DFT plus PCM calculation for pairing specificity of Watson–Crick‐type bases in aqueous solutions

This study is aimed at explaining the preference for AT and CG pairings and the possible insertion of other tautomeric DNA base pairs such as G_enolT, that respect energetic and steric requirements including at least two hydrogen bonds and 11 ± 0.5Å distance between the 9‐CH₃ of purine and 5‐CH₃ of pyrimidine. The calculated free energy of formation ΔΔG at the DFT B3LYP/6‐31G*‐PCM/BEM level pointed out the CG and AT pairs as the most favored, followed closely by G_enolT, in good agreement with Michaelis–Menten first order kinetics (CG ≈ AT > G_enolT). Unusual DNA base pairs complexes such as AG (BEM) and CT (PCM) resulted to be stable, but it is very difficult to assume that they are likely to be included in the double strand DNA. The calculated enthalpy and dipole moments of isolated DNA bases agree well with experiment. The free energy of hydration, ΔG_hyd, was found to depend on the electrostatic term, while cavitation‐dispersion components are almost constant. The stability of DNA complexes in water resulted from PCM calculations is markedly influenced by the free energy of hydration. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Broad specificity indirect competitive immunoassay for determination of nitrofurans in animal feeds

A generic hapten of nitrofurans was synthesized by derivatization of 5-nitrofurfural with diamine, and the hapten was coupled to carrier protein to prepare different immunogens and coating antigens by using diazotization method and glutaraldehyde method. The obtained novel polyclonal antibodies from immunized rabbits showed broad cross reactivity among seven nitrofurans. After assessment of four coating antigen/antibody combinations, an indirect competitive immunoassay was developed to simultaneously detect the seven nitrofurans in animal feeds. The limits of detection for these analytes were in the range of 5-16 μg kg⁻¹ depending on the compound. Recoveries from nitrofurans fortified blank feeds at levels of 30 and 100 ng g ⁻¹ were in a range of 82.6-108.4% with coefficients of variation lower than 11.4%. The immunoassay was further validated by a HPLC method and the two methods showed good correlation (r = 0.9924). Therefore, the proposed immunoassay could be used as a practical method to monitor the illicit use of nitrofurans in animal feeds.     

A model for the evolution of parasite-host interactions based on the Maculinea-Myrmica system: Numerical simulations and multiple host behavior

We present a mathematical model of parasite-host interactions inspired by the Maculinea-Myrmica system. Numerical simulations of the model were conducted in order to access the possibility of stable multiple host behavior in the model. Results indicate that multiple host behavior can be observed under natural conditions, although a division of the original parasite population into separate subpopulations, each adapted to one distinct host, is expected. Transitions from single to multiple host behavior are expected to occur if the relative host species abundances change or host’s tolerance increases. Further model development and analysis are required to extend these results.     

Ion-specific swelling behavior of poly(vinyl alcohol) gel prepared by γ-ray irradiation

Poly(vinyl alcohol) gel was prepared by γ-ray irradiation of an aqueous solution of the polymer and its swelling behavior in solutions of the alkali-metal and alkaline-earth-metal salts was investigated. The gel deswelled in solutions containing strongly hydrated anions and swelled in solutions containing strongly hydrated cations. The degree of swelling of the gel was in the following order: SO₄ ²⁻<Cl⁻<Br⁻ ≅ NO₃ ⁻<I⁻ for the anions and K⁺<Na⁺<Li⁺ and Sr²⁺<Ca²⁺<Mg²⁺ for the cations. These results were interpreted in terms of interactions between the polymer and the ions through the hydration layers. Received: 6 November 2000 Accepted: 24 May 2001     

Sequence‐Specific DNA Alkylation Targeting for Kras Codon 13 Mutation by Pyrrole–Imidazole Polyamide seco‐CBI Conjugates

Hairpin N‐methylpyrrole‐N‐methylimidazole polyamide seco‐CBI conjugates 2 – 6 were designed for synthesis by Fmoc solid‐phase synthesis, and their DNA‐alkylating activities against the Kras codon 13 mutation were compared by high‐resolution denaturing gel electrophoresis with 225 base pair (bp) DNA fragments. Conjugate 5 had high reactivity towards the Kras codon 13 mutation site, with alkylation occurring at the A of the sequence 5′‐ACGTCACC A ‐3′ (site 2), including minor 1 bp‐mismatch alkylation against wild type 5′‐ACG C CACC A ‐3′ (site 3). Conjugate 6 , which differs from conjugate 5 by exchanging one Py unit with a β unit, showed high selectivity but only weakly alkylated the A of 5′‐ACGTCACC A ‐3′ (site 2). The hairpin polyamide seco‐CBI conjugate 5 thus alkylates according to Dervan′s pairing rule with the pairing recognition which β/β pair targets T–A and A–T pairs. SPR and a computer‐minimized model suggest that 5 binds to the target sequence with high affinity in a hairpin conformation, allowing for efficient DNA alkylation.     

Neural specificity of acupuncture stimulation from support vector machine classification analysis

Acupoint specificity, as a crucial issue in acupuncture neuroimaging studies, is still a controversial topic. Previous studies have generally adopted a block-based general linear model (GLM) approach, which predicts the temporal changes in the blood oxygenation level-dependent signal conforming to the “on-off” specifications. However, this method might become impractical since the precise timing and duration of acupuncture actions cannot be specified a priori. In the current study, we applied a data-driven multivariate classification approach, namely, support vector machine (SVM), to explore the neural specificity of acupuncture at gall bladder 40 (GB40) using kidney 3 (KI3) as a control condition (belonging to different meridians but the same nerve segment). In addition, to verify whether the typical GLM approach is sensitive enough in exploring the neural response patterns evoked by acupuncture, we also employed the GLM method to the same data sets. The SVM analysis detected distinct neural response patterns between GB40 and KI3 — positive predominantly for the GB40, while negative following the KI3. By contrast, group analysis from the GLM showed that acupuncture at these different acupoints can both evoke similar widespread signal decreases in multiple brain regions, and most of these regions were spatially overlapped, mainly distributing in the limbic and subcortical structures. Our findings may provide additional evidence to support the specificity of acupuncture, relevant to its clinical efficacy. Moreover, we also proved that GLM analysis is prone to be susceptible to errors and is not appropriate for detecting neural response patterns evoked by acupuncture stimulation.