字符串匹配算法在DNA序列比对中的应用

高通量测序技术的飞速发展让生物信息领域迎来了大数据时代。新技术在提供海量生物遗传信息的同时,也给分析这些数据带来了新的挑战。DNA序列比对是信息分析流程中的关键步骤,为后续的变异检测提供序列比对信息。2015“深圳杯”数学建模夏令营B题以DNA序列比对为研究课题,希望参赛学生给出序列快速比对的最佳方案。本文简要点评了各参赛队伍的解答情况,然后介绍了现有DNA序列比对软件中用到的算法和数据结构。     

Simultaneously Probing Two Ultrafast Condensed‐Phase Molecular Symmetry Breaking Events by Two‐Dimensional Infrared Spectroscopy

In condensed phases, a highly symmetric gas‐phase molecule lowers its symmetry under perturbation of the solvent, which is vital to a variety of structural chemistry related processes. However, the dynamical aspects of solvent‐mediated symmetry‐breaking events remain largely unknown. Herein, direct evidence for two types of solvent‐mediated symmetry‐breaking events that coexist on the picosecond timescale in a highly symmetric anion, namely, hexacyanocobaltate, is presented: 1) an equilibrium symmetry‐breaking event in which a solvent‐bound species having lowered symmetry undergoes a population exchange reaction with the symmetry‐retaining species; 2) a dynamic symmetry‐breaking event that is composed of many dynamic population‐exchange reactions under fluctuating solvent interactions. Ultrafast two‐dimensional infrared spectroscopy is used to simultaneously observe and dynamically characterize these two events. This work opens a new window into molecular symmetry and structural dynamics under equilibrium and non‐equilibrium conditions.     

Chiral Monolithic Absorbent Constructed by Optically Active Helical‐Substituted Polyacetylene and Graphene Oxide: Preparation and Chiral Absorption Capacity

Chiral monolithic absorbent is successfully constructed for the first time by using optically active helical‐substituted polyacetylene and graphene oxide (GO). The preparative strategy is facile and straightforward, in which chiral‐substituted acetylene monomer (Ma), cross‐linker (Mb), and alkynylated GO (Mc) undergo copolymerization to form the desired monolithic absorbent in quantitative yield. The resulting monoliths are characterized by circular dichroism, UV–vis absorption, scanning electron microscopy (SEM), FT‐IR, Raman, energy‐dispersive spectrometer (EDS), X‐ray diffraction (XRD), Brunauer–Emmett–Teller (BET), XPS, and thermogravimetric analysis (TGA) techniques. The polymer chains derived from Ma form chiral helical structures and thus provide optical activity to the monoliths, while GO sheets contribute to the formation of porous structures. The porous structure enables the monolithic absorbents to demonstrate a large swelling ratio in organic solvents, and more remarkably, the helical polymer chains provide optical activity and further enantio‐differentiating absorption ability. The present study establishes an efficient and versatile methodology for preparing novel functional materials, in particular monolithic chiral materials based on substituted polyacetylene and GO.

     

Thermal behaviors and kinetic analysis of two natural kaolinite samples selected from Qingshuihe region in Inner Mongolia in China

Journal of Thermal Analysis and Calorimetry - The thermal characteristic behaviors of two kaolinite samples selected from Qingshuihe region in Inner Mongolia in China were studied through...     

Sparse representation-based image restoration via nonlocal supervised coding

Sparse representation (SR) and nonlocal technique (NLT) have shown great potential in low-level image processing. However, due to the degradation of the observed image, SR and NLT may not be accurate enough to obtain a faithful restoration results when they are used independently. To improve the performance, in this paper, a nonlocal supervised coding strategy-based NLT for image restoration is proposed. The novel method has three main contributions. First, to exploit the useful nonlocal patches, a nonnegative sparse representation is introduced, whose coefficients can be utilized as the supervised weights among patches. Second, a novel objective function is proposed, which integrated the supervised weights learning and the nonlocal sparse coding to guarantee a more promising solution. Finally, to make the minimization tractable and convergence, a numerical scheme based on iterative shrinkage thresholding is developed to solve the above underdetermined inverse problem. The extensive experiments validate the effectiveness of the proposed method.     

Asymmetric Coupling of Carbon-Centered Radicals Adjacent to Nitrogen: Copper-Catalyzed Cyanation and Etherification of Enamides

The first copper-catalyzed asymmetric cyanation and etherification reactions of enamides have been established, where a carbon-centered radical adjacent to a nitrogen atom (CRAN) is enantioselectively trapped by a chiral copper(II) species. Moreover, the asymmetric cyanation of vinyl esters was disclosed as well. These reactions feature very mild reaction conditions and high functional group tolerance, and give a series of chiral α-cyano amides, α-cyano esters and α-hemiaminals in good yields with excellent enantioselectivity. The chiral α-cyano amides can be easily converted into enantioenriched 1,2-diamines and amino acids.     

片段化森林中檵木幼苗种内叶经济性状变异及其驱动因子

在异质性生境中,种内功能性状变异有助于植物对环境的适应,进而影响种群更新、群落构建和生态系统过程。探讨了种内叶经济性状的变异及受生境异质性的塑造情况。以千岛湖片段化生境中的常见种檵木（Loropetalum chinense）的幼苗为研究对象,测定了200株檵木幼苗个体水平的7个叶经济性状（比叶面积SLA、叶全碳量C、叶全氮量N等）及其对应的生境因子（郁闭度、土壤全碳量、土壤全氮量等）,采用相关性检验、主成分分析和线性混合效应模型等方法探讨片段化森林中檵木幼苗的种内叶经济性状变异及生境异质性对该变异的驱动作用。结果显示：（1） 在7个叶经济性状所构成的21对相关性分析中,有12对显著相关。经主成分分析降维后,主成分1（PC1）占性状总变异的43.02%,主要与比叶面积、叶绿素浓度、叶全氮量呈正相关,与叶干物质质量分数和叶碳氮比呈负相关,体现了檵木的种内叶经济谱,可反映叶片的最大光合效率。（2）片段化对生境条件和叶经济性状均有影响。岛屿森林群落的郁闭度显著低于大陆。相对于大陆,岛屿中的檵木幼苗趋向于更小的PC1值（缓慢投资-收益策略）;大岛边缘较大岛内部偏向于更小的PC1值。（3）生境因子中,郁闭度对PC1具有显著正效应。研究表明,片段化生境中的檵木在幼苗阶段存在叶经济谱,生境片段化可通过影响生境条件进而改变檵木幼苗的叶经济性状。随着生境片段化程度的加剧,檵木幼苗的叶经济性状逐渐向缓慢投资-收益策略靠拢。     

Development of a Genus-Universal Nucleotide Signature for the Identification and Supervision of Ephedra-Containing Products

Ephedra plants generally contain ephedrine alkaloids, which are the critical precursor compounds of methamphetamine (METH). METH could cause serious physical and mental damage, and therefore Ephedra materials are strictly in supervision internationally. However, unlawful utilization of Ephedra herbs and its products still exist. Thus, it is imperative to establish a universal method for monitoring Ephedra ingredients in complex mixtures and processed products. In this study, 224 ITS2 sequences representing 59 taxa within Ephedra were collected, and a 23-bp genus-level nucleotide signature (GTCCGGTCCGCCTCGGCGGTGCG) was developed for the identification of the whole genus. The specific primers MH-1F/1R were designed, and 125 individuals of twelve Ephedra species/varieties were gathered for applicability verification of the nucleotide signature. Additionally, seven batches of Chinese patent medicines containing Ephedra herbs were used to test the application of the nucleotide signature in complex and highly processed materials. The results demonstrated that the 23-bp molecular marker was unique to Ephedra and conserved within the genus. It can be successfully utilized for the detection of Ephedra components in complex preparations and processed products with severe DNA degradation. The method developed in this study could undoubtedly serve as a strong support for the supervision of illegal circulation of Ephedra-containing products.