SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Fourier transform

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The primary structural information of proteins employed as biotherapeutics is essential if one wishes to understand their structure-function relationship, as well as in the rational design of new therapeutics and for quality control. Given both the large size (around 150 kDa) and the structural complexity of intact immunoglobulin G (IgG), which includes a variable number of disulfide bridges, its extensive fragmentation and subsequent sequence determination by means of tandem mass spectrometry (MS) are challenging. Here, we applied electron transfer dissociation (ETD), implemented on a hybrid Orbitrap Fourier transform mass spectrometer (FTMS), to analyze a commercial recombinant IgG in a liquid chromatography (LC)-tandem mass spectrometry (MS/MS) top-down experiment. The lack of sensitivity typically observed during the top-down MS of large proteins was addressed by averaging time-domain transients recorded in different LC-MS/MS experiments before performing Fourier transform signal processing. The results demonstrate that an improved signal-to-noise ratio, along with the higher resolution and mass accuracy provided by Orbitrap FTMS (relative to previous applications of top-down ETD-based proteomics on IgG), is essential for comprehensive analysis. Specifically, ETD on Orbitrap FTMS produced about 33% sequence coverage of an intact IgG, signifying an almost 2-fold increase in IgG sequence coverage relative to prior ETD-based analysis of intact monoclonal antibodies of a similar subclass. These results suggest the potential application of the developed methodology to other classes of large proteins and biomolecules.

Concepts: Immune system, Protein, Mass spectrometry, Fourier transform, Tandem mass spectrometry, Fourier transform ion cyclotron resonance, Collision-induced dissociation, Electron transfer dissociation

151

Scotch Whisky is an important product, both culturally and economically. Chemically, Scotch Whisky is a complex mixture, which comprises thousands of compounds, the nature of which are largely unknown. Here, we present a thorough overview of the chemistry of Scotch Whisky as observed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Eighty-five whiskies, representing the majority of Scotch Whisky produced and sold, were analyzed by untargeted high-resolution mass spectrometry. Thousands of chemical formulae were assigned for each sample based on parts-per-billion mass accuracy of FT-ICR MS spectra. For the first time, isotopic fine structure analysis was used to confirm the assignment of high molecular weight CHOS species in Scotch Whisky. The assigned spectra were compared using a number of visualization techniques, including van Krevelen diagrams, double bond equivalence (DBE) plots, as well as heteroatomic compound class distributions. Additionally, multivariate analysis, including PCA and OPLS-DA, was used to interpret the data, with key compounds identified for discriminating between types of whisky (blend or malt) or maturation wood type. FT-ICR MS analysis of Scotch Whisky was shown to be of significant potential in further understanding of the complexity of mature spirit drinks and as a tool for investigating the chemistry of the maturation processes. Graphical Abstract ᅟ.

Concepts: Mass spectrometry, Molecule, Chemistry, Chemical substance, Chemical compound, Fourier transform, Whisky, Scotch whisky

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The cylindrical Bessel differential equation and the spherical Bessel differential equation in the interval [Formula: see text] with Neumann boundary conditions are considered. The eigenfunctions are linear combinations of the Bessel function [Formula: see text] or linear combinations of the spherical Bessel functions [Formula: see text]. The orthogonality relations with analytical expressions for the normalization constant are given. Explicit expressions for the Lommel integrals in terms of Lommel functions are derived. The cross product zeros [Formula: see text] and [Formula: see text] are considered in the complex plane for real as well as complex values of the index [Formula: see text] and approximations for the exceptional zero [Formula: see text] are obtained. A numerical scheme based on the discretization of the two-dimensional and three-dimensional Laplace operator with Neumann boundary conditions is presented. Explicit representations of the radial part of the Laplace operator in form of a tridiagonal matrix allow the simple computation of the cross product zeros.

Concepts: Mathematics, Derivative, Fourier transform, Complex number, Laplace transform, Bessel function, Helmholtz equation, Neumann polynomial

149

Collisions of excitation pulses in dissipative systems lead usually to their annihilation. In this paper, we report electrochemical experiments exhibiting more complex pulse interaction with collision survival and pulse splitting, phenomena that have rarely been observed experimentally and are only poorly understood theoretically. Using spatially resolved in-situ Fourier transform infrared spectroscopy (FTIR) in the attenuated total reflection configuration, we monitored reaction pulses during the electrochemical oxidation of CO on Pt thin film electrodes in a flow cell. The system forms quasi-1d pulses that align parallel to the flow and propagate perpendicular to it. The pulses split once in a while, generating a second solitary wave in the backward moving direction. Upon collision, the waves penetrate each other in a soliton-like manner. These unusual pulse dynamics could be reproduced with a 3-component reaction-diffusion-migration model with two inhibitor species, one of them exhibiting a long-range spatial coupling. The simulations shed light on existence criteria of such dissipative solitons.

Concepts: Spectroscopy, Light, Refraction, Electrochemistry, Fourier transform, Electrochemical cell, Infrared spectroscopy, Fourier transform spectroscopy

69

Vitrification, a kinetic process of liquid solidification into glass, poses many potential benefits for tissue cryopreservation including indefinite storage, banking, and facilitation of tissue matching for transplantation. To date, however, successful rewarming of tissues vitrified in VS55, a cryoprotectant solution, can only be achieved by convective warming of small volumes on the order of 1 ml. Successful rewarming requires both uniform and fast rates to reduce thermal mechanical stress and cracks, and to prevent rewarming phase crystallization. We present a scalable nanowarming technology for 1- to 80-ml samples using radiofrequency-excited mesoporous silica-coated iron oxide nanoparticles in VS55. Advanced imaging including sweep imaging with Fourier transform and microcomputed tomography was used to verify loading and unloading of VS55 and nanoparticles and successful vitrification of porcine arteries. Nanowarming was then used to demonstrate uniform and rapid rewarming at >130°C/min in both physical (1 to 80 ml) and biological systems including human dermal fibroblast cells, porcine arteries and porcine aortic heart valve leaflet tissues (1 to 50 ml). Nanowarming yielded viability that matched control and/or exceeded gold standard convective warming in 1- to 50-ml systems, and improved viability compared to slow-warmed (crystallized) samples. Last, biomechanical testing displayed no significant biomechanical property changes in blood vessel length or elastic modulus after nanowarming compared to untreated fresh control porcine arteries. In aggregate, these results demonstrate new physical and biological evidence that nanowarming can improve the outcome of vitrified cryogenic storage of tissues in larger sample volumes.

Concepts: Blood, Extracellular matrix, Blood vessel, Fourier transform, Glass transition, Cryobiology, Cryopreservation, Cryoprotectant

33

Hydrophobic materials that are robust to harsh environments are needed in a broad range of applications. Although durable materials such as metals and ceramics, which are generally hydrophilic, can be rendered hydrophobic by polymeric modifiers, these deteriorate in harsh environments. Here we show that a class of ceramics comprising the entire lanthanide oxide series, ranging from ceria to lutecia, is intrinsically hydrophobic. We attribute their hydrophobicity to their unique electronic structure, which inhibits hydrogen bonding with interfacial water molecules. We also show with surface-energy measurements that polar interactions are minimized at these surfaces and with Fourier transform infrared/grazing-angle attenuated total reflection that interfacial water molecules are oriented in the hydrophobic hydration structure. Moreover, we demonstrate that these ceramic materials promote dropwise condensation, repel impinging water droplets, and sustain hydrophobicity even after exposure to harsh environments. Rare-earth oxide ceramics should find widespread applicability as robust hydrophobic surfaces.

Concepts: Oxygen, Water, Hydrogen, Chemical properties, Intermolecular forces, Atom, Fourier transform, Ceramic

28

Polystyrene (PS) is generally considered to be durable and resistant to biodegradation. Mealworms (the larvae of Tenebrio molitor Linnaeus) from different sources chew and eat Styrofoam, a common PS product. The Styrofoam was efficiently degraded in the larval gut within a retention time of less than 24 h. Fed with Styrofoam as the sole diet, the larvae lived as well as those fed with a normal diet (bran) over a period of one month. The analysis of fecula egested from Styrofoam-feeding larvae, using gel permeation chromatography (GPC), solid state 13C cross polarization/magic angle spinning nuclear magnetic resonance (CP/MAS NMR) spectroscopy and thermogravimetric Fourier transform infrared (TG-FTIR) spectroscopy, substantiated that cleavage/depolymerization of long-chain PS molecules and the formation of depolymerized metabolites occurred in the larval gut. Within a 16-day test period, 47.7% of the ingested Styrofoam carbon was converted into CO2, and the residue (ca. 49.2%) was egested as fecula with a limited fraction incorporated into biomass (ca. 0.5%). Tests with α13C- or β13C-labeled PS confirmed that the 13C-labeled PS was mineralized to 13CO2 and incorporated into lipids. The discovery of the rapid biodegradation of PS in the larval gut reveals a new fate for plastic waste in the environment.

Concepts: Protein, Spectroscopy, Nuclear magnetic resonance, Chromatography, Analytical chemistry, Fourier transform, Fourier transform spectroscopy, Fourier analysis

28

Improved methods are required for the recycling of waste printed circuit boards (WPCBs). In this study, WPCBs (1-1.5 cm2 in size) were separated into their components using dimethyl sulfoxide (DMSO) at 60°C for 45 min and a metallographic microscope used to verify their delamination. An increased incubation time of 210 min yielded a complete separation of WPCBs into their components, and copper foils and glass fibers were obtained. The separation time decreased with increasing temperature. When the WPCB size was increased to 2-3 cm2, the temperature required for complete separation increased to 90°C. When the temperature was increased to 135°C, liquid photo solder resists could be removed from the copper foil surfaces. The DMSO was regenerated by rotary decompression evaporation, and residues were obtained. Fourier transform infrared spectroscopy (FT-IR), thermal analysis, nuclear magnetic resonance, scanning electron microscopy and energy-dispersive x-ray spectroscopy were used to verify that these residues were brominated epoxy resins. From FT-IR analysis after the dissolution of brominated epoxy resins in DMSO it was deduced that hydrogen bonding may play an important role in the dissolution mechanism. This novel technology offers a method for separating valuable materials and preventing environmental pollution from WPCBs.

Concepts: Spectroscopy, Nuclear magnetic resonance, Scientific techniques, Fourier transform, Infrared spectroscopy, Fourier transform spectroscopy, Printed circuit board, FR-4

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A new ionization technique: A radio-frequency signal was used to ionize neutral organic molecules in the ultrahigh-vacuum region of a Fourier transform ion cyclotron resonance mass spectrometer. Radio-frequency ionization (RFI) yielded S/N ratios roughly six times higher than those generated by the conventional 70 eV electron impact ionization (EI).

Concepts: Mass spectrometry, Ion, Scientific techniques, Fourier transform, Ion source, Fourier transform ion cyclotron resonance, Ion cyclotron resonance, Electron ionization

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