Cathodoluminescence efficiency dependence on excitation density in n-type gallium nitride.

Cathodoluminescence (CL) spectra from silicon doped and undoped wurtzite n-type GaN have been measured in a SEM under a wide range of electron beam excitation conditions, which include accelerating voltage, beam current, magnification, beam diameter, and specimen temperature. The CL intensity dependence on excitation density was analyzed using a power-law model (I CL proportional, variant J m ) for each of the observed CL bands in this material. The yellow luminescence band present in both silicon and undoped GaN exhibits a close to cube root (m = 0.33) dependence on electron beam excitation at both 77 K and 300 K. However, the blue (at 300 K) and donor-acceptor pair (at 77 K) emission peaks observed in undoped GaN follow power laws with exponents of m = 1 and m = 0.5, respectively. As expected from its excitonic character, the near band edge emission intensity depends linearly (m = 1) in silicon doped GaN and superlinearly (m = 1.2) in undoped GaN on the electron beam current. Results show that the intensities of the CL bands are highly dependent not only on the defect concentration but also on the electron-hole pair density and injection rate. Furthermore, the size of the focussed electron beam was found to have a considerable effect on the relative intensities of the CL emission peaks. Hence SEM parameters such as the objective lens aperture size, astigmatism, and the condenser lens setting must also be considered when assessing CL data based on intensity measurements from this material.     

Structural characterization of neutral oligosaccharide mixtures through a combination of capillary electrochromatography and ion trap tandem mass spectrometry

A CEC/ESI-MS/MS combined system has been developed for the separation and on-line structural analysis of neutral oligosaccharides. Various types of isomeric oligosaccharides were first successfully separated by CEC using polar monolithic columns, while the on-line tandem mass spectrometry has been explored to differentiate and elucidate the structures of isomeric oligosaccharides. The experimentally obtained tandem spectra usually provide sequence, branching, and linkage information. Oligosaccharide isomers with a different monomeric composition and branching showed different patterns of glycosidic linkage cleavage (B- and Y-ion series), allowing us to deduce their sequence and branching points. Isomers with different linkages were distinguished by identifying cross-ring fragment ions (A-ion series). While (1-->4) linkages yielded dominant (0,2)A ions, (1-->6) linkages showed an extensive and complete cross-ring cleavage series: (0,2)A, (0,3)A, and (0,4)A ions. Although the anomeric configurations and monosaccharide identification are rarely obtained from tandem MS, the relevant mixture components can be completely resolved with high-efficiency CEC columns featuring a polar functionality.     

Reactions of Cp Ru(η-C6H5CHO) OSO2CF3 (Cp = C5Me5) with substituted anilines forming ruthenium Schiff base complexes

Cp^* Ru(η⁶-C₆H₅CHO)⁺OSO₂CF₃⁻ (1) (Cp^* = C₅Me₅) reacts with substituted anilines forming ruthenium Schiff base complexes containing an η⁶-coordinated Cp^* Ru⁺ group. The 2:1 reaction of 1 with 1,4-phenylenediamine yielded only the monocondensation product, whereas the 2:1 reaction of 1 with 1,4-xylylenediamine yielded the dicondensation product.     

Endoperoxides Revealed as Origin of the Toxicity of Graphene Oxide

Potential biomedicinal applications of graphene oxide (GO), for example, as a carrier of biomolecules or a reagent for photothermal therapy and biosensing, are limited by its cytotoxicity and mutagenicity. It is believed that these properties are at least partially caused by GO‐induced oxidative stress in cells. However, it is not known which chemical fragments of GO are responsible for this unfavorable effect. We generated four GOs containing variable redox‐active groups on the surface, including Mn²⁺, C‐centered radicals, and endoperoxides (EPs). A comparison of the abilities of these materials to generate reactive oxygen species in human cervical cancer cells revealed that EPs play a crucial role in GO‐induced oxidative stress. These data could be applied to the rational design of biocompatible nontoxic GOs for biomedical applications.     

In vitro antibiofilm activity of the freshwater bryozoan Hyalinella punctata: a case study of Pseudomonas aeruginosa PAO1

The antibiofilm and possible antiquorum sensing effects against the strain Pseudomonas aeruginosa PAO1 of five crude extracts of the freshwater bryozoan Hyalinella punctata (Hancock, 1850) were evaluated in vitro for the first time. H. punctata ethyl acetate extract (HpEtAc) exhibited the highest antibiofilm activity reducing the biofilm formation of P. aeruginosa PAO1 in the range of 80.63–88.13%. While all tested extracts reduced the twitching motility of the aforementioned bacterial strain, HpEtAc showed to be the most effective. Finally, at a concentration of 0.5 MIC, the same extract mostly inhibited the production of pyocyanin by P. aeruginosa PAO1 (71.53%). In comparison both with the positive controls used (streptomycin and ampicillin, 67.13 and 69.77%, respectively), HpEtAc was found to inhibit pyocyanin in a higher extent. An extensive chemical characterisation of this particular extract may result in isolation and identification of novel lead compounds targeting P. aeruginosa, an opportunistic human pathogen.     

A computational approach to characterizing bond linkages of glycan isomers using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry

Glycans commonly exhibit variations in their branching structures and glycosidic bond linkages, in addition to their sequence variation. These glycan features are known to be highly correlated with their biological functions. It is relatively straightforward to deduce the composition and sequence of monosaccharides of a glycan from its tandem mass spectra. However, the characterization of the linkage types of each glycosidic bond is still analytically challenging. In this paper, we present a rank-based discriminative model to differentiate between two types of glycosidic linkages (namely, 1-4 and 1-6) based on the cross-ring fragmentation patterns of the corresponding glycans observed under high-energy collision-induced dissociation (CID). To train our models, we acquired tandem mass spectra for three groups of both native and permethylated linear oligoglucoses using a matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI/TOF/TOF) instrument. Based on a 5-fold cross-validation, the prediction accuracies of our model for native glycans are determined to be about 88.4% and 92.9% for 1-6 and 1-4 linkages, respectively. The accuracies determined for permethylated glycans are slightly lower, but comparable: 85.6% and 89.0% for 1-6 and 1-4 linkages, respectively. Our method is implemented as a web-hosted utility, thus making it readily accessible to the public which can be accessed through http://ggdb.informatics.indiana.edu:8080/glycanview.     

Comparison of quantitative conformer analyses by nuclear magnetic resonance and Raman optical activity spectra for model dipeptides

Interpretation of the Raman optical activity (ROA) of peptides is difficult because of molecular flexibility and interaction with the solvent. Typically, simulations and experiments are compared in terms of a qualitative agreement between the spectra. However, on a series of the Pro-Gly, Gly-Pro, Pro-Ala, and Ala-Pro dipeptides more precise conformer ratios could be obtained with the aid of the density functional computations and numerical decomposition of the spectral shapes. All observed transitions were assigned, and the computed transition frequencies were scaled accordingly. Then the populations predicted by the optical spectroscopy agreed within a few percent with an analysis of the spin-spin coupling constants based on the Karplus equations, which was confirmed also by a comparison of calculated and experimental NMR couplings. The results are supported by molecular dynamics simulations and related to the previous conformational studies of similar molecules.     

A monolithic PNGase F enzyme microreactor enabling glycan mass mapping of glycoproteins by mass spectrometry

We demonstrate a simple and rapid single-step method to fabricate an enzyme microreactor incorporating the N-glycosidase PNGase F (peptide-N-glycosidase F) into a porous polymer-based monolith. The monolith is contained in a capillary format, while the enzyme reactor is ready to use within 1 h of preparation. The monomers making up the monolith, including N-acryloxysuccinimide for covalent immobilization of the enzyme, are mixed with PNGase F and introduced into the column by capillary force for polymerization/immobilization. Glycoproteins (ribonuclease B, asialofetuin, alpha1-acid glycoprotein, and ovalbumin) perfused through the PNGase F reactor were shown to be effectively deglycosylated on a time-scale of seconds/low minutes using low nanogram to microgram per microliter concentration (corresponding to a total sample consumption of 0.1-20 microg of a glycoprotein). The reactor enzyme activity was shown to be reproducible for at least 8 weeks when used and stored at room temperature. Evaluation was performed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.     

Convective interaction media short monolithic columns: enabling chromatographic supports for the separation and purification of large biomolecules

New therapeutics that are being developed rely more and more on large and complex biomacromolecules like proteins, DNA, and viral particles. Manufacturing processes are being redesigned and optimized both upstream and downstream to cope with the ever-increasing demand for the above target molecules. In downstream processing, LC still represents the most powerful technique for achieving high yield and high purities of these molecules. In most cases, however, the separation technology relies on conventional particle-based technology, which has been optimized for the purification of smaller molecules. New technologies are, therefore, needed in order to push the downstream processing ahead and into the direction that will provide robust, productive, and easy to implement methods for the production of novel therapeutics. New technologies include the renaissance of membranes, various improvements of existing technologies, but also the introduction of a novel concept--the continuous bed or monolithic stationary phases. Among different introduced products, Convective Interaction Media short monolithic columns (SMC) that are based on methacrylate monoliths exhibit some interesting features that make them attractive for these tasks. SMC can be initially used for fast method development on the laboratory scale and subsequently efficiently transferred to preparative and even more importantly to industrial scale. A brief historical overview of methacrylate monoliths is presented, followed by a short presentation of theoretical considerations that had led to the development of SMC. The design of these columns, as well as their scale-up to large units, together with the methods for transferring gradient separations from one scale to another are addressed. Noninvasive methods that have been developed for the physical characterization of various batches of SMC, which fulfill the regulatory requirements for cGMP production, are discussed. The applications of SMC for the separation and purification of large biomolecules, which demonstrate the full potential of this novel technology for an efficient downstream processing of biomolecules, are also presented.     

Analytical Scheme Leading to Integrated High-Sensitivity Profiling of Glycosphingolipids Together with <Emphasis Type="Italic">N</Emphasis>- and <Emphasis Type="Italic">O</Emphasis>-Glycans from One Sample

Glycoconjugates are directly or indirectly involved in many biological processes. Due to their complex structures, the structural elucidation of glycans and the exploration of their role in biological systems have been challenging. Glycan pools generated through release from glycoprotein or glycolipid mixtures can often be very complex. For the sake of procedural simplicity, many glycan profiling studies choose to concentrate on a single class of glycoconjugates. In this paper, we demonstrate it feasible to cover glycosphingolipids, N-glycans, and O-glycans isolated from the same sample. Small volumes of human blood serum and ascites fluid as well as small mouse brain tissue samples are sufficient to profile sequentially glycans from all three classes of glycoconjugates and even positively identify some mixture components through MALDI-MS and LC-ESI-MS. The results show that comprehensive glycan profiles can be obtained from the equivalent of 500-μg protein starting material or possibly less. These methodological improvements can help accelerating future glycomic comprehensive studies, especially for precious clinical samples.

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Graphical Abstract Outline of glycan profiling procedures