GlyNet: a multi-task neural network for predicting protein–glycan interactions

Advances in diagnostics, therapeutics, vaccines, transfusion, and organ transplantation build on a fundamental understanding of glycan–protein interactions. To aid this, we developed GlyNet, a model that accurately predicts interactions (relative binding strengths) between mammalian glycans and 352 glycan-binding proteins, many at multiple concentrations. For each glycan input, our model produces 1257 outputs, each representing the relative interaction strength between the input glycan and a particular protein sample. GlyNet learns these continuous values using relative fluorescence units (RFUs) measured on 599 glycans in the Consortium for Functional Glycomics glycan arrays and extrapolates these to RFUs from additional, untested glycans. GlyNet''s output of continuous values provides more detailed results than the standard binary classification models. After incorporating a simple threshold to transform such continuous outputs the resulting GlyNet classifier outperforms those standard classifiers. GlyNet is the first multi-output regression model for predicting protein–glycan interactions and serves as an important benchmark, facilitating development of quantitative computational glycobiology.

GlyNet, a neural net model of glycan-protein binding strengths. Given a glycan it outputs binding to each of several protein samples. Reproducing glycan array data, it extrapolates the binding of untested glycans against the protein samples.     

Metabolic profile of glyburide in human liver microsomes using LC‐DAD‐Q‐TRAP‐MS/MS

The sulfonylurea urea drug glyburide (glibenclamide) is widely used for the treatment of diabetes milletus and gestational diabetes. In previous studies monohydroxylated metabolites were identified and characterized for glyburide in different species, but the metabolite owing to the loss of cyclohexyl ring was identified only in mouse. Glyburide upon incubation with hepatic microsomes resulted in 10 metabolites for human. The current study identifies new metabolites of glyburide along with the hydroxylated metabolites that were reported earlier. The newly identified drug metabolites are dihydroxylated metabolites, a metabolite owing to the loss of cyclohexyl ring and one owing to hydroxylation with dehydrogenation. Among the 10 identified metabolites, there were six monohydroxylated metabolites, one dihydroxylated metabolite, two metabolites owing to hydroxylation and dehydrogenation, and one metabolite owing to the loss of cyclohexyl ring. New metabolites of glyburide were identified and characterized using liquid chromatography–diode array detector–quadruple‐ion trap–mass spectrometry/mass spectrometry (LC‐DAD‐Q‐TRAP‐MS/MS). An enhanced mass scan–enhanced product ion scan with information‐dependent acquisition mode in a Q‐TRAP‐MS/MS system was used to characterize the metabolites. Liquid chromatography with diode array detection was used as a complimentary technique to confirm and identify the metabolites. Metabolites formed in higher amounts were detected in both diode array detection and mass spectrometry detection. Copyright © 2012 John Wiley & Sons, Ltd.     

1H MRS detection of glycine residue of reduced glutathione in vivo

Glutathione (GSH) is a powerful antioxidant found inside different kinds of cells, including those of the central nervous system. Detection of GSH in the human brain using ¹H MR spectroscopy is hindered by low concentration and spectral overlap with other metabolites. Previous MRS methods focused mainly on the detection of the cysteine residue (GSH-Cys) via editing schemes. This study focuses on the detection of the glycine residue (GSH-Gly), which is overlapped by glutamate and glutamine (Glx) under physiological pH and temperature. The first goal of the study was to obtain the spectral parameters for characterization of the GSH-Gly signal under physiological conditions. The second goal was to investigate a new method of separating GSH-Gly from Glx in vivo. The characterization of the signal was carried out by utilization of numerical simulations as well as experiments over a wide range of magnetic fields (4.0–14 T). The proposed separation scheme utilizes J-difference editing to quantify the Glx contribution to separate it from the GSH-Gly signal. The presented method retains 100% of the GSH-Gly signal. The overall increase in signal to noise ratio of the targeted resonance is calculated to yield a significant SNR improvement compared to previously used methods that target GSH-Cys residue. This allows shorter acquisition times for in vivo human clinical studies.     

Regioselective synthesis of pyrano[3,2-f]quinoline and phenanthroline derivatives using molecular iodine

A series of polysubstituted pyrano[3,2-f]quinoline and phenanthroline derivatives have been synthesized by molecular iodine-catalyzed tandem reaction of various propargylic alcohols with or without substituted amines in excellent yields. Moreover, the cyclized side products are also pyrano[3,2-f]quinoline and phenanthroline derivatives.     

Ruthenium (II) Catalyzed C(sp2)−H Bond Alkenylation of 2-Arylbenzo[d]oxazole and 2-Arylbenzo[d]thiazole with Unactivated Olefins

Functionalization of the bio-relevant heterocycles 2-arylbenzo[d]oxazole and 2-arylbenzo[d]thiazole has been achieved through Ru(II)-catalyzed alkenylation with unactivated olefins leading to selective formation of the mono-alkenylated products. This approach has a broad substrate scope with respect to the coupling partners, affords high yields, and works for gram scale synthesis using a readily available Ru-based catalyst. Mechanistic studies reveal a C−H activation pathway for the dehydrogenative coupling leading to the alkenylation. However, the results of the ESI-MS-guided deuterium kinetic isotope effect studies indicate that the C−H activation stage may not be the rate-determining step of the reaction. The use of a radical scavenging agent such as TEMPO did not show any detrimental effect on the reaction outcome, eliminating the possibility of the involvement of a free-radical pathway.     

Three Bis‐BODIPY Analogous Diruthenium Redox Series: Characterization and Electronic Structure Analysis

The dianion derived from (2Z,6Z)‐3,7‐diphenyl‐N2,N6‐di(pyridin‐2‐yl)pyrrolo[2,3‐f]indole‐2,6(1H,5H)‐diimine (H₂BL), a modified BODIPY ligand precursor, is shown to be capable of bridging two metal complex fragments RuL₂, L=2,4‐pentanedionato (acac^?), 2,2’‐bipyridine (bpy) or 2‐phenylazopyridine (pap) in [Ru(acac)₂Ru(μ‐BL)Ru(acac)₂] ( 1 / 2 ), [Ru(bpy)₂Ru(μ‐BL)Ru(bpy)₂](ClO₄)₂ ([ 3 ](ClO₄)₂) and [Ru(pap)₂Ru(μ‐BL)Ru(pap)₂](ClO₄)₂ ([ 4 ](ClO₄)₂). The compounds, including a diastereoisomeric pair 1 (meso) and 2 (rac) were spectroscopically and structurally characterized. Reversible electron transfers as revealed by cyclic and differential pulse voltammetry allowed for an EPR and UV‐vis‐NIR spectroelectrochemical investigation of several neighboring charge states. Together with susceptibility measurements and TD‐DFT calculations the assignment of oxidation states reveals that 1 , 2 are diruthenium(III) species which can be oxidized or reduced by one electron whereas 3 ²⁺ and 4 ²⁺ contain ruthenium(II) and get reduced or oxidized mainly at the dianionic bridge ( 3 ²⁺) or are reduced at the ancillary ligands pap ( 4 ²⁺).     

Unusual Surface Latent Heat Flux Variations and Their Critical Dynamics Revealed before Strong Earthquakes

We focus on the possible thermal channel of the well-known Lithosphere–Atmosphere–Ionosphere Coupling (LAIC) mechanism to identify the behavior of thermal anomalies during and prior to strong seismic events. For this, we investigate the variation of Surface Latent Heat Flux (SLHF) as resulting from satellite observables. We demonstrate a spatio-temporal variation in the SLHF before and after a set of strong seismic events occurred in Kathmandu, Nepal, and Kumamoto, Japan, having magnitudes of 7.8, 7.3, and 7.0, respectively. Before the studied earthquake cases, significant enhancements in the SLHF were identified near the epicenters. Additionally, in order to check whether critical dynamics, as the signature of a complex phenomenon such as earthquake preparation, are reflected in the SLHF data, we performed a criticality analysis using the natural time analysis method. The approach to criticality was detected within one week before each mainshock.     

Symmetry reduction for molecular dynamics simulation of an imploding gas bubble

We propose a symmetry reduction technique whereby molecular dynamics (MD) simulations for spherically symmetric gas bubbles can be accelerated. Results for an imploding Xenon bubble containing 50 million particles—the smallest measured sonoluminescing system—are presented.