紫色球杆菌视紫红质光谱特性的机器学习研究

近年来，机器学习等人工智能技术被应用于蛋白质工程，其在蛋白质结构、功能预测、催化活性等研究中具有独特优势。在未知蛋白质结构的情况下，将蛋白质序列和功能特性与机器学习相结合，基于序列-活性关系（innovative sequence-activity relationship，ISAR）算法，将蛋白质氨基酸序列数字化，用快速傅里叶变换（fast four transform，FFT）进行预处理，再进行偏最小二乘回归建模，可在数据集较少情况下拟合得到最佳模型。通过机器学习对紫色球杆菌视紫红质（gloeobacter violaceus rhodopsin，GR）的突变体蛋白质氨基酸序列与光谱最大吸收波长进行建模，获得了最佳模型。用最佳索引LEVM760106建模得到的确定系数R² 为0.944，均方误差E为11.64。用小波变换进行的预处理，其R² 虽也约为0.944，但E大于11.64，不及FFT进行的预处理。方法较好地解决了蛋白质序列与功能特性之间的数学建模问题，在蛋白质工程中可为预测更优的突变体提供支持。     

Metabolomic analysis of raw Pinelliae Rhizoma and its alum‐processed products via UPLC–MS and their cytotoxicity

Alum‐processing is a traditional method to attenuate the toxicity of Pinelliae Rhizoma (tubers of Pinellia ternate, PT). The present study aimed at investigating the chemical and cytotoxic changes during alum processing. Metabolomic profiles of raw and alum‐processed PT were studied based on ultra‐performance liquid chromatography coupled with Orbitrap mass spectrometry. More than 80 chemicals in positive MS mode and 40 chemicals in negative MS mode, such as organic acids, amino acids, glucosides and nucleosides, were identified after multivariate statistical analysis, including principal component analysis and orthogonal partial least‐square discriminant analysis. Almost all of the identified chemical markers were significantly decreased ~10‐ to 100‐fold after alum processing. Meanwhile, the correlations between the chemical markers were assimilated to a positive coefficient from disorderly distribution during the processing. Raw PT extracts could inhibit the proliferation of human carcinoma cells (HCT‐116, HepG2, and A549) at the rate of 40.5, 24.8 and 31.6% more strongly than processed PT. It was concluded that the alum processing of PT could decrease the number of actively water‐soluble principles at the same time as decreasing toxicity. Given the water‐insoluble property of toxic calcium oxalate raphides in PT, we suggest that a more scientific processing method should be sought.     

Qualitative and quantitative determination of Atractylodes rhizome using ultra‐performance liquid chromatography coupled with linear ion trap–Orbitrap mass spectrometry with data‐dependent processing

A quick and effective workflow based on ultra‐performance liquid chromatography coupled with electron spray ionization and LTQ‐Orbitrap mass spectrometry (UPLC‐LTQ‐Orbitrap MS) was established for compositional analysis and screening of the characteristic compounds of three species of Atractylodes rhizome for quality evaluation. This technique was employed to determine the seven main components in Atractylodes rhizome samples. Ultimately, 78 constituents were identified; of these, seven characteristic compounds were selected for species discrimination, comprising atractylodin (63), atractylenolide I (43), atractylenolide II (49), atractylenolide III (53), atractylon (69), methyl‐atractylenolide II (54) and (4E,6E,12E)‐tetradecadecatriene‐8,10‐diyne‐1,3‐diacetate (59). The seven main compounds, including six characteristic compounds, were simultaneously determined in 29 batches of Atractylodes rhizome samples. Thus, the method validation showed acceptable results. Quantitative analysis showed significantly different contents of the seven main components among the three species of Atractylodes rhizome, which indicates possible distinctions in the pharmacological effects. This established method can simultaneously provide qualitative and quantitative results for compositional characterization of Atractylodes rhizomes and for quality control.     

Biomolecular Release Stimulated by Electrochemical Signals at a Very Small Potential Applied

DNA release electrochemically stimulated by applying ?10 mV on the modified electrode was studied. The release process was based on the local (interfacial) pH change produced upon H₂O₂ reduction electrocatalyzed by the immobilized microperoxidase‐11. SiO₂ nanoparticles attached to the electrode surface and functionalized with trigonelline and boronic acid species changed their electrical charge from positive to negative upon the interfacial pH change, thus allowing electrostatic adsorption of negatively charged DNA on the positive interface and then its repulsion/release from the negative interface. The loaded/released DNA molecules were labeled with a fluorescent dye to allow easy detection of the released DNA molecules. The important feature of the developed system is the controlled DNA release upon applying very small electrical potential on the modified electrode.     

An experimental method for eliminating effect of rigid out-of-plane motion on 2D-DIC

The out-of-plane motion is one of the most important factors that affect the precision of two-dimensional digital image correlation (2D-DIC). In this paper, a novel solution is presented to improve conventional 2D-DIC by eliminating the effect of out-of-plane motion, including translation and rotation. Firstly, an experimental technique using two projected laser strips is proposed to measure the out-of-plane motion of a planar specimen. A theoretical model is then established to predict the pseudostrains caused by out-of-plane motion based on the pin-hole imaging model. Using the measured out-of-plane displacement, the captured deformed images used in 2D-DIC are amended to eliminate the effect of out-of-plane motion by the theoretical model. Finally, two experiments were conducted to validate the effectiveness of the proposed method. Results indicate that application of the proposed method can effectively eliminate the errors caused by out-of-plane motion.     

Curvature investigation in tapered fibers and its application to sensing and mode conversion

Non-adiabatic tapered fibers are basic photonic components used in a wide range of applications. Here we investigate a way to increase their utility through the controllable bending of one of their tapered sections. The experiments carried out explain, for the first time, the mechanics of this approach showing how these tapers can be used to build more sensitive sensors. Their use as highly efficient mode converters is also discussed.     

Dual‐signal amplification strategy for ultrasensitive chemiluminescence detection of PDGF–BB in capillary electrophoresis

Many efforts have been made toward the achievement of high sensitivity in capillary electrophoresis coupled with chemiluminescence detection (CE‐CL). This work describes a novel dual‐signal amplification strategy for highly specific and ultrasensitive CL detection of human platelet‐derived growth factor–BB (PDGF–BB) using both aptamer and horseradish peroxidase (HRP) modified gold nanoparticles (HRP–AuNPs–aptamer) as nanoprobes in CE. Both AuNPs and HRP in the nanoprobes could amplify the CL signals in the luminol–H₂O₂ CL system, owing to the excellent catalytic behavior of AuNPs and HRP in the CL system. Meanwhile, the high affinity of aptamer modified on the AuNPs allows detection with high specificity. As proof‐of‐concept, the proposed method was employed to quantify the concentration of PDGF–BB from 0.50 to 250 fm with a detection limit of 0.21 fm. The applicability of the assay was further demonstrated in the analysis of PDGF–BB in human serum samples with acceptable accuracy and reliability. The result of this study exhibits distinct advantages, such as high sensitivity, good specificity, simplicity, and very small sample consumption. The good performances of the proposed strategy provide a powerful avenue for ultrasensitive detection of rare proteins in biological sample, showing great promise in biochemical analysis. Copyright © 2015 John Wiley & Sons, Ltd.     

Hexametaphosphate‐Capped Silica Mesoporous Nanoparticles Containing CuII Complexes for the Selective and Sensitive Optical Detection of Hydrogen Sulfide in Water

Cu^II‐macrocycle functionalized hexametaphosphate‐capped silica mesoporous nanoparticles have been prepared and used for the selective and sensitive detection of hydrogen sulfide in aqueous environments. The possibility of using different metal complexes combined with different capping anions and choice of different dyes or other sensing molecules as indicators makes this new protocol highly appealing for the preparation of new sensing systems for sulfide detection in different environments.