Biology subjects

Takahashi, T.

Publications and source records attributed to Takahashi, T..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

Brain Activity During Constraint Relaxation in the Insight Problem-Solving Process: An fNIRS Study

People solve insight problems that they encounter daily with a sudden sense of aha! to reach a solution. Chunk decomposition, which decomposes the factors of the problem, and constraint relaxation, which manipulates filters to organize the information necessary to solve the problem, are important in insight problem-solving. Although there have been many studies on brain activity during chunk decomposition, few have examined brain activity during constraint relaxation. Particularly, no study has observed the changes over time due to constraint relaxation during insight problem-solving. This study used a slot machine task as an insight problem to measure brain activity using functional Near-Infrared Spectroscopy (fNIRS), and eye movements to estimate constraint relaxation. The results showed that the right dorsolateral prefrontal cortex (DLPFC) and right superior temporal gyrus (STG) were activated over time in participants in whom constraint relaxation was induced. The right inferior temporal gyrus (ITG) of participants who were able to solve the insight problem after constraint relaxation was also activated. The analysis of brain activity during constraint relaxation in insight problem-solving may be useful for advancing research on the aha! phenomenon and creativity.

neuroscience↗

bioRxiv2022

Engineering of an electrically charged hydrogel implanted into a traumatic brain injury model for stepwise neuronal tissue reconstruction

Neural regeneration is extremely difficult to achieve. In traumatic brain injuries, the loss of brain parenchyma volume hinders neural regeneration. In this study, neuronal tissue engineering was performed by using electrically charged hydrogels composed of cationic and anionic monomers in a 1:1 ratio (C1A1 hydrogel), which served as an effective scaffold for the attachment of neural stem cells (NSCs). In the 3D environment of porous C1A1 hydrogels engineered by the cryogelation technique, NSCs differentiated into neuroglial cells. The C1A1 porous hydrogel was implanted into brain defects in a mouse traumatic damage model. The VEGF-immersed C1A1 porous hydrogel promoted host-derived vascular network formation together with the infiltration of macrophages/microglia and astrocytes into the gel. Furthermore, the stepwise transplantation of GFP-labeled NSCs supported differentiation to glial and neuronal cells. Therefore, this two-step method for neural regeneration may become a new approach for therapeutic brain tissue reconstruction after brain damage in the future. One Sentence SummaryBrain tissue reconstruction using charged hydrogel and stepwise NCS injection

bioengineering↗

bioRxiv2022

Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain

Survivors of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection frequently experience lingering neurological symptoms, including impairment in attention, concentration, speed of information processing and memory. This long-COVID cognitive syndrome shares many features with the syndrome of cancer therapy-related cognitive impairment (CRCI). Neuroinflammation, particularly microglial reactivity and consequent dysregulation of hippocampal neurogenesis and oligodendrocyte lineage cells, is central to CRCI. We hypothesized that similar cellular mechanisms may contribute to the persistent neurological symptoms associated with even mild SARS-CoV-2 respiratory infection. Here, we explored neuroinflammation caused by mild respiratory SARS-CoV-2 infection - without neuroinvasion - and effects on hippocampal neurogenesis and the oligodendroglial lineage. Using a mouse model of mild respiratory SARS-CoV-2 infection induced by intranasal SARS-CoV-2 delivery, we found white matter-selective microglial reactivity, a pattern observed in CRCI. Human brain tissue from 9 individuals with COVID-19 or SARS-CoV-2 infection exhibits the same pattern of prominent white matter-selective microglial reactivity. In mice, pro-inflammatory CSF cytokines/chemokines were elevated for at least 7-weeks post-infection; among the chemokines demonstrating persistent elevation is CCL11, which is associated with impairments in neurogenesis and cognitive function. Humans experiencing long-COVID with cognitive symptoms (48 subjects) similarly demonstrate elevated CCL11 levels compared to those with long-COVID who lack cognitive symptoms (15 subjects). Impaired hippocampal neurogenesis, decreased oligodendrocytes and myelin loss in subcortical white matter were evident at 1 week, and persisted until at least 7 weeks, following mild respiratory SARS-CoV-2 infection in mice. Taken together, the findings presented here illustrate striking similarities between neuropathophysiology after cancer therapy and after SARS-CoV-2 infection, and elucidate cellular deficits that may contribute to lasting neurological symptoms following even mild SARS-CoV-2 infection.

neuroscience↗

bioRxiv2021

LINE-1 activation in the cerebellum drives ataxia

Previous studies have revealed that dysregulation of long interspersed nuclear element 1 (LINE-1), a dominant class of transposable elements in the human genome, correlates with neurodegeneration1-3. Yet whether LINE-1 dysregulation is causal to disease pathogenesis has not been proven directly. Here, we demonstrate that expression of evolutionarily younger LINE-1 families is elevated in the cerebella of ataxia telangiectasia (AT) patients, which was correlated with extensive downregulation of epigenetic silencers. To examine whether LINE-1 activation causes neurologic disease, we established an approach to directly target and activate the promoter of a young family of LINE-1 in mice. LINE-1 activation in the cerebellum was sufficient to lead to robust progressive ataxia. Purkinje cells in the diseased mice exhibited marked electrophysiological dysfunctions and degeneration with a significant accumulation of cytoplasmic ribonucleoprotein LINE-1Orf1p aggregates, endoplasmic reticulum (ER) stress, and DNA damage. Treatment with lamivudine, a nucleoside reverse transcriptase inhibitor, blunted the disease progression by reducing DNA damage, attenuating gliosis and interferon gene signature, and recovering the loss of key functional molecules for calcium homeostasis in Purkinje cells. This study provides direct evidence that young LINE-1 activation drives ataxia phenotype, and points to its pleiotropic effects leading to DNA damage, inflammation, and dysfunction and degeneration of neurons.

neuroscience↗

bioRxiv2021

Microtubule assembly by soluble tau impairs vesicle endocytosis and excitatory neurotransmission via dynamin sequestration in Alzheimer's disease synapse model

Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in Alzheimers disease. We addressed whether tau elevation affects synaptic transmission at the calyx of Held in brainstem slices. Whole-cell loading of WT human tau (h-tau) in presynaptic terminals at 10-20 {micro}M caused microtubule (MT) assembly and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking MT assembly using nocodazole prevented tau-induced impairments of endocytosis and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly by WT h-tau loading was associated with an increased bound fraction of the endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin-1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced impairments of endocytosis and neurotransmission. We conclude that elevation of presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired, causing activity-dependent rundown of neurotransmission. Significance StatementWild-type human recombinant tau loaded in rodent presynaptic terminals inhibited vesicle endocytosis, thereby causing activity-dependent rundown of excitatory transmission. This endocytic block is caused by a sequestration of dynamin by excess microtubules newly assembled by tau and can be rescued by a peptide inhibiting the microtubules-dynamin interaction, or by the microtubule disassembler nocodazole. Thus, synaptic dysfunction can be induced by pathological increase of endogenous soluble tau in Alzheimer disease slice model.

neuroscience↗

bioRxiv2021

Acoustic frequency-dependent physical mechanism of sub-MHz ultrasound neurostimulation

Ultrasound is an innovative physical modality allowing non-invasive and reversible modulation of neural circuit activity in the brain with high spatial resolution. Despite growing interest in clinical applications, the safe and effective use of ultrasound neuromodulation has been limited by a lack of understanding of the physical mechanisms underlying its effects. Here, we demonstrate acoustic frequency-dependent physical effects that underlie ultrasound neuromodulation, where cavitation and radiation forces are the dominant sources of low- and high-frequency stimulation, respectively. We used 39.5 kHz and 500 kHz acoustic frequencies to stimulate cultured neural and glial cells, excised from rat cortex, to study acoustic frequency-dependent neural responses. We demonstrate increased evoked responses due to increased cavitation activity at the 39.5 kHz acoustic frequency. In contrast, notable cavitation activity was not detected at 500 kHz despite detection of evoked responses. Our work highlights the dependence of ultrasound neuromodulation on acoustic frequencies, with different physical effects underlying cell responses to low and high sub-MHz acoustic frequency ranges.

bioengineering↗

bioRxiv2021

The Relationship between Stability of Interpersonal Coordination and Inter-Brain EEG Synchronization during Anti-phase Tapping

Inter-brain synchronization is enhanced when individuals perform rhythmic interpersonal coordination tasks, such as playing instruments in music ensembles. Experimentally, synchronization has been shown to correlate with the performance of joint tapping tasks. However, it is unclear whether inter-brain synchronization is related to the stability of interpersonal coordination represented as the standard deviation of relative phase (SDRP). In this study, we simultaneously recorded electroencephalograms of two paired individuals during anti-phase tapping in three speed conditions: slow (reference inter-tap interval [ITI]: 0.5 s), fast (reference ITI: 0.25 s), and free (preferred ITI). We calculated the inter-brain synchronization within six regions of interest: frontal, central, left/right temporal, parietal, and occipital regions. We found that synchronization of the central-temporal regions was positively correlated with SDRP in the theta and alpha bands, while synchronization of the frontal-frontal and frontal-central was positively correlated with SDRP in the beta band. These results demonstrate that inter-brain synchronization occurs only when task requirements are high, and that it increases with the instability of the coordination. This may be explained by the stronger mutual prediction required in unstable coordination than that in stable coordination, which increases inter-brain synchronization.

neuroscience↗

bioRxiv2021

Evaluation of the Efficacy and Safety of a Clinical Grade Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Patch: A Pre-Clinical Study

AimsCardiomyocyte-derived induced pluripotent stem cells (iPSCs) may represent a promising therapeutic strategy for severely damaged myocardium. This study aimed to assess the efficacy and safety of clinical grade human iPSC-derived cardiomyocyte (hiPSC-CM) patches and conduct a pre-clinical proof-of-concept analysis. Methods and resultsA clinical grade hiPSC line was established from peripheral blood mononuclear cells collected from a healthy volunteer homozygous for human leukocyte antigens and differentiated into cardiomyocytes using cytokines and chemical compounds. hiPSC-CMs were cultured on temperature-responsive culture dishes to fabricate the hiPSC-CM patch. The hiPSC-CMs expressed cardiomyocyte-specific genes and proteins while electrophysiological analyses revealed that hiPSC-CMs were similar to the human myocardium. In vitro safety studies using cell growth, soft agar colony formation, and undifferentiated cell assays indicated that tumourigenic cells were not present. Moreover, no genomic mutations were discovered using whole genome and exome sequencing analysis. Tumour formation was not detected in an in vivo tumourigenicity assay using NOG mice. General toxicity tests also showed no adverse events due to hiPSC-CM patch transplantation. An efficacy study using a porcine model of myocardial infarction demonstrated significantly improved cardiac function with angiogenesis and a reduction in interstitial fibrosis, which was enhanced by cytokine secretion from hiPSC-CM patches after transplantation. No lethal arrhythmias were observed. ConclusionhiPSC-CM patches show promise for future translational research and clinical trials for ischaemic heart failure. One-sentence summaryThis pre-clinical study provides a proof-of-concept of the safety and efficacy of hiPSC-CM patches for the treatment of heart failure. Translational PerspectiveRegenerative therapy using cells and tissues is attractive as a novel approach for treating severe heart failure. We focused on human iPS cell-derived cardiomyocytes (hiPSC-CMs) as a cell source. Using basic research, the characteristics of hiPSC, hiPSC-CMs, and hiPSC-CM patches were determined in vitro and in vivo. We also conducted a pre-clinical study using a porcine model of myocardial infarction that confirmed the safety and efficacy of the hiPSC-CM patch, highlighting its potential for clinical application.

cell biology↗

bioRxiv2020

Crosstalk between repair pathways elicits Double-Strand Breaks in alkylated DNA: implications for the action of temozolomide

Temozolomide (TMZ), a DNA methylating agent, is the primary chemotherapeutic drug used in glioblastoma treatment. TMZ induces mostly N-alkylation adducts (N7-methylguanine and N3-methyladenine) and some O6-methylguanine (O6mG). Current models propose that during DNA replication, thymine is incorporated across from O6mG, promoting a futile cycle of mismatch repair (MMR) that leads to DNA double strand breaks (DSBs). To revisit the mechanism of O6mG processing, we reacted plasmid DNA with N-Methyl-N-nitrosourea (MNU), a temozolomide mimic, and incubated it in Xenopus egg extracts. We show that in this system, mismatch repair (MMR) proteins are enriched on MNU-treated DNA and we observe robust, MMR-dependent, repair synthesis. Our evidence also suggests that MMR, initiated at O6mG:C sites, is strongly stimulated in cis by repair processing of other lesions, such as N-alkylation adducts. Importantly, MNU-treated plasmids display DSBs in extracts, the frequency of which increased linearly with the square of alkylation dose. We suggest that DSBs result from two independent repair processes, one involving MMR at O6mG:C sites and the other involving BER acting at a nearby N-alkylation adducts. We propose a new, replication-independent mechanism of action of TMZ, that operates in addition to the well-studied cell cycle dependent mode of action.

biochemistry↗

bioRxiv2020

Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease

1The biomedical community is producing increasingly high dimensional datasets, integrated from hundreds of patient samples, which current computational techniques struggle to explore. To uncover biological meaning from these complex datasets, we present an approach called Multiscale PHATE, which learns abstracted biological features from data that can be directly predictive of disease. Built on a continuous coarse graining process called diffusion condensation, Multiscale PHATE creates a tree of data granularities that can be cut at coarse levels for high level summarizations of data, as well as at fine levels for detailed representations on subsets. We apply Multiscale PHATE to study the immune response to COVID-19 in 54 million cells from 168 hospitalized patients. Through our analysis of patient samples, we identify CD16hi CD66blo neutrophil and IFN{gamma}+GranzymeB+ Th17 cell responses enriched in patients who die. Further, we show that population groupings Multiscale PHATE discovers can be directly fed into a classifier to predict disease outcome. We also use Multiscale PHATE-derived features to construct two different manifolds of patients, one from abstracted flow cytometry features and another directly on patient clinical features, both associating immune subsets and clinical markers with outcome.

bioinformatics↗

bioRxiv2020

Neural correlates of temporal presentness in theprecuneus: a crosslinguistic fMRI study based on speech stimuli

AbstractsThe position of any event in time could be either present, past, or future. This temporal discrimination is vitally important in our daily conversations, but it remains elusive how the human brain distinguishes among the past, present, and future. To address this issue, we searched for neural correlates of presentness, pastness, and futurity, each of which is automatically evoked when we hear sentences such as it is raining now, it rained yesterday, or it will rain tomorrow. Here, we show that sentences that evoked presentness activated the bilateral precuneus more strongly than those that evoked pastness or futurity. Interestingly, this contrast was shared across native speakers of Japanese, English, and Chinese, languages which vary considerably in their verb tense systems. The results suggest that the precuneus serves as a key region that provides the origin, the Now, to our time perception irrespective of differences in tense systems across languages.

neuroscience↗

bioRxiv2019

A role of causal inference in non-stationary environments

Bayesian inference is the process of narrowing down the hypotheses (causes) to the one that best explains the observational data (effects). To accurately estimate a cause, a considerable amount of data is required to be observed for as long as possible. However, the object of inference is not always constant. In this case, a method such as exponential moving average (EMA) with a discounting rate is used to improve the ability to respond to a sudden change; it is also necessary to increase the discounting rate. That is, a trade-off is established in which the followability is improved by increasing the discounting rate, but the accuracy is reduced. Here, we propose an extended Bayesian inference (EBI), wherein human-like causal inference is incorporated. We show that both the learning and forgetting effects are introduced into Bayesian inference by incorporating the causal inference. We evaluate the estimation performance of the EBI through the learning task of a dynamically changing Gaussian mixture model. In the evaluation, the EBI performance is compared with those of the EMA and a sequential discounting expectation-maximization algorithm. The EBI was shown to modify the trade-off observed in the EMA.

animal behavior and cognition↗

bioRxiv2019

Role of microRNA-21 in hypertrophic cardiac remodeling

Hypertension is a major public health problem among with aging population worldwide. It causes cardiac remodeling, including hypertrophy and interstitial fibrosis, which leads to development of hypertensive heart disease (HHD). Although microRNA-21 (miR-21) is associated with fibrogenesis in multiple organs, its impact on hypertrophic cardiac remodeling in hypertension is not known. Circulating miR-21 level was higher in patients with HHD than that in the control subjects. It also positively correlated with serum myocardial fibrotic markers. MiR-21 expression levels were significantly upregulated in the mice hearts after angiotensin II (Ang II) infusion or transverse aortic constriction (TAC) compared with control mice. Expression level of programmed cell death 4 (PDCD4), a main target of miR-21, was significantly decreased in Ang II infused mice and TAC mice compared with control mice. Expression levels of transcriptional activator protein 1 (AP-1) and transforming growth factor-{beta}1 (TGF-{beta}1), which were downstream targets of PDCD4, were increased in Ang II infused mice and TAC mice compared with control mice. In vitro, mirVana-miR-21-specific inhibitor attenuated Ang II-induced PDCD4 downregulation and contributed to subsequent deactivation of AP-1/TGF-{beta}1 signaling pathway in neonatal rat cardiomyocytes. Thus, suppression of miR-21 prevents hypertrophic cardiac remodeling by regulating PDCD4, AP-1, and TGF-{beta}1 signaling pathway.

molecular biology↗

bioRxiv2019

Large scale genome-wide association study in a Japanese population identified 45 novel susceptibility loci for 22 diseases

INTRODUCTORY PARAGRAPHThe overwhelming majority of participants in current genetic studies are of European ancestry1-3, limiting our genetic understanding of complex disease in non-European populations. To address this, we aimed to elucidate polygenic disease biology in the East Asian population by conducting a genome-wide association study (GWAS) with 212,453 Japanese individuals across 42 diseases. We detected 383 independent signals in 331 loci for 30 diseases, among which 45 loci were novel (P < 5 x 10-8). Compared with known variants, novel variants have lower frequency in European populations but comparable frequency in East Asian populations, suggesting the advantage of this study in discovering these novel variants. Three novel signals were in linkage disequilibrium (r2 > 0.6) with missense variants which are monomorphic in European populations (1000 Genomes Project) including rs11235604(p.R220W of ATG16L2, a autophagy-related gene) associated with coronary artery disease. We further investigated enrichment of heritability within 2,868 annotations of genome-wide transcription factor occupancy, andidentified 378 significant enrichments across nine diseases (FDR < 0.05) (e.g. NF-{kappa}B for immune-related diseases). This large-scale GWAS in a Japanese population provides insights into the etiology of common complex diseases and highlights the importance of performing GWAS in non-European populations.

genetics↗

bioRxiv2019

Extended Bayesian inference incorporating symmetry bias

In this study, we start by proposing a causal induction model that incorporates symmetry bias. This model has two parameters that control the strength of symmetry bias and includes conditional probability and conventional models of causal induction as special cases. It can reproduce causal induction of human judgment with high accuracy. We further propose a human-like Bayesian inference method to replace the conditional probability in Bayesian inference with the aforementioned causal induction model. In this method, two components coexist: the component of Bayesian inference, which updates the degree of confidence for each hypothesis, and the component of inverse Bayesian inference that modifies the model of each hypothesis. In other words, this method allows not only inference but also simultaneous learning. Our study demonstrates that the method with both Bayesian inference and inverse Bayesian inference enables us to deal flexibly with unsteady situations where the target of inference changes occasionally.

animal behavior and cognition↗

bioRxiv2018

A regulatory module controlling stress-induced cell cycle arrest in Arabidopsis

Cell cycle arrest is an active response to stresses that enables organisms to survive under fluctuating environmental conditions. While signalling pathways that inhibit cell cycle progression have been elucidated, the putative core module orchestrating cell cycle arrest in response to various stresses is still elusive. Here we report that in Arabidopsis thaliana, the NAC-type transcription factors ANAC044 and ANAC085 are required for DNA damage-induced G2 arrest. Under genotoxic stress conditions, ANAC044 and ANAC085 enhance protein accumulation of the R1R2R3-type Myb transcription factor (Rep-MYB), which represses G2/M-specific genes. ANAC044/ANAC085-dependent accumulation of Rep-MYB and cell cycle arrest are also observed in the response to heat stress that causes G2 arrest, but not to osmotic stress that retards G1 progression. These results suggest that plants deploy the ANAC044/ANAC085-mediated signalling module as a hub which perceives distinct stress signals and leads to G2 arrest.

plant biology↗

bioRxiv2018

Direct binding of Cdt2 to PCNA is important for targeting the CRL4Cdt2 E3 ligase activity to Cdt1

The CRL4Cdt2 ubiquitin ligase complex is an essential regulator of cell-cycle progression and genome stability, ubiquitinating substrates such as p21, Set8 and Cdt1, via a display of substrate degrons on PCNA. Here, we examine the hierarchy of the ligase and substrate recruitment kinetics onto PCNA at sites of DNA replication. We demonstrate that the C-terminal end of Cdt2 bears a PCNA interaction protein motif (PIP box, Cdt2PIP), which is necessary and sufficient for binding of Cdt2 to PCNA. Cdt2PIP binds PCNA directly with high affinity, two orders of magnitude tighter than the PIP box of Cdt1. X-ray crystallographic structures of PCNA bound to Cdt2PIP and Cdt1PIP show that the peptides occupy all three binding sites of the trimeric PCNA ring. Mutating Cdt2PIP weakens the interaction with PCNA, rendering CRL4Cdt2 less effective in Cdt1 ubiquitination and leading to defects in Cdt1 degradation. The molecular mechanism we present suggests a new paradigm for bringing substrates to the CRL4-type ligase, where the substrate receptor and substrates bind to a common multivalent docking platform to enable subsequent ubiquitination.\n\nSummary blurbThe C-terminal end of Cdt2 contains a PIP-box for binding to PCNA to promote CRL4Cdt2 function, creating a new paradigm, where the substrate receptor and substrates bind to a common multivalent docking platform for ubiquitination.

molecular biology↗

bioRxiv2018

Positive-feedback defines the timing and robustness of angiogenesis

Blood vessel formation by angiogenesis is critical for tissue development, homeostasis and repair, and is frequently dysregulated in disease[1-3]. Angiogenesis is triggered by vascular endothelial growth factor receptor-2/3 (VEGFR) signalling, which induces motile endothelial cell (ECs) tip identity[4,5]. Tip cells lead new branching vessels, but also coordinate collective EC movement by repressing tip identity in adjacent ECs via Delta-Like 4 (DLL4)-Notch-mediated down-regulation of VEGFR activity[6-13]. Hence, angiogenesis is driven by lateral inhibition-mediated competition of ECs for migratory status. Recent work reveals that temporal modulation of this DLL4-Notch-mediated lateral inhibition circuit fundamentally shapes both normal and pathological angiogenesis[14-17]. However, the core regulatory network defining the timing and dynamics of EC decision-making is unclear. Here, by integrating computational modeling with in-vivo experimentation, we uncover a unique ultrasensitive switch that temporally defines EC lateral inhibition and ultimately determines the timing, magnitude and robustness of angiogenic responses. We reveal that positive-feedback to Vegfr via the atypical tetraspanin, tm4sf18, amplifies Vegfr activity and expedites EC decision-making in-vivo. Moreover, this Tm4sf18-mediated positive-feedback confers robustness to angiogenesis against changeable environmental conditions by invoking bistable-like behavior. Consequently, mutation of tm4sf18 in zebrafish delays motile EC selection, generates hypoplastic vessels, sensitizes ECs to fluctuations in pro-angiogenic signal and disrupts angiogenesis. We propose that positive-feedback transforms the normally protracted process of lateral inhibition into a quick, adaptive and robust decision-making mechanism, suggestive of a general framework for temporal modulation of cell fate specification in development and disease.

developmental biology↗