Grid Graphs,Gorenstein Polytopes,and Domino Stackings

We examine domino tilings of rectangular boards, which are in natural bijection with perfect matchings of grid graphs. This leads to the study of their associated perfect matching polytopes, and we present some of their properties, in particular, when these polytopes are Gorenstein. We also introduce the notion of domino stackings and present some results and several open questions. Our techniques use results from graph theory, polyhedral geometry, and enumerative combinatorics.     

Simultaneous determination of five coumarins in Angelicae dahuricae Radix by HPLC/UV and LC‐ESI‐MS/MS

Rapid, simple and reliable HPLC/UV and LC‐ESI‐MS/MS methods for the simultaneous determination of five active coumarins of Angelicae dahuricae Radix, byakangelicol (1), oxypeucedanin (2), imperatorin (3), phellopterin (4) and isoimperatorin (5) were developed and validated. The separation condition for HPLC/UV was optimized using a Develosil RPAQUEOUS C₃₀ column using 70% acetonitrile in water as the mobile phase. This HPLC/UV method was successful for providing the baseline separation of the five coumarins with no interfering peaks detected in the 70% ethanol extract of Angelicae dahuricae Radix. The specific determination of the five coumarins was also accomplished by a triple quadrupole tandem mass spectrometer equipped with an electrospray ionization source (LC‐ESI‐MS/MS). Multiple reaction monitoring (MRM) in the positive mode was used to enhance the selectivity of detection. The LC‐ESI‐MS/MS methods were successfully applied for the determination of the five major coumarins in Angelicae dahuricae Radix. These HPLC/UV and LC‐ESI‐MS/MS methods were validated in terms of recovery, linearity, accuracy and precision (intra‐ and inter‐day validation). Taken together, the shorter analysis time involved makes these HPLC/UV and LC‐ESI‐MS/MS methods valuable for the commercial quality control of Angelicae dahuricae Radix extracts and its pharmaceutical preparations. Copyright © 2009 John Wiley & Sons, Ltd.     

Second Order Efficient Estimating a Smooth Distribution Function and its Applications

Methodology and Computing in Applied Probability - Consider a problem of estimation of a cumulative distribution function of a random variable supported on a finite interval, with a circular random...     

Mechanism of Fenpropathrin Resistance in Red Spider Mite, <Emphasis Type="Italic">Oligonychus coffeae</Emphasis> (Acarina: Tetranychidae), Infesting Tea [<Emphasis Type="Italic">Camellia sinensis</Emphasis> L. (O. Kuntze)]

Red spider mite (RSM), Oligonychus coffeae (Nietner) (Acarina: Tetranychidae), has gained special attention in view of their widespread occurrence as a pest on tea [Camellia sinensis L. (O. Kuntze)]. The development of acaricide (fenpropathrin) resistance has been screened in field populations (FPs) of RSMs from different tea-growing regions of south India and compared with a laboratory-susceptible population (SP) based on toxicity bioassay, detoxifying enzyme activities, analysis of acetylcholine esterase gene (AChE, 2064 bp), and their expression pattern using semiquantitative RT-PCR. The increased resistance ratio (RR, 1.39 to 2.13) in LC₅₀ of fenpropathrin observed in field populations of RSM provides a baseline for screening the development of resistance to fenpropathrin. This resistance developed due to hyperexpression of detoxifying enzymes, i.e., esterase (RR of 1.43 to 2.53) and glutathione S-transferase (RR of 1.11 to 1.86), and overexpression of AChE gene at 1.4 to 2.7-fold. These results necessitate molecular studies and warrant the continuous monitoring of acaricide susceptibility and resistance pattern in order to analyze the usefulness of AChE gene as target for developing alternate pest control strategies and management of pesticide resistance in tea ecosystem.     

Steric factors override thermodynamic driving force in regioselectivity of proline hydroxylation by prolyl-4-hydroxylase enzymes

Prolyl-4-hydroxylase is an important nonheme iron-containing dioxygenase in humans involved in the regioselective hydroxylation of a proline residue in a peptide chain on the C(4) position. In biosystems this process is important to create collagen cross-linking and cellular responses to hypoxia. We have performed a series of density functional theory (DFT) studies into the origin of the regioselectivity of proline hydroxylation by P4H enzymes using a minimal active site model (where substrate is unhindered in the binding site) and a larger active site model that incorporates steric hindrance of the substrate by several secondary sphere aromatic residues. Our studies show that thermodynamically the most favorable hydrogen atom abstraction position of proline is from the C(5) position; hence, the small model gives a low reaction barrier and large exothermicity for this process. However, stereochemical repulsions of the substrate with aromatic residues of Tyr(140) and Trp(243) in the second coordination sphere prevent C(5) hydroxylation and make C(4) hydroxylation the dominant mechanism, despite a lesser driving force for the reaction. These studies explain the remarkable regioselectivity of proline hydroxylation by P4H enzymes and show that the regioselectivity is kinetically controlled but not thermodynamically. In addition, we calculated spectroscopic parameters and found good agreement with experimental data.     

Selection of aptamers for signal transduction proteins by capillary electrophoresis

High‐affinity aptamers for important signal transduction proteins, i.e. Cdc42‐GTP, p21‐activated kinase1 (PAK1) and MRCK (myotonic dystrophy kinase‐related Cdc42‐binding kinase) α were successfully selected in the low micro‐ to nanomolar range using non‐systematic evolution of ligands by exponential enrichment (SELEX) with at least three orders of magnitude enhancement from their respective bulk affinity of naïve DNA library. In the non‐SELEX procedure, CE was used as a highly efficient affinity method to select aptamers for the desired molecular target through a process that involved repetitive steps of partitioning, known as non‐equilibrium CE of equilibrium mixtures with no PCR amplification between successive steps. Various non‐SELEX conditions including the type, concentration and pH of the run buffer were optimized. Other considerations such as salt composition of selection buffer, protein concentration and sample injection size were also studied for high stringency during selection. After identifying the best enriched aptamer pool, randomly selected clones from the aptamer pool were sequenced to obtain the individual DNA sequences. The dissociation constants (K_d) of these sequences were in the low micromolar to nanomolar range, indicating high affinity to the respective proteins. The best binders were also subjected to sequence alignment to generate a phylogenetic tree. No significant consensus region based on approximately 50 sequences for each protein was observed, suggesting the high efficiency of non‐SELEX for the selection of numerous unique sequences with high selectivity.     

Fate of the resonating valence bond in graphene

We apply a variational wave function capable of describing qualitatively and quantitatively the so-called "resonating valence bond" (RVB) in realistic materials, by improving standard ab initio calculations by means of quantum Monte Carlo methods. In this framework we clearly identify the Kekulé and Dewar contributions to the chemical bond of the benzene molecule and establish the corresponding RVB energy of these structures (?0.01 eV/atom). We apply this method to unveil the nature of the chemical bond in undoped graphene, providing an estimate of the RVB energy gain, and show that this picture remains only within a small "resonance length" of a few atomic units.