Rapid Screening for Potential Epitopes Reactive with a Polycolonal Antibody by Solution-Phase H/D Exchange Monitored by FT-ICR Mass Spectrometry

The potential epitopes of a recombinant food allergen protein, cashew Ana o 2, reactive to polyclonal antibodies, were mapped by solution-phase amide backbone H/D exchange (HDX) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Ana o 2 polyclonal antibodies were purified in the serum from a goat immunized with cashew nut extract. Antibodies were incubated with recombinant Ana o 2 (rAna o 2) to form antigen:polyclonal antibody (Ag:pAb) complexes. Complexed and uncomplexed (free) rAna o 2 were then subjected to HDX-MS analysis. Four regions protected from H/D exchange upon pAb binding are identified as potential epitopes and mapped onto a homologous model.

Counting Dyck Paths by Area and Rank

The set of Dyck paths of length 2n inherits a lattice structure from a bijection with the set of noncrossing partitions with the usual partial order. In this paper, we study the joint distribution of two statistics for Dyck paths: area (the area under the path) and rank (the rank in the lattice). While area for Dyck paths has been studied, pairing it with this rank function seems new, and we get an interesting (q, t)-refinement of the Catalan numbers. We present two decompositions of the corresponding generating function: One refines an identity of Carlitz and Riordan; the other refines the notion of γ-nonnegativity, and is based on a decomposition of the lattice of noncrossing partitions due to Simion and Ullman. Further, Biane’s correspondence and a result of Stump allow us to conclude that the joint distribution of area and rank for Dyck paths equals the joint distribution of length and reflection length for the permutations lying below the n-cycle (12· · ·n) in the absolute order on the symmetric group.     

Optimizing human activity patterns using global sensitivity analysis

Implementing realistic activity patterns for a population is crucial for modeling, for example, disease spread, supply and demand, and disaster response. Using the dynamic activity simulation engine, DASim, we generate schedules for a population that capture regular (e.g., working, eating, and sleeping) and irregular activities (e.g., shopping or going to the doctor). We use the sample entropy (SampEn) statistic to quantify a schedule’s regularity for a population. We show how to tune an activity’s regularity by adjusting SampEn, thereby making it possible to realistically design activities when creating a schedule. The tuning process sets up a computationally intractable high-dimensional optimization problem. To reduce the computational demand, we use Bayesian Gaussian process regression to compute global sensitivity indices and identify the parameters that have the greatest effect on the variance of SampEn. We use the harmony search (HS) global optimization algorithm to locate global optima. Our results show that HS combined with global sensitivity analysis can efficiently tune the SampEn statistic with few search iterations. We demonstrate how global sensitivity analysis can guide statistical emulation and global optimization algorithms to efficiently tune activities and generate realistic activity patterns. Though our tuning methods are applied to dynamic activity schedule generation, they are general and represent a significant step in the direction of automated tuning and optimization of high-dimensional computer simulations.     

Intramolecular arylation of benzimidazoles via Pd(II)/Cu(I) catalyzed cross-dehydrogenative coupling

Electron poor benzimidazole substrates were arylated via an intramolecular cross-dehydrogenative coupling (CDC) reaction. These CDC reactions were catalyzed by a Pd(II)/Cu(I) catalyst system, capable of producing moderate yields on a large library of substrates. The substrate scope consisted of tethered arene-benzimidazoles that upon coupling, produced a fused polycyclic motif.     

A potent antimalarial trichothecene from hyphomycete species

Antimalarial screening of diverse fungal samples resulted in the isolation and identification of a new sesquiterpene, trichothecinol D (1), which exhibited potent in vitro activity against Plasmodium falciparum with a 200-fold selectivity for parasite versus mammalian cytotoxicity. Trichothecinol D was obtained by bioassay-guided fractionation of two hyphomycete species. Its chemical characterization was performed by detailed NMR spectroscopy and high resolution mass spectrometry. The absolute configuration of trichothecinol D was determined by X-ray crystallography.     

Detection of lectin-glycan interaction using high resolution surface plasmon resonance

We report the real-time and label-free detection of direct disaccharide binding to a lectin using a differential surface plasmon resonance detection method that allows for measurement of nanomolar concentrations of disaccharides.     

A fluorinated ruthenium porphyrin as a potential photodynamic therapy agent: synthesis, characterization, DNA binding, and melanoma cell studies

When the new porphyrin 5,10-(4-pyridyl)-15,20-(pentafluorophenyl)porphyrin is reacted with 2 equiv of Ru(bipy)(2)Cl(2) (where bipy = 2,2'-bipyridine) formation of the target ruthenated porphyrin is achieved with 40% yield. Strong electronic transitions are observed in the visible region of the spectrum associated with the porphyrin Soret and four Q-bands. A shoulder at slightly higher energy than the Soret band is attributed to the Ru(dpi) to bipy(pi*) metal to ligand charge transfer (MLCT) band. The bipyridyl pi to pi* transition occurs at 295 nm. Cyclic voltammetry experiments reveal two single-electron redox couples in the cathodic region at E(1/2) = -0.80 and -1.18 V vs Ag/AgCl associated with the porphyrin. Two overlapping redox couples at E(1/2) = 0.83 V vs Ag/AgCl due to the Ru(III/II) centers is also observed. DNA titrations using calf thymus (CT) DNA and the ruthenium porphyrin give a K(b) = 7.6 x 10(5) M(-1) indicating a strong interaction between complex and DNA. When aqueous solutions of supercoiled DNA and ruthenium porphyrin are irradiated with visible light (energy lower than 400 nm), complete nicking of the DNA is observed. Cell studies show that the ruthenated porphyrin is more toxic to melanoma skin cells than to normal fibroblast cells. When irradiated with a 60 W tungsten lamp, the ruthenium porphyrin preferentially leads to apoptosis of the melanoma cells over the normal skin cells.     

Effects of substituents on molecular devices

The current–voltage characteristics of small aliphatic chains of alkanes, alkenes, alkynes, and oligophenylene‐ethylenes, with and without substituents and terminated in sulfur attached nanosized gold electrodes are determined using ab initio procedures for discrete and extended systems in a density functional theory‐Green function's approach where most of the chemistry is considered. It is found that the current–voltage characteristics of small molecules can be tailored by the addition of substituents. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008