Biology subjects

Fukuda, T.

Publications and source records attributed to Fukuda, T..

14 recordsLinked to original sources

bioRxiv2025

Integrated Antibody and DIA Based Plasma Proteomics Uncover Temporal Host Responses to SARS CoV 2 Infection

This is a single-case longitudinal study in which we monitored antibody responses and plasma proteome dynamics over a 310-day period in a single individual who underwent COVID-19 vaccination and SARS-CoV-2 infection. To evaluate COVID-19 antibody responses, human plasma samples collected over 310 days (August 18, 2021, to June 22, 2022) were analyzed by DIA-LC-MS/MS proteomics. This led to the acquisition of a quantitative protein profile and allowed validation of the temporal behavior of expressed proteins within the samples. A total of 1,502 proteins were identified from the plasma samples. Before vaccination, after the first dose, after the second dose, and during the period after contracting the novel coronavirus, protein quantification values during each event interval were compared. Despite minimal changes before and after COVID-19 vaccination, notable proteins exhibiting distinct high-expression and low-expression patterns were identified after SARS-CoV-2 infection.

molecular biology↗

bioRxiv2025

Wasabi leaf extract changes the expression levels of cytokine related genes in dermal papilla cells, which identified by the whole transcriptome

Wasabi is a traditional food in Asian area. Wasabi leaf extract derived compounds such as 6-methylsulfinylhexyl isothiocyanate (6-MSITC) have been reported to exert anti-proliferative effects on cancer cells. The antibacterial action of wasabi leaf extract has been reported previously. However, the detailed biological effects of wasabi leaf extract are not fully understood. To get a clue for the understanding, we used next-generation sequencing to identify the upregulated or downregulated genes in immortalized human dermal papilla cells. Differentially expressed genes were identified in human papilla cells in the presence or absence of wasabi leaf extract. The effects of 6-MSITC and isosaponarin were evaluated. We found that wasabi leaf extracts upregulated or downregulated the expression of cytokine-related genes. The identified expression changes will contribute to our understanding of the biological effects of wasabi.

cell biology↗

bioRxiv2025

Mitochondrial fission during mitophagy requires both inner and outer mitofissins

Mitophagy maintains mitochondrial homeostasis through selective degradation of damaged or excess mitochondria. Recently, we identified mitofissin/Atg44, a mitochondrial intermembrane space-resident fission factor, which directly acts on lipid membranes and drives mitochondrial fission required for mitophagy in yeast. However, it remains unclear whether mitofissin is sufficient for mitophagy-associated mitochondrial fission and whether other factors act from outside the mitochondria. Here, we identify a mitochondrial outer membrane-resident mitofissin-like microprotein required for mitophagy, and we name it mitofissin 2/Mfi2 based on the following results. Overexpression of a C-terminally truncated form of Mfi2 induces mitochondrial fragmentation and partially restores mitophagy in atg44{Delta} cells. Mfi2 binds to lipid membranes and mediates membrane fission in vitro, demonstrating its intrinsic mitofissin activity. Genetic analyses reveal that Mfi2 and the dynamin-related protein Dnm1 independently facilitate mitochondrial fission during mitophagy. Thus, Atg44 and Mfi2, two mitofissins with distinct localizations, are required for mitophagy-associated mitochondrial fission.

cell biology↗

bioRxiv2023

ARBUR: a Machine Learning-based Analysis System for Relating Behaviors and Ultrasonic Vocalizations of Rats

Deciphering how different types of behavior and ultrasonic vocalizations (USVs) of rats interact can yield insights into the neural basis of social interaction. However, the behavior-vocalization interplay of rats remains elusive because of the challenges of relating the two communication media in complex social contexts. Here, we propose a machine learning-based analysis system (ARBUR) that can cluster without bias both non-step (continuous) and step USVs, hierarchically detect eight types of behavior of two freely behaving rats with high accuracy, and locate the vocal rat in 3-D space. By simultaneously recording the video and ultrasonic streams of two freely behaving rats, ARBUR reveals that rats communicate via distinct USVs when engaging in different types of social behavior. Moreover, we show that ARBUR can not only automatically reveal the well-understood behavior-associated vocalizations that were carefully concluded by other behavioral researchers, but also hold the promise to indicate novel findings that can be hardly found by manual analysis, especially regarding step USVs and the active/passive rat-associated USVs during easy-to-confuse social behaviors. This work highlights the potential of machine learning algorithms in automatic animal behavioral and acoustic analysis and could help mechanistically understand the interactive influence between the behaviors and USVs of rats.

animal behavior and cognition↗

bioRxiv2023

Role of Immature Choroid Plexus in the Pathology of Autism Spectrum Disorder

During gestation, the choroid plexus (ChP) produces protein-rich cerebrospinal fluid and matures prior to brain development. It is assumed that ChP dysfunction has a profound effect on developmental neuropsychiatric disorders, such as Autism Spectrum Disorder (ASD). However, the mechanisms linking immature ChP to the onset of ASD remain unclear. In this study, we found that ChP-specific CAMDI-knockout mice developed an immature ChP, alongside decreased multiciliogenesis and expression of differentiation marker genes following disruption of the cerebrospinal fluid barrier. These mice exhibited ASD-like behaviors, including impaired socialization with delayed critical period. Additionally, administration of Metformin, an FDA-approved drug, before the critical period achieved ChP maturation and restored social behaviors. Furthermore, ASD model mice and ASD patient-derived organoids developed immature ChP. These results indicate towards involvement of immature ChP in the pathogenesis of ASD and suggest the targeting of functional maturation of ChP as a therapeutic strategy for ASD.

neuroscience↗

bioRxiv2023

Deep proteome analysis of time-series human plasma samples applied to Covid-19 antibody test

For the purpose of Covid-19 antibody testing, the human plasma samples acquired over a period of 310 days from August 18, 2021, to June 22, 2022, were subjected to DIA LC-MS proteome analysis. This process led to the acquisition of a quantitative protein profile and allowed for the validation of the temporal behavior of expressed proteins within the samples. A total of 1502 proteins were identified from the plasma samples. Before vaccination, after the first dose, after the second dose, and during the period after contracting the novel coronavirus, protein quantification values during each event interval were compared. Despite minimal changes observed before and after Covid-19 vaccination, notable proteins exhibiting distinct high-expression and low-expression patterns were identified after contracting the novel coronavirus infection.

molecular biology↗

bioRxiv2023

Hydrogel Microdroplet-Based Digital Quantitative Polymerase Chain Reaction

Droplet digital PCR (ddPCR) is accurate in nucleic acid quantification owing to its linearity and high sensitivity. Amplification of nucleic acid in droplets, however, is limited by the stability of droplets against thermal cycling. While the use of fluorinated oil or supplementation of surfactant could improve the stability of droplets, this process has also greatly increased the cost of ddPCR and limited post-PCR analysis. Here, we report a novel method known as gel capsule-based digital PCR (gc-dPCR) which includes method to prepare hydrogel capsules encapsulating PCR reaction mix, conducting PCR reaction, and readout by either qPCR system or fluorescence microplate reader. We have compared our method to existing methods, i.e., quantitative PCR or vortex ddPCR. Our approach results in higher fluorescence intensity compared to ddPCR suggesting higher sensitivity of the system. As hydrogel capsules are more stable than droplets in fluorinated oil throughout thermal cycling, all partitions can be quantified, thus preventing loss of information from low-concentration samples. Our approach should extend to all droplet-based PCR methods. Generally, our approach has greatly improved ddPCR by increasing droplets stability and sensitivity, and reducing the cost of ddPCR, which help to remove the barrier of ddPCR in settings with limited resources. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC="FIGDIR/small/534823v2_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@15a291eorg.highwire.dtl.DTLVardef@4189e2org.highwire.dtl.DTLVardef@c35fd8org.highwire.dtl.DTLVardef@c972d0_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Structure-dependent spontaneous calcium dynamics in cultured neuronal networks on microcontact-printed substrates

Microcontact printing (CP) is widely used in neuroscience research. However, CP yields reduced cell-substrate adhesion compared with directly coating cell adhesion molecules. Here, we demonstrate that the reduced cell-substrate adhesion caused by CP, high seeding density, and the local restriction would separately contribute to more aggregated (neurons closer to each other in separate clusters) neuronal networks. Calcium recordings revealed that more aggregated networks presented fewer spontaneous calcium activity patterns, and were more likely dominated by synchronized network-wide calcium oscillation (network bursts). First, on a uniform microcontact-printed substrate, densely seeded neurons were reaggregated into a Petri dish-wide network consisting of small clusters, of which the calcium dynamics were dominated by network bursts. Next, further analysis revealed this dominance was maintained since its appearance, and the initiation and propagation of bursts in the small-cluster network shared a similar mechanism with that of homogeneous networks. Then, sparsely seeded neurons formed several networks with different aggregation degrees, in which the less clustered ones presented abundant time-varying subnetwork burst patterns. Finally, by printing locally restricted patterns, highly clustered networks formed, where dominant network bursts reappeared. These findings demonstrate the existence of structure-dependent spontaneous calcium dynamics in cultured networks on microcontact-printed substrates, which provide important insights into designing cultured networks by using CP, and into deciphering the onset and evolution of network bursts in developmental nerve systems.

neuroscience↗

bioRxiv2021

The ulcerative colitis associated gene FUT8 regulates the quantity and quality of secreted mucins

Fucosylation of mucins, the main macrocomponents of the mucus layer that protects the digestive tract from pathogens, increases their viscoelasticity and shear stress resistance. These properties are altered in patients with ulcerative colitis (UC), which is marked by a chronic inflammation of the distal part of the colon. Here we show that the levels of Fucosyltransferase 8 (FUT8) and specific mucins are increased in the distal inflamed colon of UC patients compared to normal individuals. Overexpressing FUT8, as observed in UC, in mucin-producing HT29-18N2 colonic cell line increases trafficking of MUC1 to plasma membrane and secretion of MUC2/MUC5AC. FUT8 depletion (FUT8 KD), instead, causes intracellular accumulation of MUC1 and alters the ratio of secreted MUC2 to MUC5AC. Mucins secreted by FUT8 overexpressing cells are more resistant to shear stress compared to mucins secreted by FUT8 KD cells. These data fit well with the Fut8-/- mice phenotype, which are protected against UC. Fut8-/- mice exhibit a thinner proximal colon mucus layer with an altered ratio of neutral to acidic mucins compared to Fut8+/+ mice. Together, these data reveal that FUT8 optimizes the viscoelastic properties of the extracellular mucous by controlling the quantities of mucins secreted. SIGNIFICANCE STATEMENTMucins, the major components of the mucous barrier that protects our body from pathogens, are heavily glycosylated proteins. Changes their amounts and properties will alter the viscosity of mucous. Here we show that FUT8, a glycosylation enzyme of the Golgi apparatus, can control the viscosity of secreted mucins. Mucin secreting cells of the distal colon express FUT8, but their levels are altered in Ulcerative colitis patients. As a result, mucous produced by these cells is easily washed away, which exposes them to pathogens. We suggest that a defective mucous production is the main cause of initial inflammation observed in disease. Our findings help in understanding how cells control the quality of mucins and provide a means to prevent Ulcerative colitis.

cell biology↗

bioRxiv2020

Senescent cell death as an aging resistance mechanism in naked mole-rat

Naked mole-rats (NMRs) are the longest-lived rodents, showing minimal aging phenotypes. An unsolved paradox is that NMRs exhibit low intracellular anti-oxidant defence despite minimal aging. Here, we explained a link between these “contradicting” features by a phenomenon termed “senescent cell death (SCD)”—Senescence induced cell death in NMR cells due to their inherent vulnerability to reactive oxygen species and unique metabolic system. In NMR skin, we observed few senescent cells during aging or after ultraviolet irradiation, suggesting suppression of senescent cell accumulation in NMR tissue. We discovered that senescent NMR-fibroblasts induce SCD through retinoblastoma protein activation accompanied by autophagy dysregulation, increased oxidative damage and accelerated H2O2-releasing metabolic pathways. During senescence, NMR cells showed resistance to metabolic remodelling unlike mice. Our findings provide mechanistic insights into how extraordinary aging resistance is accomplished in NMR. This will contribute to the development of senolytic drugs to regulate age-related diseases.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗

bioRxiv2019

Merger of Betula tatewakiana (Betulaceae) from northern Japan to northeast Asian B. ovalifolia based on ploidy level

It has been controversial whether Betula tatewakiana, a dwarf birch distributed in Hokkaido of northern Japan, is an endemic species or a synonym of B. ovalifolia broadly distributed in northeast Asia. The endemic hypothesis is based on the idea that B. tatewakiana is diploid while B. ovalifolia is tetraploid and that they are separated based on the ploidy level; however no chromosome data have actually been published before. Resolving the taxonomic problem is crucial also in judging the conservation priority of B. tatewakiana in a global perspective. Our chromosome observation revealed that B. tatewakiana is tetraploid as well as B. ovalifolia. Collaterally, we conducted morphological observation and clarified that B. tatewakiana is morphologically identical to B. ovalifolia in white hairs and dense resinous glands respectively on adaxial and abaxial leaf surfaces, based on which they are different from closely related species in the same section Fruticosae. We concluded that the hypothesis that B. tatewakiana is a Hokkaido endemic based on the ploidy level is not supported and that B. tatewakiana should be merged with B. ovalifolia.

plant biology↗

bioRxiv2019

Serpentine mountain uplift in northern Japan triggered the divergence of a narrow endemic from a widespread (sub)arctic Asia-Alaska species complex of Lagotis (Plantaginaceae)

In the circumboreal region, plants often have extremely-wide species ranges. Lagotis minor-glauca species complex widespread from (sub)arctic Asia to Alaska, however, have two allied narrow endemics in northern Japan: a serpentine plant L. takedana endemic to the Yubari Mountains (Mt. Yubari) and a non-serpentine plant L. yesoensis endemic to the Taisetsu Mountains (Mt. Taisetsu). Elucidating their origins sheds light on drivers for secondary-speciation of widespread circumboreal plants. To infer phylogenetic distinctiveness of two narrow endemics with those related taxa, which contained 25 out of all the 29 species of the genus, chloroplast DNA (cpDNA), nuclear ribosomal (nrITS), two low copy nuclear gene (LCN) markers and genome-wide single-nucleotide polymorphism genotyping (MIG-seq) were used. In the result of cpDNA analyses, the Lagotis minor-glauca species complex formed a clade. Within the clade, L. yesoensis and a portion of L. glauca samples formed a subclade. However, monophyly of each of the four species was not supported. In the results of nrITS and two LCN analyses, L. takedana was monophyletic, while monophyly was not recovered for each L. yesoensis, L. glauca, and L. minor. Based on a Bayesian dating analysis using nrITS data, the age of the most recent common ancestor of L. takedana was Ma (95% confidence interval: 0.05-1.75 Ma). Possible scenario is that an ancestral linage being adapted to serpentine soils migrated into the alpine habitat of Mt. Yubari, that was formed with mountain uplift by the early Pleistocene, and subsequently reproductively isolated from non-serpentine populations and speciated. The contrasting result of L. yesoensis, that was phylogenetically indistinct, is possibly explained by incorrect taxonomy, or alternatively, shallow history and incomplete lineage sorting. In Mt. Taisetsu, massive volcanic eruptions had occurred the Early Pleistocene and even after the last glacial period, suggesting that alpine plants have not migrated into and established populations in Mt. Taisetsu until very recently. To fully resolve the phylogeny of the three species L. yesoensis, L. glauca, and L. minor, further analyses using high resolution molecular markers are needed. The present study illustrated that two narrow endemics in northern Japan diverged from the widespread species include phylogenetically distinctive and indistinctive species, owing to historical orogeny and ecological factors.

ecology↗

bioRxiv2019

Two-way migration of Lychnis wilfordii caused by the circular landform of Japan-Korea-northeast China-Russian Far East region and its suggestion for conservation in northeast Asia

In northeast Asia, substantial portion of the floras, including endangered species, are shared among its component countries in the continental, peninsula, and island parts largely through Quaternary migration. To effectively conserve nationally endangered plants in Northeast Asia, transnational conservation studies are vitally needed. Lychnis wilfordii (Caryophyllaceae) has disjunct distribution in Russian Far East (Primorsky Krai), northeast China (Jilin), Korea (Gangwon-do) and Japan (Hokkaido, Aomori, Nagano), surrounding the sea, and this is designated as an endangered species in Japan and Korea. Population genetic and molecular dating analyses were conducted 1) to elucidate geographic genetic structure covering the species range, 2) to test possible scenarios of migration, and 3) to develop logical plans for effective conservation. Population genetic analyses indicated the continent and peninsula parts (north and south Primorsky Krai, Jilin, and Gangwon-do) had higher genetic diversity compared to those in the Japanese Archipelago (Hokkaido and Nagano). Five genetically distinct groups were recognized, namely, Nagano, Gangwon-do, Jilin, north and south Primorsky Krai plus Aomori, and Hokkaido. Genetic distance between Hokkaido and Nagano was larger than between Hokkaido and north Primorsky Krai, and between Nagano and Gangwon-do, crossing national borders and the natural barrier of the sea. Considering these results, L. wilfordii likely migrated from the Asian continent to the Japanese Archipelago using two routes: north route from Russian Far East to Hokkaido and Aomori, and south route from the Korean Peninsula to Nagano. Based on molecular dating, migration from the continent to the islands likely occurred from the middle Pleistocene to the Holocene. For effective conservation of L. wilfordii, Hokkaido and Nagano populations should be distinguished as different evolutionary significant units, although these two regions belong to the same country, because Hokkaido and Nagano populations are at the different ends of the two migratory routes based on the migration scenario.

evolutionary biology↗

bioRxiv2017

H2AFX AND MDC1 PROTECT GENOMIC INTEGRITY IN MALE GERM CELLS BY PROMOTING RECOMBINATION AND ACTIVATION OF THE RECOMBINATION-DEPENDENT CHECKPOINT

In somatic cells, H2afx and Mdc1 are close functional partners in DNA repair and damage response. However, it is not known whether they are also involved in the maintenance of genome integrity in meiosis. By analyzing chromosome dynamics in H2afx-/- spermatocytes, we found that synapsis of the autosomes and X-Y chromosomes were impaired in a relevant fraction of cells. Such defect correlated with an abnormal recombination profile. Conversely, Mdc1 was dispensable for the synapsis of the autosomes, and only played a minor role in X-Y synapsis, relatively to H2afx. This suggested that those genes have non-overlapping functions in chromosome synapsis. However, we observed that both genes play a similar role in the assembly of MLH3 onto chromosomes, a key step in crossover formation. Moreover, we showed that H2afx and Mdc1 cooperate in promoting the activation of the recombination-dependent checkpoint, a mechanism that restrains the differentiation of cells with unrepaired DSBs. This occurs by a mechanism that involves P53. Overall, our data showed that, in male germ cells, H2afx and Mdc1 promote the maintenance of genome integrity.

developmental biology↗