Biology subjects

Yoshida, T.

Publications and source records attributed to Yoshida, T..

82 records · Page 5Linked to original sources

bioRxiv2019

Translocational unfolding in clostridial binary iota toxin complex

Protein translocation across the membrane is critical for microbial pathogenesis and various cellular functions. Bacterial binary toxins such as anthrax toxin are composed of enzyme components and a translocation channel, which catalyses substrate unfolding and translocation. Here we report the structures of the clostridial binary toxin (iota toxin) translocation channel Ib-pore and its complex with ADP-ribosyltransferase Ia. The Ib-pore structure at atomic resolution provides a similar structural framework as observed for the catalytic {phi}-clamp of the anthrax protective antigen pore. However, the Ia-bound Ib-pore structure showed a unique binding mode of Ia: one Ia binds to the Ib-pore, and the Ia N-terminal domain interacts with Ib via two other Ib-pore bottlenecks with multiple weak interactions. Furthermore, Ib-binding induces Ia N-terminal -helix tilting and partial unfolding, whereupon the unfolded N-terminus continues to the {phi}-clamp gate. This study reveals the novel mechanism of N-terminal unfolding, which is crucial for protein translocation.

biophysics↗

bioRxiv2019

Differential scanning fluorimetric analysis of the amino-acid binding to taste receptor using a model receptor protein, the ligand-binding domain of fish T1r2a/T1r3

Taste receptor type 1 (T1r) is responsible for the perception of essential nutrients, such as sugars and amino acids, and evoking sweet and umami (savory) taste sensations. T1r receptors recognize many of the taste substances at their extracellular ligand-binding domains (LBDs). In order to detect a wide array of taste substances in the environment, T1r receptors often possess broad ligand specificities. However, the entire ranges of chemical spaces and their binding characteristics to any T1rLBDs have not been extensively analyzed. In this study, we exploited the differential scanning fluorimetry (DSF) to medaka T1r2a/T1r3LBD, a current sole T1rLBD heterodimer amenable for recombinant preparation, and analyzed their thermal stabilization by adding various amino acids. The assay showed that the agonist amino acids induced thermal stabilization and shifted the melting temperatures (Tm) of the protein. An agreement between the DSF results and the previous biophysical assay was observed, suggesting that DSF can detect ligand binding at the orthosteric-binding site in T1r2a/T1r3LBD. The assay further demonstrated that most of the tested L-amino acids, but no D-amino acid, induced Tm shifts of T1r2a/T1r3LBD, indicating the broad L-amino acid specificities of the proteins probably with several different manners of recognition. The Tm shifts by each amino acid also showed a fair correlation with the responses exhibited by the full-length receptor, verifying the broad amino-acid binding profiles at the orthosteric site in LBD observed by DSF.

biochemistry↗

bioRxiv2019

Microstimulation of primate neocortex targeting striosomes induces negative decision-making

Affective judgment and decision-making are strongly modulated by the pregenual anterior cingulate (pACC) and caudal orbitofrontal (cOFC) cortical regions. By combining MRI-guided electrical microstimulation with viral tracing methods in non-human primates, we demonstrate that circumscribed pACC and cOFC microstimulation sites that induce negative decision-making preferentially project to striosomes in the anterior striatum. These results outline a behaviorally important circuit from pACC/cOFC to striosomes causally modulating decision-making under emotional conflict.

neuroscience↗

bioRxiv2019

Microbial community-level features linked to divergent carbon flows during early litter decomposition in a constant environment

During plant litter decomposition in soils, carbon has two general fates: return to the atmosphere via microbial respiration or transport into soil where long-term storage may occur. Discovering microbial community features that drive carbon fate from litter decomposition may improve modeling and management of soil carbon. This concept assumes there are features (or underlying processes) that are widespread among disparate communities, and therefore amenable to modeling. We tested this assumption using an epidemiological approach in which two contrasting patterns of carbon flow in laboratory microcosms were delineated as functional states and diverse microbial communities representing each state were compared to discover shared features linked to carbon fate. Microbial communities from 206 soil samples from the southwestern United States were inoculated on plant litter in microcosms, and carbon flow was measured as cumulative carbon dioxide (CO2) and dissolved organic carbon (DOC) after 44 days. Carbon flow varied widely among the microcosms, with a 2-fold range in cumulative CO2 efflux and a 5-fold range in DOC quantity. Bacteria, not fungi, were the strongest drivers of DOC variation. The most significant community-level feature linked to DOC abundance was bacterial richness--the same feature linked to carbon fate in human-gut microbiome studies. This proof-of-principle study under controlled conditions suggests common features driving carbon flow in disparate microbial communities can be identified, motivating further exploration of underlying mechanisms that may influence carbon fate in natural ecosystems.

microbiology↗

bioRxiv2019

Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake

Metagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and their ecological interaction with hosts remain poorly understood. Here, we conducted a metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion (<0.22 m) and cellular (0.22-5.0 m) fractions collected spatiotemporally from a deep freshwater lake (Lake Biwa, Japan). This simultaneously reconstructed 183 complete (i.e., circular) viral genomes and 57 bacterioplankton metagenome-assembled genomes. Analysis of metagenomic read coverage revealed vertical partitioning of the viral community analogous to the vertically stratified bacterioplankton community. The hypolimnetic community was generally stable during stratification, but occasionally shifted abruptly, presumably due to lysogenic induction. Genes involved in assimilatory sulfate reduction were encoded in 20 (10.9%) viral genomes, including those of dominant viruses, and may aid viral propagation in sulfur-limited freshwater systems. Hosts were predicted for 40 (21.9%) viral genomes, encompassing 10 phyla (or classes of Proteobacteria) including ubiquitous freshwater bacterioplankton lineages (e.g., Ca. Fonsibacter and Ca. Nitrosoarchaeum). Comparison with viral genomes derived from published metagenomes revealed viral phylogeographic connectivity in geographically isolated habitats. Notably, analogous to their hosts, actinobacterial viruses were among the most diverse, ubiquitous, and abundant viral groups in freshwater systems, with potential high lytic activity in surface waters.

microbiology↗

bioRxiv2019

Nintedanib ameliorates experimental pulmonary arterial hypertension via inhibition of endothelial mesenchymal transition and smooth muscle cell proliferation

Neointimal lesion and medial wall thickness of pulmonary arteries (PAs) are common pathological findings in pulmonary arterial hypertension (PAH). Platelet-derived growth factor (PDGF) and fibroblast growth factor (FGF) signaling contribute to intimal and medial vascular remodeling in PAH. Nintedanib is a tyrosine kinase inhibitor whose targets include PDGF and FGF receptors. Although the beneficial effects of nintedanib were demonstrated for human idiopathic pulmonary fibrosis, its efficacy for PAH is still unclear. Thus, we hypothesized that nintedanib is a novel treatment for PAH to inhibit the progression of vascular remodeling in PAs. The inhibitory effects of nintedanib were evaluated both in endothelial mesenchymal transition (EndMT)-induced human pulmonary microvascular endothelial cells (HPMVECs) and human pulmonary arterial smooth muscle cells (HPASMCs) stimulated by growth factors. We also tested the effect of chronic nintedanib administration on a PAH rat model induced by Sugen5416 (a VEGF receptor inhibitor) combined with chronic hypoxia. Nintedanib was administered from weeks 3 to 5 after Sugen5416 injection, and pulmonary hemodynamics and PAs pathology were evaluated. Nintedanib attenuated the expression of mesenchymal markers in EndMT-induced HPMVECs and HPASMCs proliferation. Phosphorylation of PDGF and FGF receptors was augmented both in both intimal and medial lesions of PAs. Nintedanib blocked these phosphorylation, improved hemodynamics and reduced vascular remodeling involving neointimal lesions and medial wall thickening in PAs. Additionally, expressions Twist1, transcription factors associated with EndMT, in lung tissue was significantly reduced by nintedanib. These results suggest that nintedanib may be a novel treatment for PAH with anti-vascular remodeling effects.

physiology↗

bioRxiv2018

Hypomorphic mutation of the mouse Huntingtons disease gene orthologue

Rare individuals with hypomorphic inactivating mutations in the Huntingtons Disease (HD) gene (HTT), identified by CAG repeat expansion in the eponymous neurodegenerative disorder, exhibit variable abnormalities that imply HTT essential roles during organ development. Here we report phenotypes produced when increasingly severe hypomorphic mutations in Htt, the murine HTT orthologue (in HdhneoQ20, HdhneoQ50, HdhneoQ111 mice), were placed over a null allele (Hdhex4/5). The most severe hypomorphic allele failed to rescue null lethality at gastrulation, while the intermediate alleles yielded perinatal lethality and a variety of fetal abnormalities affecting body size, skin, skeletal and ear formation, and transient defects in hematopoiesis. Comparative molecular analysis of wild-type and Htt-null retinoic acid-differentiated cells revealed gene network dysregulation associated with organ development and proposed polycomb repressive complexes and miRNAs as molecular mediators. Together these findings demonstrate that the HD gene acts both pre- and post-gastrulation and possibly suggest pleiotropic consequences of HTT-lowering therapeutic strategies.\n\nAuthor SummaryThe HTT gene product mutated in Huntingtons Disease (HD) has essential roles during normal organism development, however, still not fully predictable are the functional consequences of its partial inactivation. Our genetic study provides a comprehensive effects description of progressively stronger suppression of Htt gene, the murine HTT counterpart. The most severe Htt reduction leads to embryo lethality, while intermediate Htt dosages yield a variety of developmental abnormalities affecting body size, skin, skeletal and ear formation, and hematopoiesis. Complementing molecular analysis in differentiating cells depleted of a functional Htt gene further elucidates genes networks dysregulated during organ development and proposes chromatin regulators and short non-coding RNAs as key molecular mediators. Together these findings demonstrate that the HD gene acts both at early and later stages of development, thus possibly suggesting long-term consequences associated to the newest HD therapeutic strategies aimed at lowering the HTT gene product.

genetics↗

bioRxiv2018

Relationships of trainee dentists’ empathy and communication characteristics with simulated patients’ assessment in medical interviews

ObjectivesWe aimed to clarify the characteristics of communication between trainee dentists and simulated patients (SPs) and to examine how the level of trainee dentists self-reported empathy influences assessment by SPs in medical interviews.\n\nMaterials and methodsThe study involved 100 trainee dentists at Okayama University Hospital and eight SPs. The trainee dentists conducted initial interviews with the SPs after completing the Japanese version of the Jefferson Scale of Empathy. Their interviews were recorded and analyzed using the Roter Interaction Analysis System. The SPs assessed the trainees communication immediately after each interview. The trainee dentists were classified into two groups (more positive and less positive groups) according to SP assessment scores.\n\nResultsCompared with the less positive trainees, the more positive trainees scored higher on the [Emotional expression] and lower on the [Medical data gathering] Roter Interaction Analysis System categories. There was no difference in [Dental data gathering] between the two groups. The SPs of more positive trainees had higher rates of [Positive talk] and [Emotional expression] and lower rates of [Medical information giving] and [Dental information giving]. The trainees with more positive ratings from SPs had significantly higher Jefferson Scale of Empathy total scores.\n\nConclusionThe results of this study suggest that responding to the SPs emotions is a relevant characteristic of dentist-SP communication to SPs positive assessment in medical interviews. Further, trainees self-reported empathy was related with the SPs assessment of trainees communication, which indicated that patient satisfaction can be improved by increasing the dentists empathy. Thus, an empathic attitude among dentists is a significant determinant of patient satisfaction.

scientific communication and education↗

bioRxiv2018

Characterization of nonlinear receptive fields of visual neurons by convolutional neural network

A comprehensive understanding of the stimulus-response properties of individual neurons is necessary to crack the neural code of sensory cortices. However, a barrier to achieving this goal is the difficulty of analyzing the nonlinearity of neuronal responses. In computer vision, artificial neural networks, especially convolutional neural networks (CNNs), have demonstrated state-of-the-art performance in image recognition by capturing the higher-order statistics of natural images. Here, we incorporated CNN for encoding models of neurons in the visual cortex to develop a new method of nonlinear response characterization, especially nonlinear estimation of receptive fields (RFs), without assumptions regarding the type of nonlinearity. Briefly, after training CNN to predict the visual responses of neurons to natural images, we synthesized the RF image such that the image would predictively evoke a maximum response (\"maximization-of-activation\" method). We first demonstrated the proof-of-principle using a dataset of simulated cells with various types of nonlinearity, revealing that CNN could be used to estimate the nonlinear RF of simulated cells. In particular, we could visualize various types of nonlinearity underlying the responses, such as shift-invariant RFs or rotation-invariant RFs. These results suggest that the method may be applicable to neurons with complex nonlinearities, such as rotation-invariant neurons in higher visual areas. Next, we applied the method to a dataset of neurons in the mouse primary visual cortex (V1) whose responses to natural images were recorded via two-photon Ca2+ imaging. We could visualize shift-invariant RFs with Gabor-like shapes for some V1 neurons. By quantifying the degree of shift-invariance, each V1 neuron was classified as either a shift-variant (simple) cell or shift-invariant (complex-like) cell, and these two types of neurons were not clustered in cortical space. These results suggest that the novel CNN encoding model is useful in nonlinear response analyses of visual neurons and potentially of any sensory neurons.

neuroscience↗

bioRxiv2018

Representation of natural image contents by sparsely active neurons in visual cortex

Natural scenes sparsely activate neurons in the primary visual cortex (V1). However, how sparsely active neurons robustly represent natural images and how the information is optimally decoded from the representation have not been revealed. We reconstructed natural images from V1 activity in anaesthetized and awake mice. A single natural image was linearly decodable from a surprisingly small number of highly responsive neurons, and an additional use of remaining neurons even degraded the decoding. This representation was achieved by diverse receptive fields (RFs) of the small number of highly responsive neurons. Furthermore, these neurons reliably represented the image across trials, regardless of trial-to-trial response variability. The reliable representation was supported by multiple neurons with overlapping RFs. Based on our results, the diverse, partially overlapping RFs ensure sparse and reliable representation. We propose a new representation scheme in which information is reliably represented while the representing neuronal patterns change across trials and that collecting only the activity of highly responsive neurons is an optimal decoding strategy for the downstream neurons

neuroscience↗