GlycoPep MassList: Software to Generate Massive Inclusion Lists for Glycopeptide Analyses

Protein glycosylation drives many biological processes and serves as markers for disease; therefore, the development of tools to study glycosylation is an essential and growing area of research. Mass spectrometry can be used to identify both the glycans of interest and the glycosylation sites to which those glycans are attached, when proteins are proteolytically digested and their glycopeptides are analyzed by a combination of high-resolution mass spectrometry (MS) and tandem mass spectrometry (MS/MS) methods. One major challenge in these experiments is collecting the requisite MS/MS data. The digested glycopeptides are often present in complex mixtures and in low abundance, and the most commonly used approach to collect MS/MS data on these species is data-dependent acquisition (DDA), where only the most intense precursor ions trigger MS/MS. DDA results in limited glycopeptide coverage. Semi-targeted data acquisition is an alternative experimental approach that can alleviate this difficulty. However, due to the massive heterogeneity of glycopeptides, it is not obvious how to expediently generate inclusion lists for these types of analyses. To solve this problem, we developed the software tool GlycoPep MassList, which can be used to generate inclusion lists for liquid chromatography tandem-mass spectrometry (LC-MS/MS) experiments. The utility of the software was tested by conducting comparisons between semi-targeted and untargeted data-dependent analysis experiments on a variety of proteins, including IgG, a protein whose glycosylation must be characterized during its production as a biotherapeutic. When the GlycoPep MassList software was used to generate inclusion lists for LC-MS/MS experiments, more unique glycopeptides were selected for fragmentation. Generally, ∼30 % more unique glycopeptides can be analyzed per protein, in the simplest cases, with low background. In cases where background ions from proteins or other interferents are high, usage of an inclusion list is even more advantageous. The software is freely publically accessible

Characterizing O-linked glycopeptides by electron transfer dissociation: fragmentation rules and applications in data analysis

Studying protein O-glycosylation remains an analytical challenge. Different from N-linked glycans, the O-glycosylation site is not within a known consensus sequence. Additionally, O-glycans are heterogeneous with numerous potential modification sites. Electron transfer dissociation (ETD) is the method of choice in analyzing these glycopeptides since the glycan side chain is intact in ETD, and the glycosylation site can be localized on the basis of the c and z fragment ions. Nonetheless, new software is necessary for interpreting O-glycopeptide ETD spectra in order to expedite the analysis workflow. To address the urgent need, we studied the fragmentation of O-glycopeptides in ETD and found useful rules that facilitate their identification. By implementing the rules into an algorithm to score potential assignments against ETD-MS/MS data, we applied the method to glycopeptides generated from various O-glycosylated proteins including mucin, erythropoietin, fetuin and an HIV envelope protein, 1086.C gp120. The site-specific O-glycopeptide composition was correctly assigned in every case, proving the merits of our method in analyzing glycopeptide ETD data. The algorithm described herein can be easily incorporated into other automated glycomics tools

A Review of Double-Walled and Triple-Walled Carbon Nanotube Synthesis and Applications

Double- and triple-walled carbon nanotubes (DWNTs and TWNTs) consist of coaxially-nested two and three single-walled carbon nanotubes (SWNTs). They act as the geometrical bridge between SWNTs and multi-walled carbon nanotubes (MWNTs), providing an ideal model for studying the coupling interactions between different shells in MWNTs. Within this context, this article comprehensively reviews various synthetic routes of DWNTs’ and TWNTs’ production, such as arc discharge, catalytic chemical vapor deposition and thermal annealing of pea pods (i.e., SWNTs encapsulating fullerenes). Their structural features, as well as promising applications and future perspectives are also discussed. Keywords: carbon nanotubes; double-walled carbon nanotubes; triple-walled carbon nanotubes; synthesis; catalytic chemical vapor deposition; arc discharge; fullerenes; pea pod

The interplay of Dzyaloshinskii-Moriya and Kitaev interactions for magnonic properties of Heisenberg-Kitaev honeycomb ferromagnets

The properties of Kitaev materials are attracting ever increasing attention owing to their exotic properties. In realistic two-dimensional materials, Kitaev interaction is often accompanied by the Dzyloshinskii-Moriya interaction, which poses a challenge of distinguishing their magnitude separately. In this work, we demonstrate that it can be done by accessing magnonic transport properties. By studying honeycomb ferromagnets exhibiting Dzyaloshinskii-Moriya and Kitaev interactions simultaneously, we reveal non-trivial magnonic topological properties accompanied by intricate magnonic transport characteristics as given by thermal Hall and magnon Nernst effects. We also investigate the effect of a magnetic field, showing that it does not only break the symmetry of the system but also brings drastic modifications to magnonic topological transport properties, which serve as hallmarks of the relative strength of anisotropic exchange interactions. Based on our findings, we suggest strategies to estimate the importance of Kitaev interactions in real materials.Comment: 6 pages, 4 figure

Comprehensive Proteome Profiling of Platelet Identified a Protein Profile Predictive of Responses to An Antiplatelet Agent Sarpogrelate

Sarpogrelate is an antiplatelet agent widely used to treat arterial occlusive diseases. Evaluation of platelet aggregation is essential to monitor therapeutic effects of sarpogrelate. Currently, no molecular signatures are available to evaluate platelet aggregation. Here, we performed comprehensive proteome profiling of platelets collected from 18 subjects before and after sarpogrelate administration using LC-MS/MS analysis coupled with extensive fractionation. Of 5423 proteins detected, we identified 499 proteins affected by sarpogrelate and found that they strongly represented cellular processes related to platelet activation and aggregation, including cell activation, coagulation, and vesicle-mediated transports. Based on the network model of the proteins involved in these processes, we selected three proteins (cut-like homeobox 1; coagulation factor XIII, B polypeptide; and peptidylprolyl isomerase D) that reflect the platelet aggregation-related processes after confirming their alterations by sarpogrelate in independent samples using Western blotting. Our proteomic approach provided a protein profile predictive of therapeutic effects of sarpogrelate. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.1

Quality destination management

Tourism is recognized as a significant industry worldwide, a key sector and source of development and income in several countries. The article focuses on quality management in tourist destinations in the Czech Republic. The overall objective of the present study is to uncover the evaluation of destination management by tourist organisations. Hence, the importance of destination management for each organisation based on the model of excellence EFQM (European Foundation for Quality Management) is evaluated. Moreover, the article highlights and assesses the difference between organisations which possess a certificate of quality and those which do not. Furthermore, the findings of the research, the data for which were collected from respondents at tourism organisations in the Czech Republic, can be used for assessing the competitiveness of destinations and for recommendations for sustainable development in the future.O

Mirror glasses for minimally invasive surgery

金沢大学大学院医学系研究科Introduction: The operator performing minimally invasive surgery is prevented from seeing the whole field with both eyes by the restricted small thoracotomy incision. To overcome this problem, we developed mirror glasses. Methods: Use of these glasses was evaluated in terms of the time required for threading of sutures with endoscopic forceps. Three surgeon ligated thread a suture five times with and without use of the glasses in the box, and the mean time was calculated for each surgeon. Results: The time required for ligation (mean ± SD) was 24.2 ± 2.9 s with mirror glasses and 27.0 ± 2.5 s without the glasses (p = 0.01). Conclusion: The mirror glasses may be found useful for fine manipulation for minimally invasive surgery. © 2006 Springer Science+Business Media, LL