A computational perspective of influenza a virus targets : neuraminidase and endonuclease.

Ph. D. University of KwaZulu-Natal, Durban 2016.Through the ages the viruses have plagued mankind claiming the lives of millions, pre-dating any advancements in the medicinal sciences. One such pathogenic virus is influenza A, which has been implicated in the 1918-Spanish flu, the 2006-avian flu outbreak and the 2009-swine flu pandemic. It is a highly sophisticated species, alluding efforts to thwart the spread of disease and infection. One of the main reasons influenza has survived this long is simple evolution. Natural mutation within the genome of virions expressed in proteins, enzymes or molecular structure render us unable to predict or take preventative measures against possible infection. Thus, research efforts toward the competitive inhibition of biological pathways that lead to the spread of disease, have become attractive targets. The influenza A virus has a number of chemotherapeutic targets, such as: 1) The surface antigens, hemagglutinin and neuraminidase, 2) RNA-dependent RNA polymerase, and 3) The M2 proton channel. Influenza RNA polymerase is composed of three large segments encoding polymerase acidic protein (PA), polymerase basic protein 1 (PB1) and polymerase basic protein 2 (PB2). The PA protein is an N-terminal domain subunit which contains the endonuclease activity. The influenza virus is incapable of synthesizing a 5’-mRNA cap, so it has adapted a cap-snatching mechanism whereby the PB2 subunit binds to the 5’-end of host mRNA, after which 10-14 nucleotides downstream the PA-subunit (aka PAN) cleaves the strand forming a primer for viral mRNA synthesis which is catalysed by the PB1 subunit. Influenza target identification is based primarily on evidence suggesting sequence conservation of each entity and its selective expression in the virus and not the host. In this thesis two enzymatic targets were investigated, the PA protein of RNA polymerase and neuraminidase. The studies focussed on using computational tools to: 1) provide insight into the mechanism of drug-resistance, 2) describe the conformational structure of the protein in the presence of point mutations and in complex with an inhibitor, 3) determine the essential binding pharmacophoric features to aid the design of new drug therapies. An array of computational techniques were employed in the studies, such as: molecular dynamics (MD) simulation, structure-based and ligand-based in silico screening, principal component analysis, radius of gyration analysis, binding free energy calculations and solventaccessible surface area analysis. The first study (Chapter 5) determined the mechanism of drug-resistance in influenza A neuraminidase as a consequence of antigenic variations. Two distinct mutations in the enzyme sequence that were investigated are H274Y and I222K. The active site residues of neuraminidase are conserved among the subtypes of influenza A. However, it was discovered that the occurrence of resistance to the drug oseltamivir, in the H1N1 species was different to the H5N1 virus. Although both systems shared a loss in hydrophobicity of the active site, the conformational distortion of the active site pocket distinguished the enzyme of the two viral entities, from one another. The discoveries made in the first study laid the foundation for the second study (Chapter 6), which was based on the in silico design and screen of potential neuraminidase inhibitors. As a result 10 characteristic molecular scaffolds were suggested as potential inhibitors. The pharmacophore design was constructed with consideration to the new conformational structure of the active site pocket. Chapter 7 is the third study of this thesis. The active site pocket enclosing the endonuclease activity of the PA subunit was investigated. Using molecular dynamics simulations and postdynamic analyses, a description of the protein conformation was offered. Subsequently, a pharmacophore was proposed as a potential scaffold to which endonuclease inhibitors may be modelled upon. It is my belief that the impact of the results derived from the above mentioned studies would greatly contribute to the development of new and effective anti-influenza drugs

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Mechanical models of proteins

textIn general, this dissertation is concerned with modeling of mechanical behavior of protein molecules. In particular, we focus on coarse-grained models, which bridge the gap in time and length scale between the atomistic simulation and biological processes. The dissertation presents three independent studies involving such models. The first study is concerned with a rigorous coarse-graining method for dynamics of linear systems. In this method, as usual, the conformational space of the original atomistic system is divided into master and slave degrees of freedom. Under the assumption that the characteristic timescales of the masters are slower than those of the slaves, the method results in Langevin-type equations of motion governed by an effective potential of mean force. In addition, coarse-graining introduces hydrodynamic-like coupling among the masters as well as non-trivial inertial effects. Application of our method to the long-timescale part of the relaxation spectra of proteins shows that such dynamic coupling is essential for reproducing their relaxation rates and modes. The second study is concerned with calibration of elastic network models based on the so-called B-factors, obtained from x-ray crystallographic measurements. We show that a proper calibration procedure must account for rigid-body motion and constraints imposed by the crystalline environment on the protein. These fundamental aspects of protein dynamics in crystals are often ignored in currently used elastic network models, leading to potentially erroneous network parameters. We develop an elastic network model that properly takes rigid-body motion and crystalline constraints into account. This model reveals that B-factors are dominated by rigid-body motion rather than deformation, and therefore B-factors are poorly suited for identifying elastic properties of protein molecules. Furthermore, it turns out that B-factors for a benchmark set of three hundred and thirty protein molecules can be well approximated by assuming that the protein molecules are rigid. The third study is concerned with the polymer mediated interaction between two planar surfaces. In particular, we consider the case where a thin polymer layer bridges two parallel plates. We consider two models of monodisperse and polydisperse for the polymer layer and obtain an analytical expression for the force-distance relationship of the two plates.Engineering Mechanic

Sensing at nanostructures for agri-food and enviromental applications

With a predicted population increase of 2.3 billion people, by 2050, agricultural productivity must be vastly improved and made sustainable. Globally, agriculture must deliver a 60% increase in food production to cope with the population demand. Moreover, this needs to be achieved against a changing climate, an exploitation of natural resources, and growing water and land scarcities. New digital technologies can optimise production efficiency and ensure food security and safety while also minimising waste within the production systems and the supply chain. To this end, new sensor technologies are being developed for applications in animal health diagnostics and environmental issues related to the global population, such as food & crop protection, pathogen and toxin detection, and environmental remediation. In this thesis, two new nanosensing diagnostic devices are developed and presented; surface enhanced Raman sensing and electrochemical sensing. Surface-enhanced Raman spectroscopy (SERS) substrates were fabricated by templating a flexible thermoplastic polymer against an aluminium drinks can followed by coating with a silver film, to produce a rough nanostructured metallic surface. SERS is used for both qualitative (molecular fingerprint) and quantitative detection of dye molecules and food toxins. In addition, the SERS technique is also applied in combination with nanoelectrochemical square wave voltammetry to detect nano-concentrations of neonicotinoid pesticides. The enhanced sensitivity and minimum sample preparation requirements provide tremendous opportunities for food safety and security sectors. An impedimetric immunosensor device (with a micro SD style pin-out) was also developed for the serological diagnosis of viruses and antibodies associated with bovine respiratory disease and bovine liver fluke. The silicon chip devices consist of six on-chip nanoband electrodes which can be independently modified with a polymer layer for covalent immobilisation of capture and target biomolecules. This electrochemical biosensor technology provides label-free and cost-efficient sensing capability in a compact size, and demonstrates the potential development of immunoassay-based point-of-use devices for on-farm diagnosis or therapeutic monitoring in animal health applications

Английский язык для биологии и медицины: бакалавров и магистров

Терминология в условиях ускорения научно-технического прогресса приобретает особое значение. Она является источником получения информации, инструментом освоения специальности. Любая область науки и техники находит своё выражение в терминах. Практически нет ни одной области знания, которая изучается, не владея терминологией. Медицинская терминология является одним из специфических пластов лексики, которая в силу особенностей структурно-семантического, словообразовательного и стилистического характера отличается от общеупотребительных слов и занимает особое место в лексической системе языка. Медицинская терминология – это пласт лексического фонда со своими специфическими особенностями, ибо в каждом профессиональном подъязыке существует номенклатурная лексика, соотносимая с определенными реалиями и объектами. Особенность словарного состава терминологии заключается в том, что её номены представлены в ней шире, многообразнее, чем в других лексических подсистемах. Выбор английского языка в качестве второго языка сопоставительного исследования обусловлен его все возрастающей коммуникативной ролью в мировом сообществе, популярностью, сегодняшней жизненной необходимостью. Учебник предназначен для бакалавров и магистров в сфере биологии и медицины. Он состоит из 4 глав и параграфов. В каждой главе дается целый ряд основных лексических номенов, помогающие понять сложные тексты из неадаптированных источников этой сферы. Также прилагается несколько десятков упражнений для лучшего понимания и усвоения данного материала. Красочные иллюстрации наглядно демонстрируют основные положения и понятия в сфере биологии и медицины

Dichotomic role of NAADP/two-pore channel 2/Ca2+ signaling in regulating neural differentiation of mouse embryonic stem cells

Poster Presentation - Stem Cells and Pluripotency: abstract no. 1866The mobilization of intracellular Ca2+stores is involved in diverse cellular functions, including cell proliferation and differentiation. At least three endogenous Ca2+mobilizing messengers have been identified, including inositol trisphosphate (IP3), cyclic adenosine diphosphoribose (cADPR), and nicotinic adenine acid dinucleotide phosphate (NAADP). Similar to IP3, NAADP can mobilize calcium release in a wide variety of cell types and species, from plants to animals. Moreover, it has been previously shown that NAADP but not IP3-mediated Ca2+increases can potently induce neuronal differentiation in PC12 cells. Recently, two pore channels (TPCs) have been identified as a novel family of NAADP-gated calcium release channels in endolysosome. Therefore, it is of great interest to examine the role of TPC2 in the neural differentiation of mouse ES cells. We found that the expression of TPC2 is markedly decreased during the initial ES cell entry into neural progenitors, and the levels of TPC2 gradually rebound during the late stages of neurogenesis. Correspondingly, perturbing the NAADP signaling by TPC2 knockdown accelerates mouse ES cell differentiation into neural progenitors but inhibits these neural progenitors from committing to the final neural lineage. Interestingly, TPC2 knockdown has no effect on the differentiation of astrocytes and oligodendrocytes of mouse ES cells. Overexpression of TPC2, on the other hand, inhibits mouse ES cell from entering the neural lineage. Taken together, our data indicate that the NAADP/TPC2-mediated Ca2+signaling pathway plays a temporal and dichotomic role in modulating the neural lineage entry of ES cells; in that NAADP signaling antagonizes ES cell entry to early neural progenitors, but promotes late neural differentiation.postprin

Microfluidics and Nanofluidics Handbook

The Microfluidics and Nanofluidics Handbook: Two-Volume Set comprehensively captures the cross-disciplinary breadth of the fields of micro- and nanofluidics, which encompass the biological sciences, chemistry, physics and engineering applications. To fill the knowledge gap between engineering and the basic sciences, the editors pulled together key individuals, well known in their respective areas, to author chapters that help graduate students, scientists, and practicing engineers understand the overall area of microfluidics and nanofluidics. Topics covered include Finite Volume Method for Numerical Simulation Lattice Boltzmann Method and Its Applications in Microfluidics Microparticle and Nanoparticle Manipulation Methane Solubility Enhancement in Water Confined to Nanoscale Pores Volume Two: Fabrication, Implementation, and Applications focuses on topics related to experimental and numerical methods. It also covers fabrication and applications in a variety of areas, from aerospace to biological systems. Reflecting the inherent nature of microfluidics and nanofluidics, the book includes as much interdisciplinary knowledge as possible. It provides the fundamental science background for newcomers and advanced techniques and concepts for experienced researchers and professionals