A critical assessment of hidden markov model sub‐optimal sampling strategies applied to the generation of peptide 3D models

Hidden Markov Model derived structural alphabets are a probabilistic framework in which the complete conformational space of a peptidic chain is described in terms of probability distributions that can be sampled to identify conformations of largest probabilities. Here, we assess how three strategies to sample sub‐optimal conformations—Viterbi k‐best, forward backtrack and a taboo sampling approach—can lead to the efficient generation of peptide conformations. We show that the diversity of sampling is essential to compensate biases introduced in the estimates of the probabilities, and we find that only the forward backtrack and a taboo sampling strategies can efficiently generate native or near‐native models. Finally, we also find such approaches are as efficient as former protocols, while being one order of magnitude faster, opening the door to the large scale de novo modeling of peptides and mini‐proteins. © 2016 Wiley Periodicals, Inc.     

Determination of volatile chlorinated hydrocarbons in water samples by static headspace gas chromatography with electron capture detection

A simple, efficient, solvent‐free, and commercial readily available approach for determination of five volatile chlorinated hydrocarbons in water samples using the static headspace sampling and gas chromatography with electron capture detection has been described. The proposed static headspace sampling method was initially optimized and the optimum experimental conditions found were 10 mL water sample containing 20% w/v sodium chloride placed in a 20 mL vial and stirred at 50ºC for 20 min. The linearity of the method was in the range of 1.2–240 μg/L for dichloromethane, 0.2–40 μg/L for trichloromethane, 0.005–1 μg/L for perchloromethane, 0.025–5 μg/L for trichloroethylene, and 0.01–2 μg/L for perchloroethylene, with coefficients of determination ranging between 0.9979 and 0.9990. The limits of detection were in the low μg/L level, ranging between 0.001 and 0.3 μg/L. The relative recoveries of spiked five volatile chlorinated hydrocarbons with external calibration method at different concentration levels in pure, tap, sea water of Jiaojiang Estuary, and sea water of waters of Xiaomendao were in the range of 91–116, 96–105, 86–112, and 80–111%, respectively, and with relative standard deviations of 1.9–3.6, 2.3–3.5, 1.5–2.7, and 2.3–3.7% (n = 5), respectively. The performance of the proposed method was compared with traditional liquid–liquid extraction on the real water samples (i.e., pure, tap, and sea water, etc.) and comparable efficiencies were obtained. It is concluded that this method can be successfully applied for the determination of volatile chlorinated hydrocarbons in different water samples.     

Ambient air monitoring with Auto-gas chromatography running in trigger mode

Speciated volatile organic compounds (VOC), either as ozone precursors or air toxics in the air, are commonly monitored by triggered canister method or continuous ozone precursor analyzer (commonly known as Auto-gas chromatography (GC)) method. In the triggered canister method, a canister sample is collected when a total non-methane organic compound (TNMOC) concentration exceeds a pre-determined trigger level. The canister sample is then analyzed in a lab in a later time. In the Auto-GC method, an online GC runs in a “continuous” mode with a sampling and analysis cycle of 1 h. Within the cycle hour, samples are collected only during the first 40 min.A new approach of Auto-GC running in trigger mode is developed in this study. This new approach uses Auto-GC but operates it in a trigger mode similar to the triggered canister sampling method. Compared to the triggered canister sample method, this system provides near real-time speciated VOC data, which are critical for responding to a high VOC concentration episode. Although the canister system generally costs less, its cost advantage may diminish if trigger events are frequent and the monitoring duration is long. Compared to continuous Auto-GC, triggered GC has its niche—it is better for capturing transient plumes with a small footprint. The continuous GC either misses a transient plume if the plume does not arrive at the sampling site during the sampling cycle or flattens the plume concentration peak by dilution with non-plume air sample.Field experience with this system for fenceline VOC monitoring is presented. The sampling and calibration strategy for trigger mode operation is described. The chromatograph retention time drift issues are discussed. The system performance is evaluated, including the method detection limit, precision and accuracy. The trigger mode configuration for VOC fenceline or near source monitoring in this work proved effective for local and transient plume identification.     

The Permeation Mechanism of Cisplatin Through a Dioleoylphosphocholine Bilayer**

The investigation of the intermolecular interactions between platinum-based anticancer drugs and lipid bilayers is of special relevance to unveil the mechanisms involved in different steps of the anticancer mode of action of these drugs. We have simulated the permeation of cisplatin through a model membrane composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids by means of umbrella sampling classical molecular dynamics simulations. The initial physisorption of cisplatin into the polar region of the lipid membrane is controlled by long-range electrostatic interactions with the choline groups in a first step and, in a second step, by long-range electrostatic and hydrogen bond interactions with the phosphate groups. The second half of the permeation pathway, in which cisplatin diffuses through the nonpolar region of the bilayer, is characterized by the drop of the interactions with the polar heads and the rise of attractive interactions with the non-polar tails, which are dominated by van der Waals contributions. The permeation free-energy profile is explained by a complex balance between the drug/lipid interactions and the energy and entropy contributions associated with the dehydration of the drug along the permeation pathway and with the decrease and increase of the membrane ordering along the first and second half of the mechanism, respectively.     

悬浮液进样-液体阴极辉光放电原子发射光谱法测定高纯氮化硅粉体中微量杂质元素

针对高纯氮化硅粉体中的9种微量杂质元素(Al、Ca、Co、Fe、K、Mg、Mn、Na、Ni),建立了悬浮液进样-液体阴极辉光放电原子发射光谱定量分析方法.考察了制备稳定悬浮液对样品颗粒度的要求,并通过六通阀将悬浮液引入液体阴极辉光放电原子发射光谱装置检测.本方法采用水溶液标准进行定量分析,无需对悬浮液的pH值进行精确调节,能够保持液体阴极辉光等离子体的稳定性.研究了仪器装置的操作电压、载液流速、光电倍增管积分时间等因素对检出限的影响.优化后得到的最佳实验条件为操作电压1080 V,载液流速1.2 mL/min,光电倍增管积分时间800 ms.利用六通阀进样系统对原有的液体阴极辉光放电原子发射光谱装置进行改进,从而实现悬浮液直接进样检测.用此装置对氮化硅实际样品进行检测,得到各种元素的检出限在0.2~53 mg/kg之间,RSD在1.1%~5.0%之间.通过对氮化硅标准参考物质ERM-ED101进行分析,其测定结果与高温高压消解-电感耦合等离子体发射光谱法一致,并与标准参考值吻合,表明此方法可用于氮化硅粉体的悬浮液直接进样检测,结果准确可靠,灵敏度高,具备应用价值.     

BayesWHAM: A Bayesian approach for free energy estimation,reweighting, and uncertainty quantification in the weighted histogram analysis method

The weighted histogram analysis method (WHAM) is a powerful approach to estimate molecular free energy surfaces (FES) from biased simulation data. Bayesian reformulations of WHAM are valuable in proving statistically optimal use of the data and providing a transparent means to incorporate regularizing priors and estimate statistical uncertainties. In this work, we develop a fully Bayesian treatment of WHAM to generate statistically optimal FES estimates in any number of biasing dimensions under arbitrary choices of the Bayes prior. Rigorous uncertainty estimates are generated by Metropolis‐Hastings sampling from the Bayes posterior. We also report a means to project the FES and its uncertainties into arbitrary auxiliary order parameters beyond those in which biased sampling was conducted. We demonstrate the approaches in applications of alanine dipeptide and the unthreading of a synthetic mimic of the astexin‐3 lasso peptide. Open‐source MATLAB and Python implementations of our codes are available for free public download. © 2017 Wiley Periodicals, Inc.     

Efficient estimation of binding free energies between peptides and an MHC class II molecule using coarse‐grained molecular dynamics simulations with a weighted histogram analysis method

We estimate the binding free energy between peptides and an MHC class II molecule using molecular dynamics (MD) simulations with the weighted histogram analysis method (WHAM). We show that, owing to its more thorough sampling in the available computational time, the binding free energy obtained by pulling the whole peptide using a coarse‐grained (CG) force field (MARTINI) is less prone to significant error induced by inadequate‐sampling than using an atomistic force field (AMBER). We further demonstrate that using CG MD to pull 3–4 residue peptide segments while leaving the remaining peptide segments in the binding groove and adding up the binding free energies of all peptide segments gives robust binding free energy estimations, which are in good agreement with the experimentally measured binding affinities for the peptide sequences studied. Our approach thus provides a promising and computationally efficient way to rapidly and reliably estimate the binding free energy between an arbitrary peptide and an MHC class II molecule. © 2017 Wiley Periodicals, Inc.     

薄膜梯度扩散技术结合相研究进展

薄膜梯度扩散(DGT)技术是一种新型原位被动采样技术,已被广泛应用于水体、土壤、沉积物中目标物的采集与测量。结合相是DGT技术的重要组成部分,决定了与目标物的结合能力、结合速度、结合容量以及目标物的形态选择性等。DGT结合相分为固态结合相和液态结合相。本文重点综述了树脂、氧化物、无机盐、活性炭、改性硅胶、分子印迹、共聚物、复合、液态等结合相在DGT技术中的应用,展望了DGT结合相的发展前景。     

Two effective post-filtering strategies for improving direct sampling methods

In this paper, we introduce two novel strategies to reduce artifacts in the direct sampling type methods (DSM). The newly proposed techniques can essentially reduce the artifacts and provide more accurate and reliable physical profiles of the scatterers compared with the original DSM. The techniques can find wide applications in the inverse scattering problems. Moreover, the novel techniques exhibit several strengths: direct, stable, robust, and ease of implementation.     

Screening disrupted molecular functions and pathways associated with clear cell renal cell carcinoma using Gibbs sampling

ObjectiveTo explore the disturbed molecular functions and pathways in clear cell renal cell carcinoma (ccRCC) using Gibbs sampling.MethodsGene expression data of ccRCC samples and adjacent non-tumor renal tissues were recruited from public available database. Then, molecular functions of expression changed genes in ccRCC were classed to Gene Ontology (GO) project, and these molecular functions were converted into Markov chains. Markov chain Monte Carlo (MCMC) algorithm was implemented to perform posterior inference and identify probability distributions of molecular functions in Gibbs sampling. Differentially expressed molecular functions were selected under posterior value more than 0.95, and genes with the appeared times in differentially expressed molecular functions ≥5 were defined as pivotal genes. Functional analysis was employed to explore the pathways of pivotal genes and their strongly co-regulated genes.ResultsIn this work, we obtained 396 molecular functions, and 13 of them were differentially expressed. Oxidoreductase activity showed the highest posterior value. Gene composition analysis identified 79 pivotal genes, and survival analysis indicated that these pivotal genes could be used as a strong independent predictor of poor prognosis in patients with ccRCC. Pathway analysis identified one pivotal pathway − oxidative phosphorylation.ConclusionsWe identified the differentially expressed molecular functions and pivotal pathway in ccRCC using Gibbs sampling. The results could be considered as potential signatures for early detection and therapy of ccRCC.