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.     

Modelling of black carbon statistical distribution and return periods of extreme concentrations

Eight datasets of 1-h black carbon (BC) concentrations measured in Warsaw agglomeration (Poland), at urban background and sub-urban sites, and in Racibórz, a small town in Upper Silesia district (regional background site) were analyzed to evaluate BC levels, daily profiles and statistical distributions of concentrations in Central-Eastern European region. The observed mean levels ranged from 1483 ng m⁻³ in suburban site during summer to 3358 ng m⁻³ in regional background site in winter. Observed diurnal patterns were bimodal in the locations dominated by traffic emissions, but unimodal, with elevated evening peak in individually heated residential area. Three theoretical frequency distributions were applied to fit analyzed datasets separately. The lognormal distribution was the most appropriate to represent the middle-range values, while the high concentrations were satisfactorily predicted by the type I two-parameter exponential distribution which was used to estimate the return periods of extreme concentrations for winter months.     

一种实用的多数据库量子信息检索协议

针对目前量子私有信息检索不能适用与云存储的多数据库问题,基于现在成熟的量子密钥分发方法,提出了一种适合在多数据库环境下,实用的量子私有信息检索协议。对于不同大小的数据库,协议可通过调节参数θ和k,在保证数据库安全及用户隐私的情况下,完成信息的检索。性能分析结果表明,协议的通信复杂度低,检索成功率高、易于实施。     

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.     

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.     

Length–weight relationships of five catfish species (Siluriformes) from the Ganga River,India

Knowledge of the length–weight relationships (LWRs) of fish is an important tool to understand fish body form, growth pattern, stock management and their conservation. The present study focused on investigating the length–weight relationships for five catfish species, Pachypterus atherinoides (Bloch, 1794), belonging to family Horabagridae; Batasio batasio (Hamilton, 1822) family Bagridae; Bagarius yarrelli (Sykes, 1839), family Gogangra viridescens (Hamilton, 1822); and Sisor rhabdophorus (Hamilton, 1822) belonging to family Sisoridae. Specimens were collected from the middle stretch of the Ganga River in India from November 2016 to May 2018. A total of 174 specimens of five fish species were collected, and their total lengths were measured to the nearest centimetre and the body weight to the nearest gram. The value of the parameter slope (b) of LWRs of the five species ranged from 2.86 (B. yarrelli) to 3.16 (G. viridescens), with a mean value of 2.99. The results of the present study documented the new maximum total length (TL) for P. atherinoides and S. rhabdophorus. The present study also provides the first reference regarding LWRs for S. rhabdophorus.     

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.