Biology subjects

Nakano, T.

Publications and source records attributed to Nakano, T..

33 records · Page 2Linked to original sources

bioRxiv2021

Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity

Diatoms adapt to various aquatic light environments and play major roles in the global carbon cycle using their unique light-harvesting system, i.e., fucoxanthin chlorophyll a/c binding proteins (FCPs). Structural analyses of photosystem II (PSII)-FCPII and photosystem I (PSI)-FCPI complexes from the diatom Chaetoceros gracilis have revealed the localization and interactions of many FCPs; however, the entire set of FCPs has not been characterized. Here, we identified 46 FCPs in the newly assembled genome and transcriptome of C. gracilis. Phylogenetic analyses suggested that these FCPs could be classified into five subfamilies: Lhcr, Lhcf, Lhcx, Lhcz, and novel Lhcq, in addition to a distinct type of Lhcr, CgLhcr9. The FCPs in Lhcr, including CgLhcr9 and some Lhcqs, had orthologous proteins in other diatoms, particularly those found in the PSI-FCPI structure. By contrast, the Lhcf subfamily, some of which were found in the PSII-FCPII complex, seemed to be diversified in each diatom species, and the number of Lhcqs differed among species, indicating that their diversification may contribute to species-specific adaptations to light. Further phylogenetic analyses of FCPs/light-harvesting complex (LHC) proteins using genome data and assembled transcriptomes of other diatoms and microalgae in public databases suggest that our proposed classification of FCPs was common among various red-lineage algae derived from secondary endosymbiosis of red algae, including Haptophyta. These results provided insights into the loss and gain of FCP/LHC subfamilies during the evolutionary history of the red algal lineage. One sentence summaryPhylogenetic analysis of fucoxanthin-chlorophyll a/c proteins in C. gracilis revealed five major subfamilies and one minor subfamily, providing insights into the diversification of light-harvesting systems in red algae.

plant biology↗

bioRxiv2021

Resting-state brain activity can predict target-independent aptitude in fMRI-neurofeedback training

Neurofeedback (NF) aptitude, which refers to an individuals ability to change its brain activity through NF training, has been reported to vary significantly from person to person. The prediction of individual NF aptitudes is critical in clinical NF applications. In the present study, we extracted the resting-state functional brain connectivity (FC) markers of NF aptitude independent of NF-targeting brain regions. We combined the data in fMRI-NF studies targeting four different brain regions at two independent sites (obtained from 59 healthy adults and six patients with major depressive disorder) to collect the resting-state fMRI data associated with aptitude scores in subsequent fMRI-NF training. We then trained the regression models to predict the individual NF aptitude scores from the resting-state fMRI data using a discovery dataset from one site and identified six resting-state FCs that predicted NF aptitude. Next we validated the prediction model using independent test data from another site. The result showed that the posterior cingulate cortex was the functional hub among the brain regions and formed predictive resting-state FCs, suggesting NF aptitude may be involved in the attentional mode-orientation modulation systems characteristics in task-free resting-state brain activity.

neuroscience↗

bioRxiv2020

Neural correlates of beauty retouching to enhance attractiveness of self-depictions in women

Beauty filters, while often employed for retouching photos to appear more attractive on social media, when used in excess cause images to give a distorted impression. The neural mechanisms underlying this change in facial attractiveness according to beauty retouching level remain unknown. The present study used functional magnetic resonance imaging in women as they viewed photos of their own face or unknown faces that had been retouched at three levels: no, mild, and extreme. The activity in the nucleus accumbens (NA) exhibited a positive correlation with facial attractiveness, whereas amygdala activity showed a negative correlation with attractiveness. Even though the participants rated others faces as more attractive than their own, the NA showed increased activity only for their mildly retouched own face and the amygdala exhibited greater activation in the others faces condition than the own face condition. Moreover, amygdala activity was greater for extremely retouched faces than for unretouched or mildly retouched faces for both conditions. Frontotemporal and cortical midline areas showed greater activation for ones own than others faces, but such self-related activation was absent when extremely retouched. These results suggest that neural activity dynamically switches between the NA and amygdala according to perceived attractiveness of ones face.

neuroscience↗

bioRxiv2020

Variation and mechanisms of life history evolution in insular dwarfism as revealed by a natural experiment

Islands are a classic focus for evolutionary studies. One subject of much interest has been the evolution of "dwarfs", significantly smaller island mammals relative to their continental counterparts. Although a consensus has been achieved that multivariate ecological causes are behind body size changes, the processes involved remain largely unexplored. Life history variables, including the age of first reproduction, growth rate, and longevity, are probably key to understanding the process of insular dwarfism. The Japanese Archipelago with numerous islands offers a unique natural experiment of evolution into different sizes within the same group of organisms, deer. Thus, we investigated eight deer populations with a total number of 52 individuals exhibiting body size variation, both extant and fossil, to clarify the effect of insularity on life history traits. We applied several methods to both extant and extinct populations to resolve life history changes among deer populations. Skeletochronology, using lines of arrested growth formed in long bones (femur and tibia), successfully reconstructed body growth curves and revealed a gradual change in growth trajectories reflecting the degree of insularity. Slower growth rates with prolonged growth periods in more isolated deer populations were revealed. An extensive examination of bone microstructure further corroborated this fact, with much slower growth and later somatic maturity evident in fossil insular deer isolated for more than 1.5 Myr. Finally, mortality patterns assessed by demographic analysis showed variation among deer populations, with a life history of insular populations shifting toward the "slow life".

evolutionary biology↗

bioRxiv2020

Candidate screening of host cell membrane proteins involved in SARS-CoV-2 entry

Coronavirus disease (COVID-19) represents a real threat to the global population, and understanding the biological features of the causative virus, i.e., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is imperative for mitigating this threat. Analyses of proteins such as primary receptors and co-receptors (co-factors), which are involved in the entry of SARS-CoV-2 into host cells, will provide important clues to help control the virus. Here, we identified host cell membrane protein candidates present in proximity to the attachment sites of SARS-CoV-2 spike proteins, using proximity labeling and proteomic analysis. The identified proteins represent key candidate factors that may be required for viral entry. DPP4, Cadherin-17, and CD133 were found to co-localize with cell membrane-bound SARS-CoV-2 spike proteins in Caco-2 cells and thus showed potential as candidate factors. The experimental infection with a SARS-CoV-2 pseudovirus indicated a 2-fold enhanced infectivity in the CD133-ACE2-coexpressing HEK293T cells compared to that in HEK293T cells expressing ACE-2 alone. The information and resources regarding these co-receptor labeling and analysis techniques could be utilized for the development of antiviral agents against SARS-CoV-2 and other emerging viruses.

biochemistry↗

bioRxiv2020

Ccr2 suppression by minocycline in Cx3cr1/Ccr2-visualized inherited retinal degeneration

Retinal inflammation accelerates photoreceptor cell death (PCD) caused by retinal degeneration. Minocycline, a semisynthetic broad-spectrum tetracycline antibiotic, has previously been reported to show PCD rescue effect in retinal degeneration. The purpose of this study was to assess the effect of minocycline on Cx3cr1 and Ccr2 expression in retinal degeneration. Mertk-/-Cx3cr1GFP/+Ccr2RFP/+ mice, which enabled observation of Cx3cr1- and Ccr2-expression pattern in inherited retinal degeneration, were used to test the effect of minocycline. Minocycline was systemically administered to Mertk-/-Cx3cr1GFP/+Ccr2RFP/+ mice. For observing the effect of minocycline on Cx3cr1 and Ccr2 expression, administration was started on 4-week-old mice and continued for 2 weeks. To assess the PCD rescue effect, minocycline was administered to 6-week-old mice for 2 weeks. The expression pattern of Cx3cr1-GFP and Ccr2-RFP were observed on retinal and retinal pigment epithelium (RPE) flat-mounts. The severity of retinal degeneration was assessed on retinal sections. Minocycline administration suppressed Ccr2 expression in Mertk-/-Cx3cr1GFP/+Ccr2RFP/+ mice as observed in retinal and RPE flat-mounts. On the contrary, Cx3cr1 expression was not affected by minocycline administration. Retinal degeneration is ameliorated in minocycline administered Mertk-/-Cx3cr1GFP/+Ccr2RFP/+ mice. In conclusions, Minocycline suppression of Ccr2 expression correlates to amelioration of retinal degeneration.

neuroscience↗

bioRxiv2020

Bimolecule detection for Extracellular Vesicle Screening

Extracellular vesicle (EV) has been investigated for use in clinical testing in recent years. Specific EV surface proteins provide distinguishing characteristics, but are insufficient for more detailed classification of EVs. Here, we suggest a novel "Bimolecular surface antigen expressed in EV" (BiEV) as a potential indicator for more efficient EV screening. A BiEV can be identified using a previously developed method, enzyme-mediated activation of radical sources, to label the components proximal (within 20 nm) to a given molecule. We examined the screening of cancer cell-secreted EV (cEV) included in serum EVs from a model mouse for lung cancer. The cEV-specific BiEVs were first identified by through a comparison of serum EVs from wild-type and lung cancer mice, showing that the CHL1-SLC4A1 bimolecule was a significant candidate for cEV-specific BiEV. Enzyme-linked immunosorbent assay quantification of CHL1-SLC4A1 BiEV appeared to suggest a potential for cancer screening of these mice. Using the same protocols, we found that CHL1-caspase 14 BiEV was significantly elevated in lung cancer patients compared with healthy persons. A BiEV strategy may be able to make a contribution to more effective EV screening, resulting in novel biological and clinical applications.

biochemistry↗

bioRxiv2020

Targeted disruption of Pparγ1 promotes trophoblast endoreplication in the murine placenta

In murine placentas, peroxisome proliferator-activated receptor (PPAR) {gamma}1, a nuclear receptor, is abundant at the late stage of pregnancy (E15-E16), but its functional roles are still elusive because PPAR{gamma}-full knockout embryos die early (E10). We generated mice disrupted in only Ppar{gamma}1, one of the two major mRNA splicing variants of PPAR{gamma}1. Ppar{gamma}1- knockout embryos developed normally until 15.5 dpc, but their growth was retarded thereafter and they did not survive. At 15.5 dpc, in the wild-type placentas, intense PPAR{gamma}-immunostaining was detected in sinusoidal trophoblast giant cells (sTGCs), a cell lineage that coordinates the maternal blood microcirculation in the labyrinth, whereas they were absent in the knockouts. Although Ppar{gamma}1-knockout placentas were normal in morphology, we observed severely dilated maternal blood sinuses in the labyrinth. The Ppar{gamma}1-knockout sTGCs had abnormally large nuclei, an enhanced endocycling phenotype, indicating insufficient differentiation. RNA-sequencing of the placentas showed increased expression of genes coding for nucleosome assembly factors. Labyrinthine gene expressions for atypical E2Fs and cyclin E, key drivers for endocycling, were increased >3-fold. These findings suggested that PPAR{gamma}1 plays a key role in endocycle termination.

developmental biology↗

bioRxiv2020

NPC1L1 inhibition disturbs lipid trafficking and induces large lipid droplet formation in intestinal absorptive epithelial cells

Ezetimibe inhibits Niemann-Pick C1-like 1 (NPC1L1) protein, which mediates intracellular cholesterol trafficking from the brush border membrane to the endoplasmic reticulum, where chylomicron assembly takes place in enterocytes or in the intestinal absorptive epithelial cells. Cholesterol is a minor lipid component of chylomicrons; however, whether or not a shortage of cholesterol attenuates chylomicron assembly is unknown. The aim of this study was to examine the effect of NPC1L1 inhibition on trans-epithelial lipid transport, and chylomicron assembly and secretion in enterocytes. Caco-2 cells, an absorptive epithelial model, grown onto culture inserts were given lipid micelles from the apical side, and chylomicron-like triacylglycerol-rich lipoprotein secreted basolaterally were analyzed after a 24-h incubation period in the presence of ezetimibe up to 50 M. The secretion of lipoprotein and apolipoprotein B48 were reduced by adding ezetimibe (30%, p<0.01 and 34%, p<0.05, respectively). Additionally, ezetimibe accelerated intracellular apoB protein degradation by approximately 2.8-fold and activated sterol regulatory element binding protein 2 by approximately 1.5-fold: These are indicators whether the cells are sensing cellular cholesterol shortage. Thus, ezetimibe appeared to limit cellular cholesterol mobilization required for lipoprotein assembly. In such conditions, large lipid droplet formation in Caco-2 cells and the enterocytes in mice were induced, implying that unprocessed triglyceride was sheltered in these compartments. Although ezetimibe did not reduce the post-prandial lipid surge appreciably in triolein-infused mice, the results of the present study indicated that NPC1L1-mediated supply chylomicron with cholesterol may participate in a novel regulatory mechanism for the efficient chylomicron assembly and secretion.

biochemistry↗

bioRxiv2020

Prolonged disturbance of proteostasis induces cellular senescence via temporal mitochondrial dysfunction and enhanced mitochondrial biogenesis in human fibroblasts

Proteolytic activities decline with age, resulting in the accumulation of aggregated proteins in aged organisms. To investigate how disturbance in proteostasis causes cellular senescence, we developed a stress-induced premature senescence (SIPS) model, in which normal human fibroblast MRC-5 cells were treated with either the proteasome inhibitor MG132 or the V-ATPase inhibitor bafilomycin A1 (BAFA1) for 5 days. Time-course studies revealed significant increase in intracellular and mitochondrial reactive oxygen species (ROS) during and after drug treatment. Mitochondrial membrane potential initially decreased, but recovered along with PGC-1-mediated mitochondrial biogenesis, especially after drug treatment. Mitochondrial antioxidant enzymes SOD2 and GPx4 were temporally depleted in mitochondria on day 1 of the treatment, which in turn could cause excess production of mitochondrial ROS. Extra-mitochondrial SOD2 colocalized with protein aggregates and lysosomes in MG132-treated cells on day 1. SOD2 partially interacted with HSC70 and LAMP2, implying that dysfunctional SOD2 was degraded through chaperon-mediated autophagy (CMA) and caused SOD2 depletion in mitochondria. SIPS induction by MG132 or BAFA1 was partially attenuated by co-treatment with rapamycin, in which generation of excess ROS and mitochondrial biogenesis were suppressed. Rapamycin co-treatment also augmented the upregulation of HSP70 and decreased protein aggregates after drug treatment. Our study proposes a possible pathway from the disturbance of proteostasis to cellular senescence via functional changes in mitochondria.

cell biology↗

bioRxiv2019

Remote control of neural function by X-ray-induced scintillation

Scintillators emit visible luminescence when irradiated with X-rays. Given the unlimited tissue penetration of X-rays, the employment of scintillators could enable remote optogenetic control of neural functions at any depth of the brain. Here we show that a yellow-emitting inorganic scintillator, Ce-doped Gd3(Al,Ga)5O12 (Ce:GAGG), could effectively activate red-shifted excitatory and inhibitory opsins, ChRmine and GtACR1, respectively. Using injectable Ce:GAGG microparticles, we successfully activated and inhibited midbrain dopamine neurons in freely moving mice by X-ray irradiation, producing bidirectional modulation of place preference behavior. Ce:GAGG microparticles were non-cytotoxic and biocompatible, allowing for chronic implantation. Pulsed X-ray irradiation at a clinical dose level was sufficient to elicit behavioral changes without reducing the number of radiosensitive cells in the brain and bone marrow. Thus, scintillator-mediated optogenetics enables less invasive, wireless control of cellular functions at any tissue depth in living animals, expanding X-ray applications to functional studies of biology and medicine.

neuroscience↗

bioRxiv2019

Epigenetic regulation of a mouse PPARγ splicing variant, Pparγ1sv, during adipogenesis in 3T3-L1 cells

We have previously reported the abundant and ubiquitous expression of a newly identified splicing variant of mouse peroxisome proliferator-activated receptor-{gamma} (Ppar{gamma}), namely Ppar{gamma}1sv that encodes PPAR{gamma}1 protein, and plays an important role in adipogenesis. Ppar{gamma}1sv has a unique 5UTR sequence, compared to those of mouse Ppar{gamma}1 and Ppar{gamma}2 mRNAs. This implies the presence of a novel transcriptional initiation site and promoter for Ppar{gamma}1sv. We found that DNA methylation of 42 CpG sites in the proximal promoter region (-733 to -76) of Ppar{gamma}1sv was largely unchanged five days after adipocyte differentiation, whereas chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) using antibodies against H3K4me3 and H3K27ac revealed that these modifications significantly elevated at the transcription start sites of Ppar{gamma}1sv and Ppar{gamma}2 after differentiation.

cell biology↗

bioRxiv2019

Micro- and nanostructural characteristics of rat masseter muscle entheses -Characteristics of masseter muscle entheses-

The entheses of the masticatory muscles differ slightly from those of the trunk and limb muscles. However, the bones of the skull are subject to various functional pressures, including masticatory force, resulting in a complex relationship between bone structure and muscle function that remains to be fully elucidated. The present study aimed to clarify aspects of masseter muscle-tendon-bone morphological characteristics and local load environment through quantitative analysis of biological apatite (BAp) crystallite alignment and collagen fiber orientation together with histological examination of the entheses.\n\nResult of histological observation, the present findings show that, in the entheses of the masseter muscle in the first molar region, tendon attaches to bone via unmineralized fibrocartilage, while some tendon collagen fibers insert directly into the bone, running parallel to the muscle fibers. Furthermore, BAp crystallites in the same region show uniaxial preferential alignment at an angle that matches the insertion angle of the tendon fibers. Conversely, in the entheses of the masseter muscle in the third molar region, the tendon attaches to the bone via a layer of thickened periosteum and chondrocytes. As in the first molar region, the results of bone quality analysis in the third molar region showed BAp crystallite alignment parallel to the orientation of the tendon fibers. This indicates that the local mechanical environment generates differences in enthesis morphology.\n\nThe present study showed a greater degree of uniaxial BAp crystallite alignment in entheses with direct insertion rather than indirect tendon-bone attachment and the direction of alignment was parallel to the orientation of tendon fibers. These findings suggest that functional pressure from the masseter muscle greatly affects bone quality as well as the morphological characteristics of the enthesis, specifically causing micro- and nanostructural anisotropy in the direction of resistance to the applied pressure.

biophysics↗

bioRxiv2018

Proximity proteomics identifies cancer cell membrane cis-molecular complex as a potential cancer target

Cancer-specific antigens expressed in the cell membrane have been used as targets for several molecular targeted strategies in recent years with remarkable success. To develop more effective cancer treatments, novel targets and strategies for targeted therapies are needed. Here, we examined the cancer cell membrane-resident \"cis-bimolecular complex\" as a possible cancer target (cis-bimolecular cancer target: BiCAT) using proximity proteomics, a technique that has attracted attention in recent years. BiCATs were detected using a previously developed method, termed the enzyme-mediated activation of radical source (EMARS), to label the components proximal to a given cell membrane molecule. EMARS analysis identified some BiCATs, such as close homolog of L1 (CHL1), fibroblast growth factor 3 (FGFR3) and 2 integrin, which are commonly expressed in mouse primary lung cancer cells and human lung squamous cell carcinoma cells. Analysis of cancer specimens from 55 lung cancer patients revealed that approximately half of patients were positive for these BiCATs. In vitro simulation of effective drug combinations used for multiple drug treatment strategy was performed using reagents targeted to BiCAT molecules. The combination treatment based on BiCAT information moderately suppressed cancer cell proliferation compared with single administration, suggesting that the information about BiCATs in cancer cells is profitable for the appropriate selection of the combination among molecular targeted reagents. Thus, BiCAT has the possibility to make a contribution to several molecular targeted strategies in future.

biochemistry↗

bioRxiv2018

Age-related macular degeneration affects the optic radiation white matter projecting to locations of retinal damage

PurposeWe investigated the impact of age-related macular degeneration (AMD) on visual acuity and the visual white matter.\n\nMethodsWe combined an adaptive cortical atlas and diffusion-weighted magnetic resonance imaging (dMRI) and tractography to separate optic radiation (OR) projections to different retinal eccentricities in human primary visual cortex. We exploited the known anatomical organization of the OR and clinically relevant data to segment the OR into three primary components projecting to fovea, mid- and far-periphery. We measured white matter tissue properties - (fractional anisotropy, linearity, planarity, sphericity) along the aforementioned three components of the optic radiation to compare AMD patients and controls.\n\nResultsWe found differences in white matter properties specific to OR white matter fascicles projecting to primary visual cortex locations corresponding to the location of retinal damage (fovea). Additionally, we show that the magnitude of white matter properties in AMD patients correlates with visual acuity. In sum, we demonstrate a specific relation between visual loss, anatomical location of retinal damage and white matter damage in AMD patients. Importantly, we demonstrate that these changes are so profound that can be detected using magnetic resonance imaging data with clinical resolution. The conserved mapping between retinal and white matter damage suggests that retinal neurodegeneration might be a primary cause of white matter degeneration in AMD patients.\n\nConclusionsThe results highlight the impact of eye disease on brain tissue, a process that may become an important target to monitor during the course of treatment.

neuroscience↗