Characterization and linear-time detection of minimal obstructions to concave-round graphs and the circular-ones property

A graph is concave-round if its vertices can be circularly enumerated so that the closed neighborhood of each vertex is an interval in the enumeration. In this study, we give a minimal forbidden induced subgraph characterization for the class of concave-round graphs, solving a problem posed by Bang-Jensen, Huang, and Yeo [SIAM J. Discrete Math., 13 (2000), pp. 179–193]. In addition, we show that it is possible to find one such forbidden induced subgraph in linear time in any given graph that is not concave-round. As part of the analysis, we obtain characterizations by minimal forbidden submatrices for the circular-ones property for rows and for the circular-ones property for rows and columns and show that, also for both variants of the property, one of the corresponding forbidden submatrices can be found (if present) in any given matrix in linear time. We make some final remarks regarding connections to some classes of circular-arc graphs.     

Change of evaporation rate of single monocomponent droplet with temperature using time-resolved phase rainbow refractometry

Droplet evaporation characterization, although of great significance, is still challenging. The recently developed phase rainbow refractometry (PRR) is proposed as an approach to measuring the droplet temperature, size as well as evaporation rate simultaneously, and is applied to a single flowing n-heptane droplet produced by a droplet-on-demand generator. The changes of droplet temperature and evaporation rate after a transient spark heating are reflected in the time-resolved PRR image. Results show that droplet evaporation rate increases with temperature, from ?1.28$\times {10}^{?8}$ m²/s at atmospheric 293 K to a range of (?1.5, ?8)$\times {10}^{?8}$ m²/s when heated to (294, 315) K, agreeing well with the Maxwell and Stefan–Fuchs model predictions. Uncertainty analysis suggests that the main source is the indeterminate gradient inside droplet, resulting in an underestimation of droplet temperature and evaporation rate. With the demonstration on simultaneous measurements of droplet refractive index as well as droplet transient and local evaporation rate in this work, PRR is a promising tool to investigate single droplet evaporation in real engine conditions.     

Design and development of a two‐dimensional system based on hydrophilic and reversed‐phase liquid chromatography with on‐line sample treatment for the simultaneous separation of excreted xenobiotics and endogenous metabolites in urine

In the present work we describe a two‐dimensional liquid chromatographic system (2D‐LC) with detection by mass spectrometry (MS) for the simultaneous separation of endogenous metabolites of clinical interest and excreted xenobiotics deriving from exposure to toxic compounds. The 2D‐LC system involves two orthogonal chromatographic modes, hydrophilic interaction liquid chromatography (HILIC) to separate polar endogenous metabolites and reversed‐phase (RP) chromatography to separate excreted xenobiotics of low and intermediate polarity. Additionally, the present proposal has the novelty of incorporating an on‐line sample treatment based on the use of restricted access materials (RAMs), which permits the direct injection of urine samples into the system. The work is focused on the instrumental coupling, studying all possible options and attempting to circumvent the problems of solvent incompatibility between the RAM device and the two chromatographic columns, HILIC and RP. The instrumental configuration developed, RAM‐HILIC‐RPLC‐MS/MS, allows the simultaneous assessment of urinary metabolites of clinical interest and excreted compounds derived from exposure to toxic agents with minimal sample manipulation. Thus, it may be of interest in areas such as occupational and environmental toxicology in order to explore the possible relationship between the two types of compounds. Copyright © 2015 John Wiley & Sons, Ltd.     

Azasugar inhibitors as pharmacological chaperones for Krabbe disease

Krabbe disease is a devastating neurodegenerative disorder characterized by rapid demyelination of nerve fibers. This disease is caused by defects in the lysosomal enzyme β-galactocerebrosidase (GALC), which hydrolyzes the terminal galactose from glycosphingolipids. These lipids are essential components of eukaryotic cell membranes: substrates of GALC include galactocerebroside, the primary lipid component of myelin, and psychosine, a cytotoxic metabolite. Mutations of GALC that cause misfolding of the protein may be responsive to pharmacological chaperone therapy (PCT), whereby small molecules are used to stabilize these mutant proteins, thus correcting trafficking defects and increasing residual catabolic activity in cells. Here we describe a new approach for the synthesis of galacto-configured azasugars and the characterization of their interaction with GALC using biophysical, biochemical and crystallographic methods. We identify that the global stabilization of GALC conferred by azasugar derivatives, measured by fluorescence-based thermal shift assays, is directly related to their binding affinity, measured by enzyme inhibition. X-ray crystal structures of these molecules bound in the GALC active site reveal which residues participate in stabilizing interactions, show how potency is achieved and illustrate the penalties of aza/iminosugar ring distortion. The structure–activity relationships described here identify the key physical properties required of pharmacological chaperones for Krabbe disease and highlight the potential of azasugars as stabilizing agents for future enzyme replacement therapies. This work lays the foundation for new drug-based treatments of Krabbe disease.     

Ozonolysis of a Series of Methylated Alkenes: Reaction Rate Coefficients and Gas‐Phase Products

The gas‐phase ozonolysis of three methylated alkenes, i.e., trans‐2,2‐dimethyl‐3‐hexene (22dM3H), trans‐2,5‐dimethyl‐3‐hexene (25dM3H), and 4‐methyl‐1‐pentene (4M1P), has been investigated in the presence of sufficient hydroxyl radical scavenger in a laminar flow reactor at ambient temperature (296 ± 2 K) and P = 1 atm of dry air (RH ≤ 5%). Ozone levels in the reactor were monitored by an automatic analyzer. Alkene and gas‐phase product concentrations were determined via online sampling either on three‐bed adsorbent cartridges followed by thermodesorption and GC/FID‐MS analysis or on 2,4‐dinitrophenylhydrazine (DNPH) cartridges for subsequent HPLC/UV analysis. Reaction rate coefficients of (3.38 ± 0.12) × 10^?17 for 22dM3H and (2.71 ± 0.26) × 10^?17 for 25dM3H, both in cm³ molecule^?1 s^?1 units, have been obtained under pseudo–first‐order conditions. Primary carbonyl products have been identified for the three investigated alkenes, and branching ratios are reported. In the case of 4M1P ozonolysis, the yield of a Criegee intermediate was indirectly determined. Kinetics and product study results are compared to those of literature when available. This work represents the first investigation of reaction products in the ozonolysis of 22dM3H, 25dM3H, and 4M1P in a flow reactor.     

Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.     

Chromatography-Free Multicomponent Synthesis of Thioureas Enabled by Aqueous Solution of Elemental Sulfur

The development of a new three-component chromatography-free reaction of isocyanides, amines and elemental sulfur allowed us the straightforward synthesis of thioureas in water. Considering a large pool of organic and inorganic bases, we first optimized the preparation of aqueous polysulfide solution from elemental sulfur. Using polysulfide solution, we were able to omit the otherwise mandatory chromatography, and to isolate the crystalline products directly from the reaction mixture by a simple filtration, retaining the sulfur in the solution phase. A wide range of thioureas synthesized in this way confirmed the reasonable substrate and functional group tolerance of our protocol.