Local structural modelling and local pair distribution function analysis for Zr-Pt metallic glass.

In disordered glass structures, the structural modelling and analyses based on local experimental data are not yet established. Here we investigate the icosahedral short-range order (SRO) in a Zr-Pt metallic glass using local structural modelling, which is a reverse Monte Carlo simulation dedicated to two-dimensional angstrom-beam electron diffraction (ABED) patterns, and local pair distribution function (PDF) analysis. The local structural modelling invariably leads to the icosahedral SRO atomic configurations that are similarly distorted by starting from some different initial configurations. Furthermore, the SRO configurations with 11-13 coordination numbers reproduce almost identical ABED patterns, indicating that these SRO structures are similar to each other. Further local PDF analysis explicitly indicates the presence of the wide distribution of atomic bond distances, which is comparable to the global PDF profile, even at the SRO level. The SRO models based on the conventional MD simulation can be strengthened by comparison with those obtained by the present local structural modelling and local PDF analysis based on the ABED data.

Activity of daily life dependency predicts the risk of mortality in patients with COVID-19 undergoing hemodialysis: a retrospective analysis of a single center with nosocomial outbreak.

Background: We experienced a nosocomial outbreak of coronavirus disease 2019 (COVID-19) from November 2020 to February 2021, during the third wave of the pandemic in Japan. Methods: We retrospectively assessed the characteristics and data of 20 inpatients undergoing hemodialysis who were hospitalized for treatment of diseases other than COVID-19 during the COVID-19 nosocomial outbreak ("inpatient," IP), and of 10 outpatients undergoing hemodialysis who were hospitalized for the care of COVID-19 under outpatient visits ("outpatient," OP). Results: Eleven patients in the IP group (55%) and one in the OP group (10%) died. Kaplan-Meier analysis showed that the IP group died more rapidly than the OP group (p = 0.02). Multivariate analysis among all hemodialysis patients showed that the IP group was not at risk of mortality independently; however, the activity of daily life (ADL) dependency was found to be an independent factor in increasing the risk of mortality (hazard ratio: 7.618). Conclusion: Our findings show that the nosocomial infected group has a worse prognosis, although it is not an independent predictor for the risk of mortality. ADL dependency could predict the risk of mortality in all hemodialysis patients with COVID-19 during the third wave pandemic in Japan.

[Coronary Artery Bypass Surgery for the Patient with a History of Anaphylaxis due to Neuromuscular Blocking Agent ; Report of a Case].

We present herein a patient with rocuronium anaphylaxis, which had been identified using skin test, underwent conventional coronary artery bypass surgery without any neuromuscular blocking agent. Immobility was achieved with sedatives and analgesics.

Miscibility phase diagram of ring-polymer blends: A topological effect.

The miscibility of polymer blends, a classical problem in polymer science, may be altered, if one or both of the component do not have chain ends. Based on the idea of topological volume, we propose a mean-field theory to clarify how the topological constraints in ring polymers affect the phase behavior of the blends. While the large enhancement of the miscibility is expected for ring-linear polymer blends, the opposite trend toward demixing, albeit comparatively weak, is predicted for ring-ring polymer blends. Scaling formulas for the shift of critical point for both cases are derived. We discuss the valid range of the present theory, and the crossover to the linear polymer blends behaviors, which is expected for short chains. These analyses put forward a view that the topological constraints could be represented as an effective excluded-volume effects, in which the topological length plays a role of the screening factor.

Membrane Protein Analyses Using Alkylated Trihydroxyacetophenone (ATHAP) as a MALDI Matrix.

Membrane proteins containing hydrophobic regions have been difficult to analyze using MALDI-MS, probably due to the use of conventional matrices with a low affinity for hydrophobic peptides. Recently, we reported 1-(2,4,6-trihydroxyphenyl)octan-1-one (alkylated trihydroxyacetophenone (ATHAP)) as a matrix for hydrophobic peptides. In this study, ATHAP was applied to analyze membrane proteins containing transmembrane domains. As a result, we detected intact molecular ions for bacteriorhodopsin (BR) containing seven transmembrane domains that are difficult to detect using 2,4,6-trihydroxyacetophenone or sinapinic acid, by using ATHAP. In addition, we detected digest ions containing all seven transmembrane domains that are difficult to detect using α-cyano-4-hydroxycinnamic acid (CHCA), by using ATHAP. Moreover, ions for hydrophobic digests containing a single transmembrane domain for cadherin 1 (CDH1), fibroblast growth factor receptor 4 (FGFR4), epithelial cell adhesion molecule (EPCAM) recombinant proteins, and human epidermal growth factor receptor type 2 (HER2) were detected with higher sensitivity using ATHAP than with CHCA, confirming that ATHAP improved the membrane protein analyses, especially for hydrophobic regions such as transmembrane domains.

Identification of human basic fetoprotein as glucose-6-phosphate isomerase by using N- and C-terminal sequence tags and terminal tag database.

Human basic fetoprotein (BFP), found in fetal serum and tissue extracts as well as in extracts of various cancer tissues, has long been known as a marker protein for cancers; however, the primary sequence has not yet been reported. This paper describes the identification of BFP using the N- and C-terminal amino acid sequence tags (Ac-AALTRDPQFQ and QQREARVQ, respectively) clarified by mass spectrometry-based methods, and a terminal tag database (ProteinCarta). In this study, BFP was identified as glucose-6-phosphate isomerase (G6PI_HUMAN).

Comparative effects of sesame seeds differing in lignan contents and composition on fatty acid oxidation in rat liver.

We compared the physiological activities of sesame seeds rich in lignans from three varieties (Gomazou, Maruhime and Maruemon), and those from a conventional cultivar (Masekin) in rats. The sum of the values of fat-soluble lignans (sesamin and sesamolin) in seeds of Gomazou, Maruhime and Maruemon varieties was approximately double the value in Masekin. Seeds from Maruemon contained fat-soluble lignan most exclusively as sesamin while other varieties contained sesamin and sesamolin at about a 2:1 ratio. After a 16 d experiment, sesame seeds, added at 200 g/kg to the experimental diets, increased the activity and mRNA levels of fatty acid oxidation enzymes. Increases were stronger with seeds rich in lignans than with seeds from Masekin. In contrast, sesame seeds lowered the activity and mRNA levels of lipogenic enzymes. However, sesame seeds from all the varieties were comparable in affecting these parameters. Serum triacylglycerol concentrations were lower in rats fed diets containing sesame seeds rich in lignans than in those fed a diet free of sesame seeds or a diet containing seeds from the Masekin variety. Serum malondialdehyde (a marker of lipid peroxidation) was lower in rats fed diets containing sesame seeds rich in lignans than in those fed a sesame seed-free diet or Masekin diet. It is apparent that sesame seeds rich in lignans, irrespective of lignan composition, more profoundly affect hepatic fatty acid oxidation and serum triacylglycerol levels and possibly attenuate oxidative stress. Therefore, consumption of sesame seeds rich in lignans hopefully results in physiological activity to promote health.

Alkylated trihydroxyacetophenone as a MALDI matrix for hydrophobic peptides.

Hydrophobic peptides are difficult to detect in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), because of the hydrophilic properties of conventional matrices and the low affinity for hydrophobic peptides. Recently, we reported on alkylated dihydroxybenzoic acid (ADHB) as a matrix additive for hydrophobic peptides; however, the peptides were detected in the rim of the matrix-analyte dried spot. Here, we report on a novel matrix, alkylated trihydroxyacetophenone (ATHAP), which is a 2,4,6-trihydroxyacetophenone derivative incorporating a hydrophobic alkyl chain on the acetyl group and thus is expected to have an affinity for hydrophobic peptides. ATHAP increased the sensitivity of hydrophobic peptides 10-fold compared with α-cyano-4-hydroxycinnamic acid (CHCA), in which the detection of hydrophilic peptides was suppressed. The peptides were detected throughout the entire matrix-analyte dried spot using ATHAP, overcoming the difficulty of finding a "sweet spot" when using ADHB. In addition, ATHAP functioned alone as a matrix, unlike ADHB as an additive. In phosphorylase b digests analysis, hydrophobic peptides, which were not detected with CHCA for 1 pmol, were detected with this matrix, confirming that ATHAP led to increased sequence coverage and may extend the range of target analytes in MALDI-MS.

Mass spectrometry based N- and C-terminal sequence determination of a hepatopancreas-type prophenoloxidase from the kuruma prawn, Marsupenaeus japonicus.

We previously identified and characterized a novel hepatopancreas-type prophenoloxidase from kuruma prawn, Marsupenaeus japonicus. In the characterization, this enzyme was indicated to have a feature of a signal peptide at its N-terminus. The putative primary structure was then proposed but its N- and C-terminal sequences remained undetermined. In the present study, the N- and C-terminal amino acid sequences of this prophenoloxidase were determined by de novo sequencing methods using matrix-assisted laser desorption ionization mass spectrometry. The sequence analyses revealed that the N-terminus of the prophenoloxidase was processed, whereas the C-terminus was not. This finding suggests that this enzyme has a signal peptide, and that it is synthesized at the endoplasmic reticulum in hepatopancreas cells and secreted to hemolymph plasma, similar to the case of hemocyanin, another member of the class III copper proteins.

Combined effect of sesamin and α-lipoic acid on hepatic fatty acid metabolism in rats.

PURPOSE: Dietary sesamin (1:1 mixture of sesamin and episesamin) decreases fatty acid synthesis but increases fatty acid oxidation in rat liver. Dietary α-lipoic acid lowers hepatic fatty acid synthesis. These changes can account for the serum lipid-lowering effect of sesamin and α-lipoic acid. It is expected that the combination of these compounds in the diet potentially ameliorates lipid metabolism more than the individual compounds. We therefore studied the combined effect of sesamin and α-lipoic acid on lipid metabolism in rats. METHODS: Male Sprague-Dawley rats were fed diets supplemented with 0 or 2 g/kg sesamin and containing 0 or 2.5 g/kg α-lipoic acid for 22 days. RESULTS AND CONCLUSIONS: Sesamin and α-lipoic acid decreased serum lipid concentrations and the combination of these compounds further decreased the parameters in an additive fashion. These compounds reduced the hepatic concentration of triacylglycerol, the lignan being less effective in decreasing this value. The combination failed to cause a stronger decrease in hepatic triacylglycerol concentration. The combination of sesamin and α-lipoic acid decreased the activity and mRNA levels of hepatic lipogenic enzymes in an additive fashion. Sesamin strongly increased the parameters of hepatic fatty acid oxidation enzymes. α-Lipoic acid antagonized the stimulating effect of sesamin of fatty acid oxidation through reductions in the activity of some fatty acid oxidation enzymes and carnitine concentration in the liver. This may account for the failure to observe strong reductions in hepatic triacylglycerol concentration in rats given a diet containing both sesamin and α-lipoic acid.

Enriching C-terminal peptide from endopeptidase ArgC digest for protein C-terminal analysis.

This Letter describes a method for enriching C-terminal peptide of protein for C-terminal sequence analysis. This method employs endopeptidase ArgC digestion and C-terminal peptide enrichment using m-aminophenylboronic acid-agarose as an arginine-capture material. The selectively recovered C-terminal peptide incorporates no artificial derivatization. Therefore, the widely used functional groups (e.g. α-NH(2) and α-COOH) can be used for any necessary transformation. In this research, a TMPP mass tag was attached to the α-NH(2) group to clarify the amino acid sequence of the C-terminal peptide.

Mass spectrometry-based sequencing of protein C-terminal peptide using α-carboxyl group-specific derivatization and COOH capturing.

An approach to mass spectrometry (MS)-based sequence analysis of selectively enriched C-terminal peptide from protein is described. This approach employs a combination of the specific derivatization of α-carboxyl group (α-COOH), enzymatic proteolysis using endoproteinase GluC, and enrichment of C-terminal peptide through the use of COOH-capturing material. Highly selective derivatization of α-COOH was achieved by a combination of specific activation of α-COOH through oxazolone chemistry and amidation using 3-aminopropyltris-(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-propylamine). This amine component was used to simplify fragmentation in tandem mass spectrometry (MS/MS) measurement, which facilitated manual sequence interpretation. The peptides produced after GluC digestion were then treated with a COOH scavenger to enrich the C-terminal peptide that is only devoid of COOH groups, and the obtained C-terminal peptide was readily sequenced by matrix-assisted laser desorption/ionization (MALDI)-MS/MS due to the TMPP mass tag.

C-terminal sequencing of protein by MALDI mass spectrometry through the specific derivatization of the α-carboxyl group with 3-aminopropyltris-(2,4,6-trimethoxyphenyl)phosphonium bromide.

We present here an approach to C-terminal sequencing of proteins by the procedure consisting of the following: (1) derivatization of the C-terminal α-carboxyl group with 3-aminopropyltris(2,4,6-trimethoxyphenyl)-phosphonium bromide (TMPP-propylamine) through oxazolone chemistry, (2) enzymatic proteolysis of the TMPP-derivatized protein, and (3) MALDI-MS/MS analysis of the peptide mixture, in which the C-terminal peptide incorporating the TMPP group is preferably detected. In this protocol, it is possible to choose any endoproteinase such as trypsin, GluC, and AspN for digestion so that a C-terminal peptide with length appropriate for mass spectrometric sequencing could be generated. The peptide labeled with TMPP-propylamine at the C terminus tends to exhibit y-type ions in MS/MS spectra, allowing manual sequence interpretation with the simplified fragmentation pattern. The efficacy of the method was verified with five proteins, which demonstrated that the C-terminal peptides were readily distinguishable by their peak intensity and characteristic mass signature peak in MALDI-PSD analysis.

A method for N-terminal de novo sequencing of Nα-blocked proteins by mass spectrometry.

A method for de novo sequencing of N(α)-blocked proteins by mass spectrometry (MS) is presented. The approach consists of enzymatic digestion of N(α)-blocked protein, recovery of N-terminal peptide by depletion of non-N-terminal peptides from the digest pool, and selective derivatization of a C-terminal α-carboxyl group of isolated N-terminal peptide. The C-terminal α-carboxyl group of the N-terminal peptide was selectively derivatized with 3-aminopropyl-tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-propylamine), according to oxazolone chemistry. The reagent TMPP-propylamine was designed to facilitate sequence analysis with MALDI-MS by mass- and charge-tagging. All of the identities and N-terminal sequences of two N(α)-acetylated proteins (rabbit phosphorylase b and bovine calmodulin) and human orexin A, which has pyroglutamic acid at the N-terminus, were successfully analyzed by allowing for the y-type ions almost exclusively.

A new approach for detecting C-terminal amidation of proteins and peptides by mass spectrometry in conjunction with chemical derivatization.

We describe a mass spectrometric method for distinguishing between free and modified forms of the C-terminal carboxyl group of peptides and proteins, in combination with chemical approaches for the isolation of C-terminal peptides and site-specific derivatization of the C-terminal carboxyl group. This method could most advantageously be exploited to discriminate between peptides having C-terminal carboxyl groups in the free (COOH) and amide (CONH(2)) forms by increasing their mass difference from 1 to 14 Da by selectively converting the free carboxyl group into methylamide (CONHCH(3)). This method has been proven to be applicable to peptides containing aspartic and glutamic acids, because all the carboxyl groups except the C-terminal one are inert to derivatization, according to oxazolone chemistry. The efficiency of the method is illustrated by a comparison of the peaks of processed peptides obtained from a mixture of adrenomedullin, calcitonin, and BSA. Among these components of the mixture, only the C-terminal peptide of BSA exhibited the mass shift of 13 Da upon treatment, eventually unambiguously validating the C-terminal amide structures of adrenomedullin and calcitonin. The possibility of extending this method for the analysis of C-terminal PTMs is also discussed.

Phase of neural excitation relative to basilar membrane motion in the organ of Corti: theoretical considerations.

Although the auditory transduction process is dependent on neural excitation of the auditory nerve in relation to motion of the basilar membrane (BM) in the organ of Corti (OC), specifics of this process are unclear. In this study, therefore, an attempt was made to estimate the phase of the neural excitation relative to the BM motion using a finite-element model of the OC at the basal turn of the gerbil, including the fluid-structure interaction with the lymph fluid. It was found that neural excitation occurs when the BM exhibits a maximum velocity toward the scala vestibuli at 10 Hz and shows a phase delay relative to the BM motion with increasing frequency up to 800 Hz. It then shows a phase advance until the frequency reaches 2 kHz. From 2 kHz, neural excitation again shows a phase delay with increasing frequency. From 800 Hz up to 2 kHz, the phase advances because the dominant force exerted on the hair bundle shifts from a velocity-dependent Couette flow-induced force to a displacement-dependent force induced by the pressure difference. The phase delay that occurs from 2 kHz is caused by the resonance process of the hair bundle of the IHC.