水菖蒲的化学成分研究和忍冬属植物的色谱分析

本论文由三章组成。第一章阐述了藏药水菖蒲的化学成分研究，共分离鉴定了39个化学成分，其中6个为新化合物。第二章报道了几种忍冬属植物的HPLC、HPLC-MS、GC分析以及抑菌活性、重金属含量测定结果。第三章概述了菖蒲属植物的研究进展。 第一章报道了水菖蒲(Acorus calamus L.)化学成分的分离纯化与结构鉴定。采用正、反相硅胶柱层析等分离方法，从水菖蒲的根中共分离出41个化合物，通过红外、质谱、核磁共振及X-ray单晶衍射等波谱方法和模拟计算方法鉴定了其中39个化合物的结构，主要为倍半萜、苯丙素、甾体类化合物。其中含有5个新的倍半萜类化合物和1系列新的甾体皂苷衍生物。经波谱分析将它们的结构鉴定为 1b, 7a(H)-cadinane-4a, 6a, 10a-triol (1), (2R,6R,7S,9S)-1(10), 4-cadinadiene-2, 9-diol (2), 1a, 5b-guaiane-10a-O-ethyl-4b, 6b-diol (7), 6b, 7b(H)-cadinane-1a, 4a, 10a-triol (13)，(1R,4R,6S,10R)-1-hydroxy-7(11)-cadinen-5, 8-dione (14)， 4′-O-正n碳酰基-3-O- β-D-葡萄糖基谷甾醇(n=14, 16, 18, 22) (15)。 第二章包括四个部分。第一部分报道了忍冬属三种植物40个样品的HPLC测定和对主要活性成分绿原酸的定量分析结果，以及运用HPLC-MS技术对色谱图中8个峰进行指认。在此基础上，考察了种植和采收多个因素对绿原酸含量的影响。第二部分报道了忍冬属三种植物27个样品的GC分析，根据样品的挥发性成分的保留时间对不同样品进行了定性比较，并考察了花期及海拔高度对植物挥发性成分的影响。第三、四部分分别阐述了灰毡毛忍冬和红腺忍冬的体外抑菌活性研究和重金属含量测定结果。 第三章全面系统地概述了菖蒲属植物的化学成分和药理活性研究进展。 This dissertation is composed by three chapters. The first chapter elaborates the phytochemical investigation of Acorus calamus L. Thirty-nine compounds including six new compounds were isolated and identified. The second chapter reports the research on genus Lonicera by HPLC, HPLC-MS and GC. Antifungal activity and heavy metals measurement of genus Lonicera were reported. The third chapter is a review about the research progress on the plant family of Acorus. The first chapter focuses on the isolation and identification of chemical constituents from Acorus calamus L.. Forty-one compounds were isolated from the root of Acorus calamus L. by repeat column chromatography over normal and reversed phase silica gel, the structure of thirty-nine compounds was identified by spectroscopic methods and computational methods, including IR, MS, NMR and X-ray. Those compounds mainly belonged to sesquiterpene, phenylpropanoid and steroid. Among them, five are new sesquiterpenes and one series are new steroid glycoside derivatives. Their structure were suggested as 1b, 7a(H)-cadinane-4a, 6a, 10a-triol (1), (2R,6R,7S,9S)-1(10), 4-cadinadiene-2, 9-diol (2), 1a, 5b-guaiane-10a-O-ethyl-4b, 6b- diol (7), 6b, 7b(H)-cadinane-1a, 4a, 10a-triol (13), (1R,4R,6S,10R)-1-hydroxy-7(11)- cadinen-5, 8-dione (14), 4′-O-carbonyl-3-O-β-D-glucosyl-sitosterol (carbonyl = tetradecanoyl, hexadecanoyl, octadecyl, docosanoyl) (15). The second chapter consists of four parts. The first part reports the HPLC analysis of forty samples of the genus Lonicera, and the quantitative investigation of chlorogenic acid in these samples by HPLC analysis. Relationship between the content of chlorogenic acid in different samples and their planting conditions and harvesting time were discussed. Furthermore, eight compounds were identified or tentatively characterized based on their mass spectra and UV spectra profiles. The second part is about qualitative analysis of the volatile constituent in twenty-seven samples of genus Lonicera by GC. The effect of planting altitude and harvesting time on the volatile constituent was also investigated. The third and fourth parts describe the antifungal activity and content of some kinds of heavy metals of L. macranthoides Hand.-Mazz. and L. hypoglauca Miq.. The third chaspter is a review about the research progress of the plant family of Acorus.

Exploitation of Ebola Virus VP35 Protein to identify new drugs counteracting its type I IFN antagonism

Ebolaviruses (EBOVs) are among the most virulent and deadly pathogens ever known, causing fulminant haemorrhagic fevers in humans and non-human primates. The 2014 outbreak of Ebola virus disease (EVD) in West Africa has claimed more lives than all previous EVD outbreaks combined. The EBOV high mortality rates have been related to the virus-induced impairment of the host innate immunity reaction due to two virus-coded proteins, VP24 and VP35. EBOV VP35 is a multifunctional protein, it is essential for viral replication as a component of the viral RNA polymerase and it also participates in nucleocapsid assembly. Early during EBOV infection, alpha-beta interferon (IFN-α/β) production would be triggered upon recognition of viral dsRNA products by cytoplasmic retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs). However, this recognition is efficiently prevented by the double-stranded RNA (dsRNA) binding activity of the EBOV VP35 protein, which hides RLRs binding sites on the dsRNA phosphate backbone as well the 5’-triphosphate (5’-ppp) dsRNA ends to RIG-I recognition. In addition to dsRNA binding and sequestration, EBOV VP35 inhibits IFN-α/β production preventing the activation of the IFN regulatory factor 3 (IRF-3) by direct interaction with cellular proteins. Previous studies demonstrated that single amino acid changes in the VP35 dsRNA binding domain reduce EBOV virulence, indicating that VP35 is an attractive target for antiviral drugs development. Within this context, here we report the establishment of a novel method to characterize the EBOV VP35 inhibitory function of the dsRNA-dependent RIG-I-mediated IFN-β signaling pathway in a BLS2 cell culture setting. In such system, a plasmid containing the promoter region of IFN-β gene linked with a luciferase reporter gene was transfected, together with a EBOV VP35 mammalian expression plasmid, into the IFN-sensitive A549 cell line, and the IFN-induction was stimulated through dsRNA transfection. Through alanine scanning mutational studies with biochemical, cellular and computational methods we highlighted the importance of some VP35 residues involved in dsRNA end-capping binding, such as R312, K282 and R322, that may serve as target for the development of small-molecule inhibitors against EBOV. Furthermore, we identified a synthetic compound that increased IFN-induction only under antiviral response stimulation and subverted VP35 inhibition, proving to be very attractive for the development of an antiviral drug. In conclusion, our results provide the establishment of a new assay as a straightforward tool for the screening of antiviral compounds that target i) dsRNA-VP35 or cellular protein-VP35 interaction and ii) dsRNA-dependent RIG-I-mediated IFN signaling pathway, in order to potentiate the IFN response against VP35 inhibition, setting the bases for further drug development.

Identyfikacja domen WG/GW zaangażowanych w wiązanie białek Argonaute oraz analiza mechanizmów molekularnych odpowiedzialnych za ich zmienność

Wydział Biologii: Instytut Biologii Molekularnej i Biotechnologii

De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex.

The de novo design of membrane proteins remains difficult despite recent advances in understanding the factors that drive membrane protein folding and association. We have designed a membrane protein PRIME (PoRphyrins In MEmbrane) that positions two non-natural iron diphenylporphyrins (Fe(III)DPP's) sufficiently close to provide a multicentered pathway for transmembrane electron transfer. Computational methods previously used for the design of multiporphyrin water-soluble helical proteins were extended to this membrane target. Four helices were arranged in a D(2)-symmetrical bundle to bind two Fe(II/III) diphenylporphyrins in a bis-His geometry further stabilized by second-shell hydrogen bonds. UV-vis absorbance, CD spectroscopy, analytical ultracentrifugation, redox potentiometry, and EPR demonstrate that PRIME binds the cofactor with high affinity and specificity in the expected geometry.

Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.

A steady increase in knowledge of the molecular and antigenic structure of the gp120 and gp41 HIV-1 envelope glycoproteins (Env) is yielding important new insights for vaccine design, but it has been difficult to translate this information to an immunogen that elicits broadly neutralizing antibodies. To help bridge this gap, we used phylogenetically corrected statistical methods to identify amino acid signature patterns in Envs derived from people who have made potently neutralizing antibodies, with the hypothesis that these Envs may share common features that would be useful for incorporation in a vaccine immunogen. Before attempting this, essentially as a control, we explored the utility of our computational methods for defining signatures of complex neutralization phenotypes by analyzing Env sequences from 251 clonal viruses that were differentially sensitive to neutralization by the well-characterized gp120-specific monoclonal antibody, b12. We identified ten b12-neutralization signatures, including seven either in the b12-binding surface of gp120 or in the V2 region of gp120 that have been previously shown to impact b12 sensitivity. A simple algorithm based on the b12 signature pattern was predictive of b12 sensitivity/resistance in an additional blinded panel of 57 viruses. Upon obtaining these reassuring outcomes, we went on to apply these same computational methods to define signature patterns in Env from HIV-1 infected individuals who had potent, broadly neutralizing responses. We analyzed a checkerboard-style neutralization dataset with sera from 69 HIV-1-infected individuals tested against a panel of 25 different Envs. Distinct clusters of sera with high and low neutralization potencies were identified. Six signature positions in Env sequences obtained from the 69 samples were found to be strongly associated with either the high or low potency responses. Five sites were in the CD4-induced coreceptor binding site of gp120, suggesting an important role for this region in the elicitation of broadly neutralizing antibody responses against HIV-1.

WormSizer: high-throughput analysis of nematode size and shape.

The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating volume either coarsely model the nematode as a cylinder or assume the worm shape or opacity is invariant. Our estimate is more robust to changes in morphology or optical density as it only assumes radial symmetry. This open source software is written as a plugin for the well-known image-processing framework Fiji/ImageJ. It may therefore be extended easily. We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series. We confirm quantitatively that a Dumpy (Dpy) mutant is short and fat and that a Long (Lon) mutant is long and thin. We show that daf-2 insulin-like receptor mutants are larger than wild-type upon hatching but grow slow, and WormSizer can distinguish dauer larvae from normal larvae. We also show that a Small (Sma) mutant is actually smaller than wild-type at all stages of larval development. WormSizer works with Uncoordinated (Unc) and Roller (Rol) mutants as well, indicating that it can be used with mutants despite behavioral phenotypes. We used our complete data set to perform a power analysis, giving users a sense of how many images are needed to detect different effect sizes. Our analysis confirms and extends on existing phenotypic characterization of well-characterized mutants, demonstrating the utility and robustness of WormSizer.

CFD approach for solid mechanics analysis

A cell-centred finite volume(CC-FV) solid mechanics formulation, based on a computational fluid dynamics(CFD) procedure, is presented. A CFD code is modified such that the velocity variable is used as to the displacement variable. Displacement and pressure fields are considered as unknown variables. The results are validated with finite element(FE) and cell-vertex finite volume(CV-FV) predictions based on discretisation of the equilibrium equations. The developed formulation is applicable for both compressible and incompressible solids behaviour. The method is general and can be extended for the simultaneous analysis of problems involving flow-thermal and stress effects.

Multi-physics modelling for the fabrication, packaging and reliability of micro-systems components

The latest advances in multi-physics modelling both using high fidelity techniques and reduced order and behavioural models will be discussed. Particular focus will be given to the application and validation of these techniques for modelling the fabrication, packaging and subsequent reliability of micro-systems based components. The paper will discuss results from a number of research projects with particular emphasis on the techniques being developed in a major UK Goverment funded project - 3D-MINTEGRATION (www.3d-mintegration.com).

Multiphysics simulation of microwave processing using a multidomain coupled solver approach

Microwave processing of materials is numerically simulated using a coupled solver approach. Microwave heating is a complex coupled process due to the variation in dielectric properties during heating. The effects of heating an object in a electromagnetic field directly influence the manner in which it interacts with the field. Simplifying assumptions and empirical solutions do not capture the fundamental physics involved and, in general, do not provide usefully accurate solutions in a number of practical problems. In order to capture the underlying processes involved in microwave heating, the problem must be looked at in a holistic manner rather than a number of discrete processes. This contribution outlines a coupled-solver multiphysics analysis approach to the solution of practical microwave heating problems.

Effects of magnetic fields on crystal growth

The effects of a constant uniform magnetic field on thermoelectric currents during dendritic solidification were investigated using an enthalpy based numerical model. It was found that the resulting Lorentz force generates a complex flow influencing the solidification pattern. Experimental work of material processing under high magnetic field conditions has shown that the microstructure can be significantly altered. There is evidence that these effects can be atrtributed to the Lorentz force created through the thermoelectric magentohydrodynamic interactions.[1,2] However the mechanism of how this occurs is not very well understood. In this paper, our aim is to investigate the flow field created from the Lorentz force and how this influences the morphology of dendritic growth for both pure materials and binary alloys.

Spectroscopic studies of oligomers containing 2,5-trans furanoid sugar amino acids

Sugar amino acids and their oligomers, known as carbopeptoids, are commonly studied as foldamers. However, study of their conformational preference is often challenging when the adopted conformations are extended and/or disordered. This study is the first to explore the disordered nature of such carbopeptoids by utilizing a family of 2,5-trans carbopeptoids. An array of spectroscopic techniques has been used to investigate the conformational preference of these carbopeptoids. However, using this data alone it has not been possible to assign conformational preference as an ordered extended conformation or as a disordered family of closely related conformations. Computational methods need to be employed to achieve reliable interpretation of the spectroscopic data. Chirality, 2008. © 2008 Wiley-Liss, Inc.

Multiphoton absorption by helium, magnesium and H-2 at high frequencies and intensities

We review principally some recent work carried out in Belfast and Heraklion which handles the few-electron dynamics of atomic and molecular systems exposed to high frequency. high intensity laser fields. The design and application of the quantitatively accurate computational methods is discussed. The Belfast work is illustrated by results for double ionization of helium and the hydrogen molecule where in each case the two electrons have been handled in full-dimensionality. The first results for multiphoton, double ionization of a complex atom, namely magnesium demonstrate an important application of the Heraklion approach.