Biology subjects

Tsuji, Y.

Publications and source records attributed to Tsuji, Y..

10 recordsLinked to original sources

bioRxiv2026

Avatar-Induced Postural Responses during a Virtual Full-Body Illusion

Body ownership over an artificial body can alter perceptual and autonomic responses, but its influence on online postural control remains less understood. We investigated whether ownership-related body-avatar correspondence modulates postural responses to an unexpected change in avatar posture. Thirty-six healthy male participants were randomly assigned to an Embodiment condition, in which body-avatar correspondence was maintained, or a Disruption condition, in which the avatar's arm temporarily moved independently of the participant before the critical event. During a standing virtual-reality session with synchronous visuotactile stimulation, the avatar unexpectedly leaned forward. We introduced Avatar-Induced Postural Response (AIPR), an event-related index of anterior-posterior center-of-pressure displacement following the avatar's movement. Ownership-related questionnaire ratings were higher in the Embodiment condition, whereas self-location-related ratings did not differ between conditions. AIPR was greater in the Embodiment condition and was greater than zero only in this condition. AIPR was also positively correlated with skin conductance responses in the Embodiment condition, but was not associated with questionnaire ratings. These findings suggest that an unexpected change in avatar posture can influence the participant's own postural regulation when ownership-related body-avatar correspondence is maintained. AIPR may provide a complementary behavioral index of a postural-control component of avatar embodiment not fully reflected in explicit subjective reports.

neuroscience↗

bioRxiv2026

Brief online mindfulness meditation training modulates heart rate variability during post-stress meditation

Mindfulness-based interventions are increasingly delivered online, yet evidence for short programs often relies on self-report outcomes. We tested whether a brief online mindfulness meditation training produces detectable changes in autonomic regulation during a standardized stress-to-meditation sequence. Healthy adults with no meditation experience were randomized to a four-week online mindfulness meditation program (MG) or an active health-management program (CG). Before and after training, participants completed a laboratory session consisting of rest, a mental arithmetic stress task, guided focused-attention breathing meditation, and post-rest while ECG was recorded. Across the training period, both groups showed reduced negative affective symptoms, but only the mindfulness group showed an increase in the Observing facet. Critically, frequency-domain HRV indices during the laboratory protocol showed a group-specific post-training pattern: MG exhibited lower LF/HF and higher normalized HF power (nHF) compared with pre-training, and MG differed from CG in the post-training session. Within MG, training-related improvement in FFMQ Non-reactivity was positively associated with nHF during the post-stress meditation period. These findings indicate that a brief online mindfulness program can modulate HRV during a stress-to-meditation context and that post-stress autonomic modulation during meditation covaries with acceptance-related skill acquisition.

neuroscience↗

bioRxiv2024

Assessing Target of Rapamycin (TOR) activity in the diatom Phaeodactylum tricornutum using commercially available materials

Target of rapamycin (TOR) is a conserved protein kinase that regulates the balance between catabolic and anabolic processes in response to nutrient availability. Although the central role of TOR kinase in nutrient stress responses is well-recognized, little is known about the molecular basis of TOR signaling in ecologically important secondary algae with plastids of red algal origin, such as diatoms, as assessing in vivo TOR kinase activity is a difficult task. To assess TOR kinase activity, the phosphorylation status of downstream components, such as ribosomal protein S6 (RPS6), must be measured. Unlike for model organisms, an antibody that detects phosphorylated (P-) RPS6 in diatoms is not commercially available. Therefore, we developed a convenient method in which P-RPS6 and non-P-RPS6 were detected via Phos-tag affinity electrophoresis and immunoblotting with a commercial antibody that cross-reacts with RPS6 (both P- and non-P-RPS6) in the diatom, Phaeodactylum tricornutum. Using this Phos-tag-based method, we observed a dose-dependent decrease in the P-RPS6/total RPS6 ratio in P. tricornutum cells treated with the TOR kinase inhibitor, AZD-8055. We also observed a reduction in the P-RPS6/total RPS6 ratio during the nitrogen-deficient culture of P. tricornutum, which indicated the inactivation of TOR kinase in response to nitrogen deficiency. Finally, we demonstrated the potential application of the Phos-tag-based method to other ecologically, evolutionarily, and industrially important secondary algae, such as Nannochloropsis oceanica (Stramenopiles), the haptophyte Tisochrysis lutea, and Euglena gracilis (Euglenid). As all experimental materials are commercially available, the Phos-tag-based method can be used to promote studies on TOR in diverse algae in different contexts.

biochemistry↗

bioRxiv2024

Periplasmic carbonic anhydrase CAH1 contributes to high inorganic carbon affinity in Chlamydomonas reinhardtii

Carbonic anhydrase (CA), an enzyme conserved across species, is pivotal in the interconversion of inorganic carbon (Ci; CO2 and HCO3-). Compared to the well-studied intracellular CA, the specific role of extracellular CA in photosynthetic organisms is still not well understood. In the green alga Chlamydomonas reinhardtii, CAH1, located at the periplasmic space, is strongly induced under CO2-limiting conditions by the Myb transcription factor LCR1. While it has been observed that the lcr1 mutant shows decreased Ci-affinity, the detailed mechanisms behind this phenomenon are yet to be elucidated. In this study, we aimed to unravel the LCR1-dependent genes essential for maintaining high Ci-affinity. To achieve this, we identified a total of 12 LCR1-dependent inducible genes under CO2-limiting conditions, focusing specifically on the most prominent ones - CAH1, LCI1, LCI6, and Cre10.g426800. We then created mutants of these genes using the CRISPR-Cas9 system, all from the same parental strain, and compared their Ci-affinity. Contrary to earlier findings (Van and Spalding, 1999) that reported no reduction in Ci-affinity in the cah1 mutant, our newly created cah1-1 mutant exhibited a significant decrease in Ci-affinity under high HCO3-/CO2-ratio conditions. Additionally, when we treated wild-type cells with a CA inhibitor with low membrane permeability, a similar reduction in Ci-affinity was observed. Moreover, the addition of exogenous CA to the cah1 mutant restored the decreased Ci-affinity. These results, highlighting the crucial function of the periplasmic CAH1 in maintaining high Ci-affinity in Chlamydomonas cells, provide new insights into the functions of periplasmic CA in algal carbon assimilation. One-sentence summaryCAH1, a periplasmic carbonic anhydrase in Chlamydomonas reinhardtii, plays a crucial role in maintaining a high affinity for inorganic carbon, particularly under CO2-limiting conditions.

plant biology↗

bioRxiv2023

Diatom pyrenoids are encased in a protein shell that enables efficient CO2 fixation

Pyrenoids are subcompartments of algal chloroplasts that concentrate Rubisco enzymes and their CO2 substrate, thereby increasing the efficiency of carbon fixation. Diatoms perform up to 20% of global CO2 fixation, but their pyrenoids remain poorly characterized at a molecular level. Here, we used in vivo photo-crosslinking to catalogue components of diatom pyrenoids and identified a pyrenoid shell (PyShell) protein, which we localized to the pyrenoid periphery of both the pennate diatom, Pheaodactylum tricornutum, and the centric diatom, Thalassiosira pseudonana. In situ cryo-electron tomography (cryo-ET) revealed that the pyrenoids of both diatom species are encased in a lattice-like protein sheath. Disruption of PyShell expression in T. pseudonana resulted in the absence of this protein sheath, altered pyrenoid morphology, and a high-CO2 requiring phenotype, with impaired growth and reduced carbon fixation efficiency under standard atmospheric conditions. Pyrenoids in mutant cells were fragmented and lacked the thylakoid membranes that normally traverse the Rubisco matrix, demonstrating how the PyShell plays a guiding role in establishing pyrenoid architecture. Recombinant PyShell proteins self-assembled into helical tubes, enabling us to determine a 3.0 [A]-resolution PyShell structure. We then fit this in vitro structure into an in situ subtomogram average of the pyrenoids protein sheath, yielding a putative atomic model of the PyShell within diatom cells. The structure and function of the diatom PyShell provides a new molecular view of how CO2 is assimilated in the ocean, a crucial biome that is on the front lines of climate change.

cell biology↗

bioRxiv2023

Low-CO2 inducible bestrophins in diatom thylakoid membranes sustain high photosynthetic efficacy at distant locations from the pyrenoid

Anion transporters are important to sustain a variety of physiological states in cells. Bestrophins are a family of Cl- and/or HCO3- transporters conserved in bacteria, animals, algae, and plants. Recently, bestrophin paralogs were found in the green alga Chlamydomonas reinhardtii as up- regulated components in low CO2 conditions that play an essential role in the CO2- concentrating mechanism (CCM). Bestrophin orthologs are also conserved in diatoms, a group of secondary endosymbiotic algae harboring red-type plastids, but their physiological functions are not known yet. Here, we characterized the subcellular localization and expression profile of bestrophins in the marine diatoms Phaeodactylum tricornutum (PtBST1-4) and Thalassiosira pseudonana (TpBST1 and 2). PtBST1 and PtBST2 were localized at the stromal thylakoid membrane outside of the pyrenoid, and PtBST3 was localized in the pyrenoid. Contrarily, TpBST1 and TpBST2 were both localized in the pyrenoid. These bestrophin proteins were accumulated in cells grown in atmospheric CO2 but not in 1% CO2-grown cells. To assess the physiological functions, we generated knock-out mutants for PtBST1 by genome editing. The lack of PtBST1 decreased affinity of photosynthesis for dissolved inorganic carbon closer to that of the cells grown in 1% CO2. Additionally, non-photochemical quenching was 1.5-2.0 times higher in the mutants than that of the wild type cells. These data suggests that HCO3- transport at the stroma thylakoid membranes by PtBST1 is a critical part of the CO2 evolving system of the pyrenoid in the fully induced CCM, and simultaneously that PtBST1 modulates photoprotection in response to CO2 availability in P. tricornutum. Significant statementMarine diatoms are responsible for nearly half of oceanic primary production, owing to the high-affinity photosynthesis for dissolved inorganic carbon which is supported by CO2- concentrating mechanism (CCM). This study uncovered that a bestrophin family protein at the stoma thylakoid membrane operates to import HCO3- to the thylakoid lumen and mobilizes it towards the CO2 evolving system at the pyrenoid-penetrating thylakoid in the diatom Phaeodactylum tricornutum. This HCO3- collecting system not only enhances the CCM but also down regulates the photoprotection capacity of photosystem II, presumably by affecting the thylakoid lumen acidification. This study experimentally demonstrates the molecular mechanism how diatoms optimize the use of CO2 and light energy, giving an insight into the reason of ecological successfulness of marine diatoms.

plant biology↗

bioRxiv2022

Topologically frustrated dynamics in an uncharged Tetra-PEG gel

Based on our previous discovery of non-diffusive topologically frustrated dynamics in a charged system where electrostatic interactions between the charged guest and the charged host gel play a role (Nature Communications, 2018, 9, 2248; Physical Review Letters, 2021, 126, 057802), we have investigated the onset of this effect in an uncharged gel matrix. Using sodium (polystyrene sulfonate) as the guest macromolecule and the ideal tetra-PEG gel, we find the emergence of the non-diffusive topologically frustrated dynamical state with a hierarchy of segmental dynamics represented by a stretched exponential of exponent {beta} around 1/3. Our results demonstrate the universal behavior of the topologically frustrated dynamical state.

biophysics↗

bioRxiv2021

Nuclear activation in dual-durotaxing cells on a matrix with cell-scale stiffness-heterogeneity

Living organisms are typically composed of various tissues with microscopic cell-scale stiffness-heterogeneity, in which some cells receive dynamically fluctuating mechanical stimuli from the heterogeneous extracellular milieu during long-term movement. Although intracellular stress dynamics (ISD), which are closely related to the regulation of cell functions such as proliferation and differentiation, can be characteristically modulated in cells migrating on a matrix with stiffness-heterogeneity, it has been unclear how the mode of fluctuation of ISD affects cell functions. In the present study, we demonstrate that mesenchymal stem cells (MSCs) dual-durotaxing (i.e., both forward and reverse durotaxis) on microelastically-patterned gels with stiff triangular domains markedly amplify the fluctuation of ISD, nuclear shape, and the spatial distribution of chromatins, which makes the cells remain far from tensional equilibrium. We provide evidence that amplified chromatin fluctuation in the dual-durotaxing MSCs can cause activation of cellular vigor and maintenance of the stemness.

biophysics↗

bioRxiv2021

Decrease of Functional Connectivity within the Default Mode Network by a Brief Training of Focused Attention on the Breath in Novices

Experienced meditators reduce the activity of the default mode network (DMN), a brain system preferentially active when people are not engaged in specific tasks. However, the neural modulation of the DMN in novices remain largely unexplored. By using electroencephalography, we investigated the DMN functional connectivity in two groups of novices: the meditation group practiced six consecutive days of focused attention on the breath; the control group practiced only on the first and last days. After the brief training, results showed a decrease in the DMN functional connectivity between the ventromedial prefrontal cortex and the posterior cingulate cortex in theta and alpha bands during the focused attention condition, in the meditation group compared to the control group. The change in DMN functional connectivity was significantly correlated with the increase in state-level mindfulness scores. These data elucidate DMN modifications already arising at the initial stages of mindfulness meditation training in novices.

neuroscience↗

bioRxiv2019

Effects of a rifampicin pre-treatment on linezolid pharmacokinetics

Linezolid is an oxazolidinone antibiotic that effectively treats methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE). Since rifampicin induces other antibiotic effects, it is combined with linezolid in therapeutic regimes. However, linezolid blood concentrations are reduced by this combination, which increases the risk of the emergence of antibiotic-resistant bacteria. We herein demonstrated that the combination of linezolid with rifampicin inhibited its absorption and promoted its elimination, but not through microsomal enzymes. Our results indicate that the combination of linezolid with rifampicin reduces linezolid blood concentrations via metabolic enzymes.

molecular biology↗