Real-Time Duplex Applications of Loop-Mediated AMPlification (LAMP) by Assimilating Probes

Isothermal nucleic-acid amplification methods such as Loop-Mediated isothermal AMPlification (LAMP) are increasingly appealing alternatives to PCR for use in portable diagnostic system due to the low cost, weight, and power requirements of the instrumentation. As such, interest in developing new probes and other functionality based on the LAMP reaction has been intense. Here, we report on the development of duplexed LAMP assays for pathogen detection using spectrally unique Assimilating Probes. As proof of principle, we used a reaction for Salmonella enterica as a model coupled with a reaction for λ-phage DNA as an internal control, as well as a duplexed assay to sub-type specific quarantine strains of the bacterial wilt pathogen Ralstonia solanacearum. Detection limits for bacterial DNA analyzed in individual reactions was less than 100 genomic equivalents in all cases, and increased by one to two orders of magnitude when reactions were coupled in duplexed formats. Even so, due to the more robust activity of newly available strand-displacing polymerases, the duplexed assays reported here were more powerful than analogous individual reactions reported only a few years ago, and represent a significant advance for incorporation of internal controls to validate assay results in the field.     

Tetrahydroindoles as Multipurpose Screening Compounds and Novel Sirtuin Inhibitors

Indoles are privileged structures in medicinal and bioorganic chemistry that are particularly well suited to serve as platforms for diversity. Among many other therapeutic areas, the indole scaffold has been used to design aromatic compounds useful to interfere with enzymes engaged in the regulation of substrate acylation status, such as sirtuins. However, the planarity of the indole ring is not necessarily optimal for all target enzymes, especially when functionalization with aromatic side chains is required. Replacement of flat scaffolds by nonplanar molecular cores dominated by sp³ hybridization is a common strategy to avoid the disadvantages associated with poor solubility and high promiscuity, while covering less-well-explored areas of chemical space. Thus, we synthesized fragment-like tetrahydroindoles suitable for fragment-based drug discovery as well as a well-characterized small library intended as multipurpose screening compounds. For proof of principle, these compounds were screened against sirtuins 1–3, enzymes known to be addressable by indoles. We found that 2,6,6-trimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indole-3-carboxamides are potent and selective SIRT2 inhibitors. Compound 16 t displayed an IC₅₀ value of 0.98 μm and could serve as exquisite starting point for hit-to-lead profiling.     

灵芝菌丝体多糖的分离纯化及其单糖组成分析与分子量测定

前期杂交优化后赤芝菌种经液体深层发酵后,提取灵芝菌丝体多糖,并过DEAE-Sepharose Fast Flow柱分离纯化,利用高效体积排阻色谱(HPSEC)检测多糖级分的纯度,采用完全酸水解PMP柱前衍生化RP—HPLC测定多糖级分的单糖组成,多角度光散射仪联用装置(SEC—MALLS)测定其绝对重均分子量(Mw),并且根据分子旋转半径与分子摩尔数的关系曲线斜率初步推断其空间构象。结果显示:分离纯化得到3个多糖级分GLMP1、GLMP2和GLMP3,HPSEC检测其峰面积百分比分别为93.58%,97.64%,99.19%,单糖组成分析结果表明GLMP1、GLMP2和GLMP3均含有甘露糖、鼠李糖、半乳糖醛酸、葡萄糖、半乳糖、木糖、阿拉伯糖和岩藻糖,但单糖摩尔比各异。SEC—MALLS测试GLMP1、GLMP2和GLMP3的Mw分别为4.526×105,4.603×104,3.760×103 g/mol,3个多糖级分构象可能均为高度紧缩且具有分支结构的聚合物。     

Sofosbuvir Selects for Drug-Resistant Amino Acid Variants in the Zika Virus RNA-Dependent RNA-Polymerase Complex In Vitro

The nucleotide analog sofosbuvir, licensed for the treatment of hepatitis C, recently revealed activity against the Zika virus (ZIKV) in vitro and in animal models. However, the ZIKV genetic barrier to sofosbuvir has not yet been characterized. In this study, in vitro selection experiments were performed in infected human hepatoma cell lines. Increasing drug pressure significantly delayed viral breakthrough (p = 0.029). A double mutant in the NS5 gene (V360L/V607I) emerged in 3 independent experiments at 40–80 µM sofosbuvir resulting in a 3.9 ± 0.9-fold half- maximal inhibitory concentration (IC₅₀) shift with respect to the wild type (WT) virus. A triple mutant (C269Y/V360L/V607I), detected in one experiment at 80 µM, conferred a 6.8-fold IC₅₀ shift with respect to the WT. Molecular dynamics simulations confirmed that the double mutant V360L/V607I impacts the binding mode of sofosbuvir, supporting its role in sofosbuvir resistance. Due to the distance from the catalytic site and to the lack of reliable structural data, the contribution of C269Y was not investigated in silico. By a combination of sequence analysis, phenotypic susceptibility testing, and molecular modeling, we characterized a double ZIKV NS5 mutant with decreased sofosbuvir susceptibility. These data add important information to the profile of sofosbuvir as a possible lead for anti-ZIKV drug development.     

不同润湿表面液体沸腾的分子动力学模拟

采用分子动力学方法研究纳米尺度下液氩在过热基板上的沸腾过程。通过调节固液间相互作用的方式改变壁面润湿性，模拟并分析了壁面润湿性对沸腾过程中能量传递和液体运动情况的影响。结果表明：不同润湿性表面均会发生固液分离的现象，但是固体表面附近吸附的氩原子数密度随润湿性增强而增大；润湿性较强时，液体的能量上升快，热通量高，液体内部温度梯度大，发生固液分离时间早，系统中氩的温度和能量低，上升过程中液氩密度、厚度变化小；润湿性较弱时，液体的能量上升慢，热通量小，液体内部温度梯度小，发生固液分离时间延后，系统中氩的温度、能量更高，上升过程中液氩密度、厚度变化较大。下部气体压力整体上大于上部气体压力，发生固液分离时润湿性越强的表面上液体上下压差越大，首次上升过程能达到的高度越高，所需时间越短。     

介孔分子硅剂改善茶浓缩膜结构特性应用研究

为有效提高功能性茶浓缩反渗透膜的回收效率和抗污性能,探究了3种介孔分子硅材料(MCM-41、SBA-15和MCFs)对浓缩膜面聚酰胺层聚合形成过程的结构影响。结果表明,添加质量分数0.02%经磺化预处理的MCM-41于间苯二胺水相可接枝酰氯基团,形成的聚酰胺结构层峰谷粗糙跨度仅为220 nm且交联紧致,膜抗拉伸强度增加37.8%;SBA-15和MCFs相膜面峰谷跨度达500~780 nm,横向褶皱和团聚,结构存在孔道塌陷;改性膜在3 h内对茶多酚、茶多糖、茶蛋白即可达到最大浓缩度,减少50%浓缩时间;MCM-41和SBA-15膜长时间运行的浓缩降率仅为2.8%~6.1%,48 h下降率比显示改性膜达标使用时长增加112.5%~137.5%,亲水性和抗污堵能力均大幅提升,可有效满足功能化茶浓缩精度。     

Fine-tuned,molecular-composite,organosilica membranes for highly efficient propylene/propane separation via suitable pore size

Fine-tuned, molecular-composite, organosilica membranes were fabricated via the co-condensation of organosilica precursors bis(triethoxysilyl)acetylene (BTESA) and bis(triethoxysilyl)benzene (BTESB). Fourier transform infrared and UV–vis spectra confirmed the co-condensation behaviors of BTESA and BTESB. The evolution of the network structure indicated that the incorporated BTESB decreased the membrane pore size, which was determined by a modified gas translation model according to the steric effect of the phenyl groups. The incorporation of BTESB to BTESA finely tuned the membrane structure and endowed the resultant composite membrane with improved separation properties. The BTESAB 9:1 membrane (molar ratio of BTESA/BTESB was 9:1) exhibited high C₃H₆ permeance at 4.5 × 10⁻⁸ mol m⁻² s⁻¹ Pa⁻¹ and a C₃H₆/C₃H₈ permeance ratio of 33 at 50°C. One of the most important developments of this study involved clearly defining the relationship between membrane pore size and C₃H₆/C₃H₈ separation performance for organosilica membranes in single and binary separation systems.     

Electrocatalytic Reduction of CO2 to Ethylene by Molecular Cu‐Complex Immobilized on Graphitized Mesoporous Carbon

The electrochemical reduction of carbon dioxide (CO₂) to hydrocarbons is a challenging task because of the issues in controlling the efficiency and selectivity of the products. Among the various transition metals, copper has attracted attention as it yields more reduced and C2 products even while using mononuclear copper center as catalysts. In addition, it is found that reversible formation of copper nanoparticle acts as the real catalytically active site for the conversion of CO₂ to reduced products. Here, it is demonstrated that the dinuclear molecular copper complex immobilized over graphitized mesoporous carbon can act as catalysts for the conversion of CO₂ to hydrocarbons (methane and ethylene) up to 60%. Interestingly, high selectivity toward C2 product (40% faradaic efficiency) is achieved by a molecular complex based hybrid material from CO₂ in 0.1 m KCl. In addition, the role of local pH, porous structure, and carbon support in limiting the mass transport to achieve the highly reduced products is demonstrated. Although the spectroscopic analysis of the catalysts exhibits molecular nature of the complex after 2 h bulk electrolysis, morphological study reveals that the newly generated copper cluster is the real active site during the catalytic reactions.     

Genes Identification,Molecular Docking and Dynamics Simulation Analysis of Laccases from Amylostereum areolatum Provides Molecular Basis of Laccase Bound to Lignin

An obligate mutualistic relationship exists between the fungus Amylostereum areolatum and woodwasp Sirex noctilio. The fungus digests lignin in the host pine, providing essential nutrients for the growing woodwasp larvae. However, the functional properties of this symbiosis are poorly described. In this study, we identified, cloned, and characterized 14 laccase genes from A. areolatum. These genes encoded proteins of 508 to 529 amino acids and contained three typical copper-oxidase domains, necessary to confer laccase activity. Besides, we performed molecular docking and dynamics simulation of the laccase proteins in complex with lignin compounds (monomers, dimers, trimers, and tetramers). AaLac2, AaLac3, AaLac6, AaLac8, and AaLac10 were found that had low binding energies with all lignin model compounds tested and three of them could maintain stability when binding to these compounds. Among these complexes, amino acid residues ALA, GLN, LEU, PHE, PRO, and SER were commonly present. Our study reveals the molecular basis of A. areolatum laccases interacting with lignin, which is essential for understanding how the fungus provides nutrients to S. noctilio. These findings might also provide guidance for the control of S. noctilio by informing the design of enzyme mutants that could reduce the efficiency of lignin degradation.     

Sequence-Dependent Nanofiber Structures of Phenylalanine and Isoleucine Tripeptides

The molecular design of short peptides to achieve a tailor-made functional architecture has attracted attention during the past decade but remains challenging as a result of insufficient understanding of the relationship between peptide sequence and assembled supramolecular structures. We report a hybrid-resolution model to computationally explore the sequence–structure relationship of self-assembly for tripeptides containing only phenylalanine and isoleucine. We found that all these tripeptides have a tendency to assemble into nanofibers composed of laterally associated filaments. Molecular arrangements within the assemblies are diverse and vary depending on the sequences. This structural diversity originates from (1) distinct conformations of peptide building blocks that lead to different surface geometries of the filaments and (2) unique sidechain arrangements at the filament interfaces for each sequence. Many conformations are available for tripeptides in solution, but only an extended β-strand and another resembling a right-handed turn are observed in assemblies. It was found that the sequence dependence of these conformations and the packing of resulting filaments are determined by multiple competing noncovalent forces, with hydrophobic interactions involving Phe being particularly important. The sequence pattern for each type of assembly conformation and packing has been identified. These results highlight the importance of the interplay between conformation, molecular packing, and sequences for determining detailed nanostructures of peptides and provide a detailed insight to support a more precise design of peptide-based nanomaterials.