Glycan analysis by ion mobility-mass spectrometry and gas-phase spectroscopy

Due to the existence of numerous isomers, the in-depth analysis of glycans represents a major challenge. Currently, the majority of glycans are analysed using mass spectrometry (MS)-based techniques, which can provide information on regioisomers but usually fail to differentiate stereoisomers. A promising approach to overcome this limitation is to implement ion mobility spectrometry (IMS) as an additional gas-phase separation dimension. This review highlights recent developments in which IM-MS was used as a tool for comprehensive glycan analysis or as rapid screening method for glycan feature analysis. Furthermore, we summarize a series of very recent investigations in which gas-phase spectroscopy is applied to study glycans and discuss the potential of the hyphenation between IM-MS and infrared (IR) spectroscopy as a future tool for glycomics and glycoproteomics

Mass Spectrometry-Based Techniques to Elucidate the Sugar Code

Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the “sugar code” and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility–mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves

Dextran as internal calibrant for N-glycan analysis by liquid chromatography coupled to ion mobility-mass spectrometry

LC–MS is one of the most important tools for the comprehensive characterization of N-glycans. Despite many efforts to speed up glycan analysis via optimized sample preparation (e.g., faster enzyme digestion in combination with instant or rapid labeling dyes), a major bottleneck remains the rather long measurement times of HILIC chromatography. Further compli- cation arises from the necessity to concomitantly calibrate with an external standard to allow for accurate retention times and the conversion into more robust GU values. Here we demonstrate the use of an internal calibration strategy for HILIC chromatography to speed up glycan analysis. By reducing the number of utilized dextran oligosaccharides, the calibrant can be spiked directly into the sample such that external calibration runs are no longer required. The minimized dextran ladder shows accurate GU calibration with a minor deviation of well below 1% and can be applied without modifications in sample preparation or data processing. We further demonstrate the simultaneous use of the minimized dextran ladder as calibrant for the estimation of CCS values in traveling wave ion mobility spectrometry. In both cases, the minimized dextran ladder enables the measurement of calibrant and sample in a single HPLC run without losing information or accuracy

Global turbulence simulations of the tokamak edge region with GRILLIX

Turbulent dynamics in the scrape-off layer (SOL) of magnetic fusion devices is intermittent with large fluctuations in density and pressure. Therefore, a model is required that allows perturbations of similar or even larger magnitude to the time-averaged background value. The fluid-turbulence code GRILLIX is extended to such a global model, which consistently accounts for large variation in plasma parameters. Derived from the drift reduced Braginskii equations, the new GRILLIX model includes electromagnetic and electron-thermal dynamics, retains global parametric dependencies and the Boussinesq approximation is not applied. The penalisation technique is combined with the flux-coordinate independent (FCI) approach [F. Hariri and M. Ottaviani, Comput.Phys.Commun. 184:2419, (2013); A. Stegmeir et al., Comput.Phys.Commun. 198:139, (2016)], which allows to study realistic diverted geometries with X-point(s) and general boundary contours. We characterise results from turbulence simulations and investigate the effect of geometry by comparing simulations in circular geometry with toroidal limiter against realistic diverted geometry at otherwise comparable parameters. Turbulence is found to be intermittent with relative fluctuation levels of up to 40% showing that a global description is indeed important. At the same time via direct comparison, we find that the Boussinesq approximation has only a small quantitative impact in a turbulent environment. In comparison to circular geometry the fluctuations are reduced in diverted geometry, which is related to a different zonal flow structure. Moreover, the fluctuation level has a more complex spatial distribution in diverted geometry. Due to local magnetic shear, which differs fundamentally in circular and diverted geometry, turbulent structures become strongly distorted in the perpendicular direction and are eventually damped away towards the X-point

Mid-infrared quantum cascade detectors for applications inspectroscopy and pyrometry

In this paper, we give an overview of quantum cascade detector technology for the near- and mid-infrared wavelength range. Thanks to their photovoltaic operating principle, the most advanced quantum cascade detectors offer great opportunities in terms of high detection speed, reliable room temperature operation, and excellent Johnson noise limited detectivity. Besides some important features dealing with their fabrication and their general characteristics, we will also briefly present some possibilities for performance improvement. Elementary theoretical considerations adopted from photoconductive detectors confirm that optimization of such devices always involves various trade-off

Two-point phase correlations of a one-dimensional bosonic Josephson junction

We realize a one-dimensional Josephson junction using quantum degenerate Bose gases in a tunable double well potential on an atom chip. Matter wave interferometry gives direct access to the relative phase field, which reflects the interplay of thermally driven fluctuations and phase locking due to tunneling. The thermal equilibrium state is characterized by probing the full statistical distribution function of the two-point phase correlation. Comparison to a stochastic model allows to measure the coupling strength and temperature and hence a full characterization of the system

Humanized hemato-lymphoid system mice

Over the last decades, incrementally improved xenograft mouse models, supporting the engraftment and development of a human hemato-lymphoid system, have been developed and now represent an important research tool in the field. The most significant contributions made by means of humanized mice are the identification of normal and leukemic hematopoietic stem cells, the characterization of the human hematopoietic hierarchy, and their use as preclinical therapy models for malignant hematopoietic disorders. Successful xenotransplantation depends on three major factors: tolerance by the mouse host, correct spatial location, and appropriately cross-reactive support and interaction factors such as cytokines and major histocompatibility complex molecules. Each of these can be modified. Experimental approaches include the genetic modification of mice to faithfully express human support factors as non-cross-reactive cytokines, to create free niche space, the co-transplantation of human mesenchymal stem cells, the implantation of humanized ossicles or other stroma, and the implantation of human thymic tissue. Besides the source of hematopoietic cells, the conditioning regimen and the route of transplantation also significantly affect human hematopoietic development in vivo. We review here the achievements, most recent developments, and the remaining challenges in the generation of pre-clinically-predictive systems for human hematology and immunology, closely resembling the human situation in a xenogeneic mouse environment

Artery tertiary lymphoid organs control multi-layered territorialized atherosclerosis B cell responses in aged ApoE-/- mice

Objective: Explore aorta B cell immunity in aged ApoE-/- mice. Approach and Results: Transcript maps, FACS, immunofluorescence analyses, cell transfers, and Ig-ELISPOT assays showed multi-layered atherosclerosis B cell responses in artery tertiary lymphoid organs (ATLOs). Aging-associated aorta B cell-related transcriptomes were identified and transcript atlases revealed highly territorialized B cell responses in ATLOs versus atherosclerotic lesions: ATLOs showed upregulation of bona fide B cell genes including Cd19, Ms4a1 (Cd20), Cd79a/b, and Ighm though intima plaques preferentially expressed molecules involved in non-B effector responses towards B cell-derived mediators, i.e. Fcgr3 (Cd16), Fcer1g (Cd23), and the C1q family. ATLOs promoted B cell recruitment. ATLO B-2 B cells included naïve, transitional, follicular, germinal center, switched IgG1+, IgA+, and IgE+ memory cells, plasmablasts, and long-lived plasma cells (PCs). ATLOs recruited large numbers of B-1 cells whose subtypes were skewed towards IL-10+ B-1b cells versus IL-10- B-1a cells. ATLO B-1 cells and PCs constitutively produced IgM and IgG and a fraction of PCs expressed IL-10. Moreover, ApoE-/- mice showed increased germinal center B cells in renal lymph nodes, IgM-producing PCs in the bone marrow, and higher IgM and anti-MDA-LDL IgG serum titers. Conclusions: ATLOs orchestrate dichotomic, territorialized, and multi-layered B cell responses in the diseased aorta; germinal center reactions indicate generation of autoimmune B cells within the diseased arterial wall during aging