Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study.

Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.

Translating and validating a Japanese version of the instrument for patient assessment of medical professionalism (J-IPAMP): a cross-sectional survey.

BACKGROUND: Although there are many tools to assess medical professionalism, they rarely address patients' perspectives. The instrument for patient assessment of medical professionalism (IPAMP) comprises 11 items and has been established and validated as a valuable tool for assessing trainees' professionalism from the patient's perspective. However, there is no instrument to assess professionalism from the patient's perspective in Japan. The purpose of the present study was to develop a Japanese version of the IPAMP (J-IPAMP) and test its validity and reliability. METHODS: We conducted a cross-sectional survey to examine the reliability and validity of the J-IPAMP in two hospitals (one each in an urban and rural area) in Japan. Receptionists or surveyors distributed the anonymous questionnaire to 276 inpatients; all participants were aged above 20 years and assigned to medical trainees. We evaluated its structural and criterion-related validity, as well as internal consistency reliability. RESULTS: Data of 235 (85.1%) patients were analyzed. Using the split-half validation technique, we performed an exploratory factor analysis (EFA) along with a confirmatory factor analysis (CFA). The EFA showed a one-factor solution. Then, to compare the model fitness between two models (the two-factor model from the original English version vs. unidimensional model suggested by the EFA), the CFA was performed. The CFA showed that almost all of the fit indices met their respective criteria and were approximately the same for the two models. Thus, we adopted a single-factor model. The Pearson correlation coefficients between the total J-IPAMP scores and the global ratings were 0.738, indicating adequate criterion-related validity. The Cronbach's alpha of the 11 items of the instrument was 0.96 (95% confidence interval: 0.96-0.97) and the omega value was 0.96, demonstrating acceptable internal consistency reliability. CONCLUSIONS: We developed the Japanese version of the IPAMP. Its validity and reliability were verified through analysis. This instrument can be utilized for professionalism education in the postgraduate training setting.

Epicatechin increases the persistence of long-term memory formed by conditioned taste aversion in Lymnaea.

We examined the effects of epicatechin (Epi), a flavonoid abundant in green tea and cocoa, on long-term memory (LTM) formed following conditioned taste aversion (CTA) training in Lymnaeastagnalis In CTA training, the snails learnt to avoid a food that initially they liked (i.e. sucrose). Twenty-four hours after CTA training, 67% of the trained snails showed a significant decrease in the feeding behaviour elicited by sucrose. Placing snails in the Epi solution in CTA training did not alter the percentage of snails exhibiting LTM, but it significantly increased LTM persistence. We also examined changes following Epi exposure in spontaneous activity of the cerebral giant cells (CGCs) that modulate feeding behaviour and are necessary for CTA-LTM. Our data suggest that Epi causes a decrease in CGC activity and increases LTM persistence, possibly via a GABAergic mechanism.

Quantifying scaling exponents for neurite morphology of in vitro-cultured human iPSC-derived neurons using discrete Loewner evolution: A statistical-physical approach to the neuropathology in Alzheimer's disease.

Defining the morphological disorders causing neurodegenerative diseases is an unresolved problem. In this study, we propose a statistical-physical approach to quantify neurite morphology and evaluate the pathological states induced by Alzheimer's disease (AD). We analyzed the two-dimensional morphologies of neurites of in vitro-cultured human induced-pluripotent stem cell-derived neurons, reprogrammed from both a healthy person and a patient with AD, using discrete chordal Loewner evolution. For the numerically calculated Loewner driving forces, detrended fluctuation analysis was performed, and the morphological characteristics of the neurites were quantified using short-range and long-range scaling exponents. The day in vitro (DIV)-dependent behaviors of the scaling exponents and the associated neurite-type categorizations suggested that differences between healthy and AD neurites can be observed from the early stage (DIV3) of their development. Notably, AD neurites have less long-range autocorrelations than healthy neurites, particularly in the earlier stages (DIV3-10). Immunofluorescence-staining results suggested that these differences precede significant expressions of ß-amyloid and phosphorylated tau, which are known as biological factors causing AD. We expect that these results will lead to a theoretical interpretation of the neurogenerative disease, providing the physical properties of individual neurites with different morphologies.

Non-Equilibrium Entropy and Irreversibility in Generalized Stochastic Loewner Evolution from an Information-Theoretic Perspective.

In this study, we theoretically investigated a generalized stochastic Loewner evolution (SLE) driven by reversible Langevin dynamics in the context of non-equilibrium statistical mechanics. Using the ability of Loewner evolution, which enables encoding of non-equilibrium systems into equilibrium systems, we formulated the encoding mechanism of the SLE by Gibbs entropy-based information-theoretic approaches to discuss its advantages as a means to better describe non-equilibrium systems. After deriving entropy production and flux for the 2D trajectories of the generalized SLE curves, we reformulated the system's entropic properties in terms of the Kullback-Leibler (KL) divergence. We demonstrate that this operation leads to alternative expressions of the Jarzynski equality and the second law of thermodynamics, which are consistent with the previously suggested theory of information thermodynamics. The irreversibility of the 2D trajectories is similarly discussed by decomposing the entropy into additive and non-additive parts. We numerically verified the non-equilibrium property of our model by simulating the long-time behavior of the entropic measure suggested by our formulation, referred to as the relative Loewner entropy.

Loewner driving force of the interface in the 2-dimensional Ising system as a chaotic dynamical system.

The interfaces in the 2-dimensional (2D) ferromagnetic Ising system below and at the critical temperature Tc were numerically analyzed in the framework of discrete Loewner evolution. We numerically calculated Loewner driving forces corresponding to the interfaces in the 2D Ising system and analyzed them using nonlinear time series analyses. We found that the dynamics of the Loewner driving forces showed chaotic properties wherein their intermittency, sensitivity to initial condition, and autocorrelation change depending on the temperature T of the system. It is notable that while the Loewner driving forces have deterministic properties, they have Gaussian-type probability distributions whose variance increases as T→Tc, indicating that they are examples of the Gaussian chaos. Thus, the obtained Loewner driving forces can be considered a chaotic dynamical system whose bifurcation is dominated by the temperature of the Ising system. This perspective for the dynamical system was discussed in relation to the extension and/or generalization of the stochastic Loewner evolution.

[A Case of Wernicke's Encephalopathy Presenting with Acute Deterioration of Consciousness Caused by Peripheral Parenteral Nutrition].

We report the case of a 67-year-old woman with Wernicke's encephalopathy(WE), who had been suffering from repeated vomiting and poor oral intake due to both reflux esophagitis and atrophic gastritis. She presented with altered of consciousness, horizontal nystagmus, and gait disturbance, and acute deterioration of consciousness was observed after starting peripheral parenteral nutrition (PPN). Brain MRI showed bilateral high intensity lesions in the medial thalamus and the dorsal midbrain on FLAIR and T2-weighted images. Although brain MRI characteristics are useful for diagnosing WE, it is possible that there are no abnormal MRI findings in its early stages. In addition, only 10-20% of WE cases present with the classical clinical triad of confusion, ophthalmoplegia, and ataxia. Therefore, confirming the diagnosis can be challenging. In general, rapid improvement of symptoms is observed with prompt vitamin B1 supplementation. However, delays in treatment can result in irreversible amnesia and ataxia. Furthermore, in the state of vitamin B1 deficiency, even PPN, not just total parenteral nutrition, can worsen symptoms, and this deterioration is attributed to the glucose load.

Binding properties of thyroxine to nuclear extract from sea urchin larvae.

We previously reported that thyroid hormones are involved in the formation of the adult rudiment and adult-type skeleton in sea urchin larvae, as well as in the resorption of larval tissues. In the present study, to search for the presence of thyroid hormone receptor in sea urchin larvae, we performed a ligand-binding assay between radiolabeled thyroid hormones and nuclear extracts from the larvae of the sea urchin Hemicentrotus pulcherrimus. The presence of binding sites with a high affinity to thyroxine (T4) was detected in the nuclear extract, but not in the cytoplasmic fraction. The dissociation constants for the T4 binding to the nuclear extracts were estimated to be about 18 pM from the mesenchyme-blastula stage to the four-armed pluteus stage. The quantity of T4 binding sites in the nuclear extracts increased during larval development. These results suggest that the binding affinity to T4 in the nuclear extracts was caused by a putative nuclear thyroid hormone receptor in sea urchin larvae.

Phosphorylation of endogenous α-synuclein induced by extracellular seeds initiates at the pre-synaptic region and spreads to the cell body.

Accumulation of phosphorylated α-synuclein aggregates has been implicated in several diseases, such as Parkinson's disease (PD) and dementia with Lewy bodies (DLB), and is thought to spread in a prion-like manner. Elucidating the mechanisms of prion-like transmission of α-synuclein is important for the development of therapies for these diseases, but little is known about the details. Here, we injected α-synuclein fibrils into the brains of wild-type mice and examined the early phase of the induction of phosphorylated α-synuclein accumulation. We found that phosphorylated α-synuclein appeared within a few days after the intracerebral injection. It was observed initially in presynaptic regions and subsequently extended its localization to axons and cell bodies.　These results suggest that extracellular α-synuclein fibrils are taken up into the presynaptic region and seed-dependently convert the endogenous normal α-synuclein that is abundant there to an abnormal phosphorylated form, which is then transported through the axon to the cell body.

Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community.

The simultaneous conservation of species richness and evenness is important to effectively reduce biodiversity loss and keep ecosystem health. Environmental DNA (eDNA) metabarcoding has been used as a powerful tool for identifying community composition, but it does not necessarily provide quantitative information due to several methodological limitations. Thus, the quantification of eDNA through metabarcoding is an important frontier of eDNA-based biomonitoring. Particularly, the qMiSeq approach has recently been developed as a quantitative metabarcoding method and has attracted much attention due to its usefulness. The aim here was to evaluate the performance of the qMiSeq approach as a quantitative monitoring tool for fish communities by comparing the quantified eDNA concentrations with the results of fish capture surveys. The eDNA water sampling and the capture surveys using the electrical shocker were conducted at a total of 21 sites in four rivers in Japan. As a result, we found significant positive relationships between the eDNA concentrations of each species quantified by qMiSeq and both the abundance and biomass of each captured taxon at each site. Furthermore, for seven out of eleven taxa, a significant positive relationship was observed between quantified DNA concentrations by sample and the abundance and/or biomass. In total, our results demonstrated that eDNA metabarcoding with the qMiSeq approach is a suitable and useful tool for quantitative monitoring of fish communities. Due to the simplicity of the eDNA analysis, the eDNA metabarcoding with qMiSeq approach would promote further growth of quantitative monitoring of biodiversity.

Perinatal Exposure of Bisphenol A Differently Affects Dendritic Spines of Male and Female Grown-Up Adult Hippocampal Neurons.

Perinatal exposure to Bisphenol A (BPA) at a very low dose may modulate the development of synapses of the hippocampus during growth to adulthood. Here, we demonstrate that perinatal exposure to 30 µg BPA/kg per mother's body weight/day significantly altered the dendritic spines of the grownup rat hippocampus. The density of the spine was analyzed by imaging of Lucifer Yellow-injected CA1 glutamatergic neurons in adult hippocampal slices. In offspring 3-month male hippocampus, the total spine density was significantly decreased by BPA exposure from 2.26 spines/µm (control, no BPA exposure) to 1.96 spines/µm (BPA exposure). BPA exposure considerably changed the normal 4-day estrous cycle of offspring 3-month females, resulting in a 4∼5 day estrous cycle with 2-day estrus stages in most of the subjects. In the offspring 3-month female hippocampus, the total spine density was significantly increased by BPA exposure at estrus stage from 2.04 spines/µm (control) to 2.25 spines/µm (BPA exposure). On the other hand, the total spine density at the proestrus stage was moderately decreased from 2.33 spines/µm (control) to 2.19 spines/µm (BPA exposure). Thus, after the perinatal exposure to BPA, the total spine density in males became lower than that in females. Concerning the BPA effect on the morphology of spines, the large-head spine was significantly changed with its significant decrease in males and moderate change in females.

Contribution of the trifluoroacetyl group in the thermodynamics of antigen-antibody binding.

We analyzed the binding of the 7C8 antibody to the chloramphenicol phosphonate antigens-one containing a trifluoroacetyl group (CP-F) and the other containing an acetyl group (CP-H)-by using isothermal titration calorimetry (ITC). The thermodynamic difference due to the substitution of F by H was evaluated using free energy calculations based on molecular dynamics (MD) simulations. We have previously shown that another antibody, namely, 6D9, binds more weakly to CP-H than to CP-F, mainly due to the different hydration free energies of the dissociated state and not due to the unfavorable hydrophobic interactions with the antibody in the bound state. Unlike in the binding of the trifluoroacetyl group with 6D9, in its binding with 7C8, it is exposed to the solvent, as seen in the crystal structure of the complex of 7C8 with CP-F. The thermodynamic analysis performed in this study showed that the binding affinity of 7C8 for CP-H is similar to that for CP-F, but this binding to CP-H is accompanied with less favorable enthalpy and more favorable entropy changes. The free energy calculations indicated that, upon the substitution of F by H, enthalpy and entropy changes in the associated and dissociated states were decreased, but the magnitude of enthalpy and entropy changes in the dissociated state was larger than that in the associated state. The differences in binding free energy, enthalpy, and entropy changes determined by the free energy calculations for the substitution of F by H are in good agreement with the experimental results.

Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms.

The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field.

A simple method for environmental cell depressurization for use with an electron microscope.

With the aid of the environmental cell (EC) in electron microscopy, hydrated specimens have been observed at high resolutions that optical microscopy cannot attain. Due to the ultra-high vacuum conditions of the inner column of the electron microscope, the EC requires sealing films that are sufficiently thin to allow electron transmission and that are sufficiently tough to withstand the pressure difference between the inside and outside of the EC. However, most hydrated specimens can be observed at low vacuum because the saturated vapor pressure of water is known to be 0.02 atm at room temperature. These concepts have been used in the differential pumping system, but it is complicated and relatively expensive. In this work, we propose a simple method for depressurization of the EC using a 'balloon structure' and demonstrate the theoretical benefits and practical improvement for specimen observations in low-vacuum conditions.

Clinical Search for Undiagnosed Mesenteric Phlebosclerosis at Outpatient Departments Specializing in Herbal (Kampo) Medicine.

OBJECTIVE: Mesenteric phlebosclerosis (MP) is a disease characterized by calcification of the mesenteric vein, which causes chronic mesenteric ischemia. Recently, the long-term intake of gardenia fruit ('Sanshishi' in Japanese) has been attracting attention as a possible cause. Usually, only advanced, severe MP cases get reported. However, we suspected that some latent cases of this disease may exist. We performed this study in order to determine the prediagnostic cases at our outpatient departments of herbal (Kampo) medicine, with particular attention paid to the initial changes, such as any slight color change of the colon, as shown in colonoscopy. METHODS: We recommend colonoscopy and computed tomography (CT) scans for patients with a long-term history of taking herbal medicines containing gardenia fruit. Clinical examinations were performed upon receiving patients' consent from December 2013 to November 2014. RESULTS: Of the 103 patients who took gardenia fruit long-term, 29 agreed to be checked for MP. 14 patients underwent colonoscopy. Four patients were confirmed to have MP due to the presence of fibrotic deposition of the colonic membrane on histological inspection. Twenty-one patients underwent abdominal CT screening. Characteristic calcification of the mesenteric vein was observed on CT scans in 2 patients. All 4 MP patients took Kampo formulas containing gardenia fruit for more than 6.8 years. The other patients did not develop MP, despite long-term gardenia fruit intake. CONCLUSION: We detected the latent and undiagnosed MP cases. All diagnoses were made while paying careful attention to any slight changes in colonoscopy and CT scans.