Biology subjects

Nishida, T.

Publications and source records attributed to Nishida, T..

9 recordsLinked to original sources

bioRxiv2025

Crowdsourced Wildlife Observations Uncover Ecotourism Assets-Sites and Species

Ecotourism plays a vital role in conserving ecosystems and revitalising rural economies. Sustainable management requires strategies that effectively balance conservation needs with tourism promotion, necessitating a clear understanding of which landscapes and species attract visitors. However, identifying these "charismatic" assets has traditionally relied on costly and spatially limited surveys. This study leverages crowdsourced biodiversity data from digital platforms (iNaturalist and Biome) to identify nature-based recreation sites and visitor-preferred species in Inabe City, a rural Japanese municipality with high recreational visitation. We analysed 12,764 observations within the city and 238,625 reference observations from across Japan. By applying the Out-of-Area Activity Index (OAAI) to biological recording data, we distinguished visitors from residents with high accuracy. Spatial analyses using hurdle models revealed distinct preferences: while both groups frequented recreational facilities, residents concentrated on lowland forests, whereas visitors were significantly drawn to wetlands and mountain habitats. To quantify specific biological interests, we developed the Visitor Preference Index (VPI). This index highlighted that visitors disproportionately recorded aquatic insects (e.g., dragonflies) and endangered understory plants compared to their observations elsewhere, identifying these taxa as key ecological assets. These findings underscore the critical importance of managing highland forests and wetlands--habitats often vulnerable to degradation--to support both biodiversity and tourism. This study illustrates how crowdsourced biodiversity data can contribute to understanding human-nature interactions and offer a scalable tool for regional planning that integrates ecological conservation with sustainable tourism development.

ecology↗

bioRxiv2025

Golgi retention of KIT in gastrointestinal stromal tumour cells is phospholipase D activity-dependent

A constitutively active mutant of the receptor protein-tyrosine kinase KIT is a major cause of gastrointestinal stromal tumours (GISTs). Recently, we discovered that during biosynthetic transport, the KIT mutant (KITmut) is retained in the Golgi/trans-Golgi network (TGN), where it activates downstream molecules. This retention is dependent on the phospholipase C{gamma}2-protein kinase D2-PI4 kinase III{beta} (PLC{gamma}2-PKD2-PI4KIII{beta}) pathway, which KITmut activates at the Golgi/TGN. The activated cascade aberrantly recruits GGA1 and the {gamma}-adaptin subunit of AP1, resulting in KITmut retention in the Golgi/TGN. However, the precise mechanisms, including the mediators and effectors in the pathway, remain unclear. In humans, the phosphatidic acid-generating enzymes, phospholipase D1 (PLD1) and PLD2, are known downstream proteins of PKD. In the presence of the PLD inhibitor CAY10594, KITmut is released from the Golgi/TGN and subsequently degraded in lysosomes, leading to signal inactivation. Knockdown experiments indicated that PLD2 plays a role in KITmut retention. KITmut activates PLD2 through PKD2, but not PI4KIII{beta}, for Golgi/TGN retention. PLD activity is required for the association of {gamma}-adaptin with GGA1. Therefore, the KIT-PLC{gamma}2-PKD2 pathway separately activates PLD2 and PI4KIII{beta} to recruit {gamma}-adaptin and GGA1. Collectively, these results suggest that KITmut retention is dependent on the activation of the PLC{gamma}2-PKD2-PLD2 cascade in GIST.

cell biology↗

bioRxiv2023

Brefeldin A and M-COPA block the export of RTKs from the endoplasmic reticulum via simultaneous inactivation of ARF1, ARF4, and ARF5

Normal receptor tyrosine kinases (RTKs) need to reach the plasma membrane (PM) for ligand-induced activation, whereas its cancer-causing mutants can be activated before reaching the PM in organelles, such as the Golgi/trans-Golgi network (TGN). Inhibitors of protein export from the endoplasmic reticulum (ER), such as brefeldin A (BFA) and 2-methylcoprophilinamide (M-COPA), can suppress the activation of mutant RTKs in cancer cells, suggesting that RTK mutants cannot initiate signaling in the ER. BFA and M-COPA block the function of ADP-ribosylation factors (ARFs) that play a crucial role in ER-Golgi protein trafficking. However, which ARFs among AFR family proteins are inhibited by BFA or M-COPA, that is, which ARFs are involved in RTKs transport from the ER, remain unclear. In this study, we showed that M-COPA blocked the export of not only KIT but also PDGFRA/EGFR/MET RTKs from the ER. ER-retained RTKs could not fully transduce anti-apoptotic signals, thereby leading to cancer cell apoptosis. Moreover, single knockdown of ARF1, ARF3, ARF4, ARF5, or ARF6 could not block ER export of RTKs, indicating that BFA/M-COPA treatment cannot be mimicked by knockdown of only one ARF member. Interestingly, simultaneous transfection of ARF1, ARF4, and ARF5 siRNAs mirrored the effect of BFA/M-COPA treatment. Consistent with these results, in vitro pulldown assays showed that BFA/M-COPA blocked the function of ARF1, ARF4, and ARF5. Taken together, these results suggest that BFA/M-COPA targets at least ARF1, ARF4, and ARF5; in other words, RTKs require the simultaneous activation of ARF1, ARF4, and ARF5 for their ER export.

cell biology↗

bioRxiv2023

Liver-specific LXR inhibition represses reverse cholesterol transport in cholesterol-fed mice

ObjectiveHigh density lipoprotein (HDL) exerts an anti-atherosclerotic effect via reverse cholesterol transport (RCT). Several phases of RCT are transcriptionally controlled by Liver X receptors (LXRs). Although macrophage LXRs reportedly promote RCT, it is still uncertain whether hepatic LXRs affect RCT in vivo. Approach and ResultsTo address this question, we induced hepatic overexpression of sulfotransferase family cytosolic 2B member 1 (Sult2b1) in mice. Sult2b1 facilitates generation of sulfated cholesterol, resulting in reduced production of LXR ligands (oxysterols), which impairs LXR signaling. Adenoviral vectors expressing Sult2b1 (Ad-Sult2b1) or luciferase were intravenously injected into mice under a normal or high-cholesterol diet. Hepatic Sult2b1 overexpression resulted in reduced expression of LXR-target genes - ATP-binding cassette transporter G5/G8, cholesterol 7 hydroxylase and LXR itself - respectively reducing or increasing cholesterol levels in HDL and apolipoprotein B-containing lipoproteins (apoB-L). A macrophage RCT assay revealed that Sult2b1 overexpression inhibited fecal excretion of macrophage-derived 3H-cholesterol only under a high-cholesterol diet. In a HDL kinetic study, Ad-Sult2b1 promoted catabolism/hepatic uptake of HDL-derived cholesterol, thereby reducing fecal excretion. We next performed an in vitro lipoprotein production assay which revealed a Sult2b1-mediated reduction/increase in HDL or apoB-L secretion from hepatocytes, respectively. Finally, in LXR/{beta} double knockout mice, hepatic Sult2b1 overexpression increased apoB-L levels, but there were no differences in HDL levels or RCT compared to the control, indicating that Sult2b1-mediated effects on HDL/RCT and apoB-L were distinct: the former was LXR-dependent, but not the latter. ConclusionsHepatic LXR inhibition negatively regulates circulating HDL levels and RCT by reducing LXR-target gene expression. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/527401v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@18ff927org.highwire.dtl.DTLVardef@12e776corg.highwire.dtl.DTLVardef@1a26ebaorg.highwire.dtl.DTLVardef@113b5c6_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2022

Golgi retention and oncogenic KIT signaling via PLCγ2-PKD2-PI4KIIIβ activation in GIST cells

Most gastrointestinal stromal tumors (GISTs) develop due to gain-of-function mutations in the tyrosine kinase, KIT. We recently showed that mutant KIT mislocalizes to the Golgi area and initiates uncontrolled signaling. However, the molecular mechanisms underlying its Golgi retention remain unknown. Here, we show that protein kinase D2 (PKD2) is activated by the mutant, which causes KITs Golgi retention. In PKD2-inhibited cells, KIT migrates from the Golgi region to lysosomes and subsequently undergoes degradation. Importantly, delocalized KIT is unable to trigger downstream activation. In the Golgi area, KIT activates the PKD2-phosphatidylinositol 4-kinaseIII{beta} (PKD2-PI4KIII{beta}) pathway through phospholipase {gamma}2 (PLC{gamma}2) to generate a PI4P-rich membrane domain, where the AP1-GGA1 complex is aberrantly recruited. Disruption of any factors in this cascade results in KIT release from the Golgi region, indicating that these PKD2-related pathways are responsible for the Golgi retention of KIT. Our findings unveil the molecular mechanisms underlying KIT mislocalization and provide evidence for a new strategy for inhibition of oncogenic signaling.

cancer biology↗

bioRxiv2021

FLT3-ITD transduces autonomous growth signals during its biosynthetic trafficking in acute myelogenous leukemia cells.

FMS-like tyrosine kinase 3 (FLT3) in hematopoietic cells binds to its ligand at the plasma membrane (PM), then transduces growth signals. FLT3 gene alterations that lead the kinase to assume its permanently active form, such as internal tandem duplication (ITD) and D835Y substitution, are found in 30~40% of acute myelogenous leukemia (AML) patients. Thus, the drugs for molecular targeting of FLT3 mutants have been developed for the treatment of AML. Several groups have reported that compared with wild-type FLT3 (FLT3-wt), FLT3 mutants are retained in organelles, resulting in low levels of PM localization of the receptor. However, the precise subcellular localization of mutant FLT3 remains unclear, and the relationship between oncogenic signaling and the mislocalization is not completely understood. In this study, we show that in cell lines established from AML patients, endogenous FLT3-ITD but not FLT3-wt clearly accumulates in the perinuclear region. Our co-immunofluorescence assays demonstrate that Golgi markers are co-localized with the perinuclear region, indicating that FLT3-ITD mainly localizes to the Golgi region in AML cells. FLT3-ITD biosynthetically traffics to the Golgi apparatus and remains there in a manner dependent on its tyrosine kinase activity. A tyrosine kinase inhibitor midostaurin (PKC412) markedly decreases in FLT3-ITD retention and increases in the PM levels of the mutant. FLT3-ITD activates downstream in the endoplasmic reticulum (ER) and the Golgi apparatus during its biosynthetic trafficking. Results of our trafficking inhibitor treatment assays show that FLT3-ITD in the ER activates STAT5, whereas that in the Golgi can cause the activation of AKT and ERK. We provide evidence that FLT3-ITD signals from the early secretory compartments before reaching the PM in AML cells.

cancer biology↗

bioRxiv2020

Lipooligosaccharide, Vag8, and pertussis toxin of Bordetella pertussis cooperatively cause coughing in mice

Whooping cough, a contagious respiratory disease caused by Bordetella pertussis, is characterized by paroxysmal coughing; however, the mechanism has not been studied because of the lack of versatile animal models that reproduce the cough. Here, we present a mouse model that reproduces coughing after intranasal inoculation with the bacteria or its components and demonstrate that lipooligosaccharide (LOS), pertussis toxin (PTx), and Vag8 of the bacteria cooperatively function to cause coughing. LOS-induced bradykinin sensitized a transient receptor potential ion channel, TRPV1, which acts as a sensor to evoke the cough reflex. Vag8 further increased bradykinin levels by inhibiting the C1 esterase inhibitor, the major downregulator of the contact system, which generates bradykinin. PTx inhibits intrinsic negative regulation systems for TRPV1 through inactivation of Gi GTPases. Our findings provide a basis for answering long-standing questions on the pathophysiology of the pertussis cough.

microbiology↗

bioRxiv2020

Focusing on human haplotype diversity in numerous individual genomes demonstrates an evolutional feature of each locus

The application of current genome-wide sequencing techniques on human populations helps elucidate the considerable gene flow among genus Homo, which includes modern and archaic humans. Gene flow among current human populations has been studied using frequencies of single nucleotide polymorphisms. Unlike single nucleotide polymorphism frequency data, haplotype data are suitable for identifying and tracing rare evolutionary events. Haplotype data can also conveniently detect genomic location and estimate molecular function that may be a target of selection. We analyzed eight loci of the human genome using the same procedure for each locus to infer human haplotype diversity and reevaluate past explanations of the evolutionary mechanisms that affected these loci. These loci have been recognized by separate studies because of their unusual gene genealogy and geographic distributions that are inconsistent with the recent out-of-Africa model. For each locus, we constructed genealogies for haplotypes using sequence data of the 1000 Genomes Project. Then, we performed S* analysis to estimate distinct gene flow events other than out-of-Africa events. Furthermore, we also estimated unevenness of selective pressure between haplotypes by Extended Haplotype Homozygosity analysis. Based on the patterns of results obtained by this combination of analyses, we classified the examined loci without using a specific population model. This simple method helped clarify evolutionary events for each locus, including rare evolutionary events such as introgression, incomplete lineage sorting, selection, and haplotype recombination that may be hard to discriminate from each other.

evolutionary biology↗

bioRxiv2019

2-Cl-C.OXT-A Stimulates Contraction through the Suppression of Phosphodiesterase Activity in Human Induced Pluripotent Stem Cell-derived Cardiac Organoids

Background2-Cl-C.OXT-A (COA-Cl) is a novel synthesized adenosine analog that activates S1P1 receptor (S1P1R) and combines with adenosine A1 receptor (A1R) in G proteins and was shown to enhance angiogenesis and improve the brain function in rat stroke models. However, the role of COA-Cl in hearts remains unclear. COA-Cl, which has a similar structure to xanthine derivatives, has the potential to suppress phosphodiesterase (PDE), which is an important factor involved in the beating of heart muscle. Methods and resultsCardiac organoids with fibroblasts, human induced pluripotent stem cell-derived cardiac myocytes (hiPSC-CMs), and hiPSC-derived endothelial cells (hiPSC-ECs) were cultured until they started beating. The beating and contraction of organoids were observed before and after the application of COA-Cl. COA-Cl significantly increased the beating rate and fractional area change in organoids. To elucidate the mechanism underlying these effects of COA-Cl on cardiac myocytes, pure hiPSC-CM spheroids were evaluated in the presence/absence of Suramin (antagonist of A1R). The effects of COA-Cl, SEW2871 (direct stimulator of S1P1R), two positive inotropes (Isoproterenol [ISO] and Forskolin [FSK]), and negative inotrope (Propranolol [PRP]) on spheroids were assessed based on the beating rates and cAMP levels. COA-Cl stimulated the beating rates about 1.5-fold compared with ISO and FSK, while PRP suppressed the beating rate. However, no marked changes were observed with SEW2871. COA-Cl, ISO, and FSK increased the cAMP level. In contrast, the level of cAMP did not change with PRP or SEW2871 treatment. The results were the same in the presence of Suramin as absence. Furthermore, an enzyme analysis showed that COA-Cl suppressed the PDE activity by half. ConclusionsCOA-Cl, which has neovascularization effects, suppressed PDE and increased the contraction of cardiac organoids, independent of S1P1R and A1R. These findings suggest that COA-Cl may be useful as an inotropic agent for promoting angiogenesis in the future.

pharmacology and toxicology↗