Biology subjects

Nagai, H.

Publications and source records attributed to Nagai, H..

15 recordsLinked to original sources

bioRxiv2026

Synaptic mitochondrial oxidative stress drives individual variability in age-related cognitive decline in mice

Aging leads to cognitive decline with considerable individual variability, yet the biological mechanisms remain unclear. Here we performed ultrastructural and proteomic analyses of the medial prefrontal cortex (mPFC) alongside behavioral assessments of attentional set shifting in mice across age groups. Although reduced synaptic density did not consistently lead to cognitive decline, proteomic analyses of synaptosomes and whole tissue revealed that the molecular signatures associated with individual variability in cognitive decline were distinct from those associated with chronological aging, and that synaptic mitochondria and their proteins were more abundant in aged mice with greater cognitive decline. Moreover, treatment with the mitochondria-targeted antioxidant MitoQ reduced the abundance of synaptic mitochondrial proteins, including pro-apoptotic proteins, and mitigated age-related cognitive decline. These findings demonstrate that synaptic mitochondrial oxidative stress in the mPFC, distinct from chronological age-related processes, contributes to individual variability in age-related cognitive decline and offers a potential target for prevention and intervention.

animal behavior and cognition↗

bioRxiv2026

Aging Converts Microglial Repopulation into Maladaptive Reprogramming that Exacerbates Cognitive Deficits

Background and PurposeAging has been associated with neuroinflammation and cognitive decline. Microglial repopulation after pharmacological depletion has been proposed as a strategy to alleviate microglia-driven neuropathology. However, the effects of microglial repopulation on age-related cognitive decline remain largely unexplored. In the present study, we examined how microglial repopulation affects the transcriptomic profiles of cortical microglia and the decline in prefrontal cortex-dependent cognitive function in aged mice. Experimental ApproachYoung and aged male C57BL/6J mice were used in this study. Microglial depletion was induced by treatment with PLX3397, a CSF1R inhibitor, followed by microglial repopulation after drug withdrawal. Microglia isolated from the entire cerebral cortex were subjected to bulk RNA-sequencing analysis. The visual discrimination test followed by the response direction test was conducted to assess sensory learning and attentional set shifting abilities, respectively. Key ResultsRepopulated cortical microglia in aged, but not young, mice exhibited aberrant gene expression patterns, including reduced expression of microglial identity genes, reprogramming of innate and adaptive immune-related gene expression, and derepression of neuronal gene expression. Furthermore, microglial repopulation selectively impaired visual discrimination learning and attentional set shifting in aged mice. Conclusion and ImplicationsThese findings demonstrate that aging converts microglial repopulation into maladaptive reprogramming that exacerbates cognitive decline, possibly through aberrant gene expression programs. Therefore, the therapeutic potential of this approach must be carefully evaluated with respect to specific behavioral domains and disease contexts, including aging.

neuroscience↗

bioRxiv2025

Lateralized vagal oxytocin signaling separately controls feeding and socioemotional functions via hypothalamic oxytocin signaling

Oxytocin neurons in the paraventricular hypothalamus (PVHOxt) regulate feeding, anxiety, and social behaviors. Activation of Oxt receptor (Oxtr) -expressing vagal sensory neurons engages these PVHOxt neurons and improves hyperphagic obesity; however, their roles in anxiety and sociability remain unclear. Here, we activated vagal Oxtr-expressing neurons in male mice using a single intraperitoneal (IP) Oxt injection or chemogenetics. IP Oxt reduced anxiety-like behavior, enhanced social interaction, and suppressed feeding while activating both vagal sensory neurons and PVHOxt neurons. These effects were abolished by chemogenetic inhibition of PVHOxt neurons or central Oxtr blockade. Subdiaphragmatic vagotomy revealed lateralized functions: right-side vagotomy eliminated anxiolytic and prosocial effects, whereas left-side vagotomy blocked feeding suppression. Consistently, chemogenetic activation of left-sided neurons suppressed feeding, while right-sided activation reduced anxiety and increased sociability. These findings identify Oxtr-expressing vagal sensory neurons as a major peripheral pathway in which left- and right-sided inputs differentially control feeding and socioemotional behaviors.

physiology↗

bioRxiv2025

Fine modulation of carbon flow in the central carbon metabolism via ribosome-binding site modification in Escherichia coli

Optimization of flux distribution in central carbon metabolism is important to improve the microbial productivity. As the number of precursors required for synthesis differs for each target compound, optimal flux distribution also varies. A library of mutant strains with diverse flux distributions can aid in optimal strain screening. Therefore, in this study, we aimed to construct a library of Escherichia coli strains with stepwise changes in flux distribution by introducing mutations into the ribosome-binding sites of key enzyme genes on its chromosome. We focused on the flux ratios at the glucose-6-phosphate and acetyl-CoA nodes to enhance mevalonate production. Mutations were introduced into the ribosome-binding sites of pgi and gltA to vary the flux ratios of the two pathway branches. Furthermore, a combinatorial repression library comprising 16 strains was constructed by varying pgi and gltA expression at four levels, and a plasmid expressing mevalonate synthesis genes was introduced into each strain. Batch cultures were performed to obtain strains with mevalonate titers and yields were 2.4- and 3.4-fold higher than those of the parent strain. Overall, our combinatorial suppression library of pgi and gltA facilitated the effective identification of mutants with optimal metabolism for mevalonate production.

molecular biology↗

bioRxiv2025

Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in the adult Drosophila midgut

Cellular plasticity, the ability of a differentiated cell to adopt another phenotypic identity, is restricted under basal conditions, but can be elicited upon damage to facilitate regeneration. Such damage-induced cellular plasticity restores homeostasis and prevents pathology, yet its underlying molecular basis remains largely unexplored. Here, we reported damage-induced cellular plasticity of secretory enteroendocrine cells (EEs) in the adult Drosophila midgut. We found that ionizing radiation enhanced EE plasticity such that it promoted EEs to dedifferentiate into ISCs and subsequently re-differentiate towards ECs. We identified that radiation induced the production of a stress-inducible transcription factor Xrp1 in EE lineages, and its upregulation was necessary for EE plasticity. Single-cell RNA sequencing of guts with EE-specific Xrp1 overexpression revealed ectopic expression of progenitor-specific genes in EEs, which was necessary for Xrp1 to drive EE plasticity. Our work provides a mechanistic framework for understanding cellular plasticity and suggests its potential role in damage-induced responses.

cell biology↗

bioRxiv2025

BubR1 and Mad2 regulate adult midgut remodeling in Drosophila diapause

Diapause is a survival strategy in which growth and aging are temporarily suspended, enabling animals to withstand unfavorable environments. Various insects, including the fruit fly Drosophila, enter reproductive diapause, or dormancy, in response to colder temperatures and/or shorter day lengths. During reproductive diapause, ovarian development halts, and non-reproductive organs also undergo remodeling at both morphological and metabolic levels: however, the mechanisms underlying this remodeling and its physiological impact remain largely unclear. Here, we show that the Drosophila adult midgut undergoes extensive remodeling in diapause, marked by a sustained suspension of growth due to the cell cycle arrest of intestinal stem cells (ISCs) that revert to normal upon returning to recovery conditions. During dormancy, BubR1 and Mad2, key regulators of mitosis, are highly expressed and localized in the cytoplasm of ISCs rather than at the kinetochore, and both BubR1 and Mad2 are essential for diapause-specific midgut remodeling. Furthermore, disruption of midgut growth arrest during diapause reduces the resistance to starvation in adult flies. Together, our findings identify a novel role for BubR1 and Mad2 in ISCs-promoting proper midgut remodeling during dormancy-and highlight the importance of this process for survival under adverse environments.

developmental biology↗

bioRxiv2025

Cleavage cascade of the sigma regulator FecR orchestrates TonB-dependent signal transduction

TonB-dependent signal transduction is a versatile mechanism observed in gram-negative bacteria, integrating energy-dependent substrate transport with signal relay. In Escherichia coli, the TonB-ExbBD motor complex energizes the TonB-dependent transporter FecA, facilitating ferric citrate import. FecA also functions as a sensor, transmitting signals to the cytoplasmic membrane protein FecR. We previously demonstrated that FecR undergoes a three-step cleavage process, culminating in the activation of the cytoplasmic sigma factor FecI, which drives fec gene transcription. Here, we describe the complete mechanism of FecR cleavage-mediated ferric citrate signaling involving FecA and TonB. The cleavage cascade begins with FecR autoproteolysis prior to membrane integration. The soluble C-terminal domain (CTD) fragment of FecR is co-translocated with the N-terminal domain (NTD) fragment through a Tat system-mediated process. In the periplasm, the interaction between the CTD and NTD fragments prevents further cleavage. This inhibition is lifted by TonB-mediated motor function, which releases the CTD, allowing the cleavage cascade to proceed. This process is essential for ferric citrate signal-induced activation of fec gene expression. Our findings reveal that the regulation of FecR cleavage, relying on the TonB-FecA axis, plays a central role in bacterial response to ferric citrate signals. Significance StatementScarcity of iron, an essential element for life, has driven bacteria to evolve intricate acquisition systems, yet the molecular basis of their signal transduction mechanisms remains elusive. Unlike conventional pathways, iron transport systems employ outer membrane receptors that mediate signal transduction across both the outer and cytoplasmic membranes, powered by TonB. Using the Escherichia coli Fec system, we uncovered the mechanism by which FecRs cleavage cascade orchestrates ferric citrate signaling through TonB-mediated energy transfer. These findings shed light on similar mechanisms in gram-negative bacteria and have significant implications for understanding bacterial adaptation and pathogenesis.

immunology↗

bioRxiv2024

Compatibility of time-lapse dry incubator on in vitro production of bovine embryos

Embryo culture is crucial to achieve successful outcomes in assisted reproductive technology (ART) for cattle. This study explored the innovative use of dry incubators integrated with time-lapse monitoring systems for bovine embryo culture, building on their advantages in human medicine, such as reduced contamination risk, stable temperature control, and lower gas consumption. Our research demonstrates the feasibility of this approach, showing that although the osmotic pressure gradually increases over the culture period, it remains below the critical threshold for developmental impairment. Embryos cultured in dry incubators exhibited morphokinetics comparable to those cultured in conventional humidified time-lapse incubators. Furthermore, RNA-seq revealed that the transcriptomic profiles of blastocysts cultured in dry incubators closely matched those of blastocysts cultured in humidified incubators. These findings highlight the significant potential of dry incubators with time-lapse monitoring systems for the in vitro production of bovine embryos, marking a promising advancement in assisted reproductive technologies for the livestock industry and research setting.

developmental biology↗

bioRxiv2023

Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut

BackgroundThe remarkable regenerative abilities observed in planarians and cnidarians are closely linked to the active proliferation of adult stem cells and the precise differentiation of their progeny, both of which typically deteriorate during aging in low regenerative animals. While regeneration-specific genes conserved in highly regenerative organisms may confer regenerative abilities and long-term maintenance of tissue homeostasis, it remains unclear whether introducing these regenerative genes into low regenerative animals can improve their regeneration and aging processes. ResultsHere we ectopically express high regenerative species-specific JmjC domain-encoding genes (HRJDs) in Drosophila, a widely used low regenerative model organism. Surprisingly, HRJD expression impedes tissue regeneration in the developing wing disc but extends organismal lifespan when expressed in the intestinal stem cell lineages of the adult midgut under non-regenerative conditions. Notably, HRJDs enhance the proliferative activity of intestinal stem cells while maintaining their differentiation fidelity, ameliorating age-related decline in gut barrier functions. ConclusionsThese findings together suggest that the introduction of highly regenerative species-specific genes can improve stem cell functions and promote a healthy lifespan when expressed in aging animals.

developmental biology↗

bioRxiv2023

Multi-tiered actions of Legionella effectors to modulate host Rab10 dynamics

Rab GTPases are representative targets of manipulation by intracellular bacterial pathogens for hijacking membrane trafficking. Legionella pneumophila recruits many Rab GTPases to its vacuole and exploits their activities. Here, we found that infection-associated regulation of Rab10 dynamics involves ubiquitin signaling cascades mediated by the SidE and SidC families of Legionella ubiquitin ligases. Phosphoribosyl-ubiquitination of Rab10 catalyzed by the SidE ligases is crucial for its recruitment to the bacterial vacuole. SdcB, the previously uncharacterized SidC family effector, resides on the vacuole and contributes to retention of Rab10 at the late stages of infection. We further identified MavC as a negative regulator of SdcB. By the transglutaminase activity, MavC crosslinks ubiquitin to SdcB and suppresses its function, resulting in elimination of Rab10 from the vacuole. These results demonstrate that the orchestrated actions of many L. pneumophila effectors fine-tune the dynamics of Rab10 during infection.

microbiology↗

bioRxiv2023

Nutrient-driven dedifferentiation of enteroendocrine cells promotes adaptive intestinal growth

Post-developmental organ resizing improves organismal fitness under constantly changing nutrient environments. Although stem cell abundance is a fundamental determinant of adaptive resizing, our understanding of its underlying mechanisms remains primarily limited to the regulation of stem cell division. Here we demonstrate that nutrient fluctuation induces dedifferentiation in the Drosophila adult midgut to drive adaptive intestinal growth. From lineage tracing and single-cell RNA-sequencing, we identify a subpopulation of enteroendocrine cells (EEs) that convert into functional intestinal stem cells (ISCs) in response to dietary glucose and amino acids by activating the JAK-STAT pathway. Genetic ablation of EE-derived ISCs severely impairs ISC expansion and midgut growth despite the retention of resident ISCs, and in silico modeling further indicates that EE dedifferentiation enables efficient increase in the midgut cell number while maintaining epithelial cell composition. Our findings uncover a physiologically-induced dedifferentiation that ensures ISC expansion during adaptive organ growth in concert with nutrient conditions.

developmental biology↗

bioRxiv2022

Mechanism of Lys6 poly-ubiquitin specificity by the L. pneumophila deubiquitinase LotA

The versatility of ubiquitination to impose control over vast domains of eukaryotic biology is due, in part, to diversification through differently-linked poly-ubiquitin chains. Deciphering the signaling roles for some poly-ubiquitin chain types, including those linked via K6, has been stymied by a lack of stringent linkage specificity among the implicated regulatory proteins. Forged through strong evolutionary pressures, pathogenic bacteria have evolved intricate mechanisms to regulate host ubiquitin, and in some cases even with exquisite specificity for distinct poly-ubiquitin signals. Herein, we identify and characterize a deubiquitinase domain of the secreted effector protein LotA from Legionella pneumophila that specifically regulates K6-linked poly-ubiquitin during infection. We demonstrate the utility of LotA as a tool for studying K6 poly-ubiquitin. By determining apo and diUb-bound structures, we identify the mechanism of LotA activation and K6 poly-ubiquitin specificity, and identify a novel ubiquitin-binding domain utilized among bacterial deubiquitinases.

biochemistry↗

bioRxiv2020

Isolation and characterization of a novel phage SaGU1 that infects Staphylococcus aureus clinical isolates from patients with atopic dermatitis

The bacterium Staphylococcus aureus, which grows on healthy human skin, may cause diseases such as atopic dermatitis (AD). Treatment for such AD cases involves antibiotic use; however, alternate treatments are preferred owing to the development of antimicrobial resistance. This study aimed to characterize the novel bacteriophage SaGU1 as a potential agent for phage therapy to treat S. aureus infections. SaGU1 that infects S. aureus strains previously isolated from the skin of patients with AD was screened from sewage samples in Gifu, Japan. Its genome was sequenced and analyzed using bioinformatics tools, and the morphology, lytic activity, stability, and host range of the phage were determined. The SaGU1 genome consisted of 140,909 bp with an average GC content of 30.2%. The viral chromosome contained putative 225 protein-coding genes and four tRNA genes, carrying neither toxic nor antibiotic resistance genes. Electron microscopy analysis revealed that SaGU1 belongs to the Myoviridae family. Stability tests showed that SaGU1 was heat-stable under physiological and acidic conditions. Host-range testing revealed that SaGU1 could infect a broad range of S. aureus clinical isolates present on the skin of patients with AD, whereas it did not kill strains of Staphylococcus epidermidis, which are symbiotic bacteria in the human skin microbiota. Our data suggest that SaGU1 is a potential candidate for developing a phage therapy to treat AD caused by pathogenic S. aureus.

microbiology↗

bioRxiv2019

Mesenchymal-Epithelial Transition Regulates Initiation of Pluripotency Exit before Gastrulation

The pluripotent epiblast gives rise to all tissues and organs in an adult body. Its differentiation starts at gastrulation when the epiblast generates mesoderm and endoderm germ layers through a process called epithelial-mesenchymal transition (EMT). Although gastrulation EMT coincides with loss of epiblast pluripotency, pluripotent cells in development and in vitro can adopt either mesenchymal or epithelial morphology. The relationship between epiblasts cellular morphology and its pluripotency is not well understood. In this work, using chicken epiblast and mammalian pluripotency stem cell (PSC) models, we show that PSCs undergo a mesenchymal-epithelial transition (MET) prior to EMT-associated pluripotency loss. Epiblast MET and its subsequent EMT are two distinct processes. The former, a partial MET, is associated with reversible initiation of pluripotency exit; whereas the latter, a full EMT, is associated with complete and irreversible pluripotency loss. We provide evidence that integrin-mediated cell-matrix interaction is a key player in pluripotency exit regulation. We propose that epiblast partial MET is an evolutionarily conserved process among all amniotic vertebrates and its developmental function is to mediate planar symmetry-breaking within an epithelialized epiblast, taking place after epiblast MET but before gastrulation EMT.

developmental biology↗

bioRxiv2018

Microglial SIRPα regulates the emergence of CD11c+ microglia and demyelination damage in white matter

A characteristic subset of microglia expressing CD11c appears in response to brain damage. However, the functional role of CD11c+ microglia, as well as the mechanism of its induction, are poorly understood. Here we report that the genetic ablation of signal regulatory protein (SIRP), a membrane protein, induced CD11c+ microglia in the brain white matter. Mice lacking CD47, a physiological ligand of SIRP, and microglia-specific SIRP knockout mice exhibited the same phenotype, suggesting the interaction between microglial SIRP and CD47 on neighbouring cells suppressed the emergence of CD11c+ microglia. A lack of SIRP did not cause detectable damage in the white matter, but resulted in the increased expression of genes characteristic of the repair phase after demyelination. In addition, cuprizone-induced demyelination was alleviated by the microglia-specific ablation of SIRP. Thus, microglial SIRP suppresses the induction of CD11c+ microglia that have the potential to accelerate the repair of damaged white matter.

neuroscience↗