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Rohatschek Andreas - One of the best experts on this subject based on the ideXlab platform.

  • Disinfection of Enterobacteria Phage MS2 by Chlorine dioxide as related to the Tailing phenomenon
    2015
    Co-Authors: Rohatschek Andreas
    Abstract:

    Diese Arbeit untersucht eine spezielle Abweichung der Inaktivierungskinetik, die bei der Desinfektion von EnterobakterioPhage MS2 mit Chlordioxid auftritt und als Tailing Phänomen bezeichnet wird. Drei Hypothesen wurden überprüft: (1) Verlust der bioziden Wirkung der Versuchlösung, (2) Aggregation von Viruspartikeln und (3) Existenz einer resistenten Virussubpopulation. Um Hypothese 1 zu überprüfen wurden zwei verschiedene Experimente durchgeführt. Einerseits wurde im Startbereich von Tailing erneut die gleichen Menge an Virus zur Versuchslösung zugegeben, andererseits wurde vor dem Beginn des Experiments, Chlorit zugegeben. Ein Lauf wurde mit der vollen Dosis und ein zweiter Lauf mit der halben Dosis Chlorit durchgeführt. Um Hypothese 2 zu überprüfen wurden neben Desinfektionsexperimenten auch Messungen der dynamischen Lichtstreuung (DLS) durchgeführt. Bei den DLS Messungen im Zuge eines Standarddesinfektionsexperiments konnte keine Aggregatbildung nachgewiesen werden. Neben physikalischer - Filtration, Ultraschallbehandlung vor Beginn und im Startbereich von Tailing - und chemischer Behandlung der Versuchlösung - Chloroform-Extraktion, Puffer mit höherer Natriumchlorid-Konzentration - wurde auch eine geringer konzentrierte Viruslösung eingesetzt, um den Verlauf der Desinfektion zu beeinflussen. Um Hypothese 3 zu überprüfen, wurden zwei verschiedene Experimente durchgeführt. In beiden Fällen wurde ein Standarddesinfektionsexperiment durchgeführt und jeweils im Startbereich von Tailing unterbrochen. Einmal wurde die Versuchslösung gewaschen und das Experiment wieder gestartet. Im anderen Fall wurde die Konzentration der zugegebenen Chlordioxid Lösung erhöht. Schlussendlich mussten alle drei aufgestellten Hypothesen verworfen werden. Die im Rahmen dieser Arbeit erhaltenen Ergebnisse der Überprüfung von Hypothese 3 waren Ausgangspunkt für weitere Untersuchungen, die schließlich zur Aufklärung des Tailing Phänomens führten.This thesis investigates a particular deviation of disinfection kinetics, known as Tailing phenomenon, that appears in case of the disinfection of Enterobacteria Phage MS2 by Chlorine dioxide. Three hypotheses were tested: (1) Loss of biocidal properties of the experimental solution, (2) Aggregation of virus particles and (3) Existence of a resistant virus subpopulation. To verify Hypothesis 1 two differnet experiments were perfomed. First, the same amount of virus was added to the experimental solution in the time range when Tailing started. Second, Chlorite was added before starting. One run was conducted with a full dose and a second run with a half dose of Chlorite. To verify Hypothesis 2 beside disinfection experiments also Dynamic Light Scattering (DLS) measurements have been performed. The results of the DLS measurements showed no aggregate formation in the case of a standard disinfection experiment. Besides the physical - filtration, sonication before starting and in the time range of tailing - and chemical treatment of the experimental solution - Chloroform extraction, buffer with a higher Sodium chloride concentration - a lower virus concentration has also been used to influence the course of disinfection. To verfiy Hypothesis 3, two different experiments were performed. In both cases, a standard disinfection experiment was performed until the time range when Tailing started. In one case, the experimental solution was washed and then the experiment was restarted again. In the other case the concentration of the added Chlorine dioxide solution was increased. For all performed experiments the received disinfection curves possessed Tailing behaviour. Consequently all three proposed hypotheses had to be rejected. The results of Hypothesis 3 - especially for the experiment with a washing pause - constituted the starting point for further investigations that finally disclosed the tailing phenomenon.Andreas RohatschekZsfassung in dt. SpracheWien, Univ. für Bodenkultur, Masterarb., 2015(VLID)112765

Pötsch Florian - One of the best experts on this subject based on the ideXlab platform.

  • MS2 virus and the RNA/protein complementarity hypothesis
    2018
    Co-Authors: Pötsch Florian
    Abstract:

    Trotz der enormen Bedeutung von RNA-Protein Interaktionen bleibt unser Verständnis dieser jedoch unvollständig. Im Detail betrifft dies vor allem Interaktionen von Protein codierenden mRNA Sequenzen. Diesbezüglich jedoch haben wissenschaftliche Arbeiten, auf diesem Gebiet, die Komplementäre Verwandtschaft von mRNA codierenden Sequenzen zu Nukleobasen Affnitätsprofilen von deren codierenden Protein Sequenzen nachgewiesen. Dieses wurde als Grundlage genommen für die Vermutung, dass mRNAs und die Proteine für die diese codieren in einer direkten, gerichteten komplementären Weise miteinander interagieren, besonders wenn die Partner unstrukturiert sind. In dieser Arbeit untersuchten wir die Hypothese der RNA/Protein Komplementarität in Bezug auf ihre Gültigkeit, im Rahmen eines konkreten biologisch relevanten Systems, dem Enterobacteria Virus MS2. Von diesem Virus MS2 ist bekannt, dass sein eigenes Coat-Protein in mehreren Stellen an die eigene genomische RNA bindet und diese Eigenschaft könnte eine wesentliche Verbindung mit der vorher erwähnten Hypothese aufweisen. Die erste Frage, die wir uns stellten war, ob es möglich ist Interaktionen vom MS2 Coat-Protein und dem Genome des Virus selber festzustellen, gestützt nur auf die Analyse der Primären Sequenzen mit Hilfe der Komplementaritaetshypothese. Die zweite Frage war, ob man feststellen könnte, mithilfe der Fourier Transform, ob eine definitive Periodizität zwischen den Interaktionsmustern von der viralen RNA und dessen Coat-Protein vorhanden ist. Unter der Benützung von bereits wissenschaftlich bekannten Nukleobasen/Aminosäuren Affinitäten waren wir in der Lage 10 der 13 potentiell detektierbaren, experimentell bestätigten Bindungsstellen vorherzusagen. Die Komplementaritaetshypothese scheint daher eine sehr vielversprechende Methode zu bieten für das Erforschen und Vorhersagen von RNA/Protein Interaktionen. Da jedoch die genaue Beziehung zwischen den individuellen RNA Basen und deren Profilen noch nicht genau geklärt ist, ist es bisher noch nicht möglich gewesen ein robustes und universelles System zu bieten, welches die RNA-Protein Interaktionen im generellen beschreibt und weitere Forschung in diesem Bereich ist von Nöten. Des weiteren zeigte unse Analyse keine dedektierbare Periodizität in den Interaktionsmustern zwischen der MS2 RNA und dem Coat-Protein, welche über zufällige Kontrollen hinausgehen würde.Despite their importance, our understanding of RNA-protein interactions remains incomplete. This, in particular, concerns the interactions involving protein-coding mRNA sequences. In this regard, recent work has demonstrated a complementary relationship between nucleobase-density profiles of mRNA coding sequences and nucleobase-affnity profiles of their cognate protein sequences. This has been taken as a suggestion that mRNAs and their cognate proteins may directly interact in a co-aligned, complementary fashion, especially if unstructured. Here, we explore the RNA/protein complementarity hypothesis and study its limits of validity in a concrete biological system, the Enterobacteria Phage MS2. Namely, the MS2 coat protein is known to bind in multiple locations to its own genomic RNA, providing a potential link with the complementarity hypothesis. First, we asked whether it is possible to detect interactions between the MS2 coat protein and its genome from sequence information only, following the methodical framework of the complementarity hypothesis. Second, we analyzed apparent periodicities in the interaction patterns between the MS2 RNA and coat protein via Fourier transform. Using the known nucleobase/amino-acid affinity scales, we were indeed able to identify 10 out of 13 possible detectable binding locations between the MS2 RNA and coat protein as reported experimentally. The complementarity hypothesis thus appears to provide a potentially promising approach for investigating and predicting specific RNA/protein interactions. However, as the relationship between individual RNA nucleobase profiles and protein nucleobase-affinity profiles remains unclear, further studies are needed in order to use it to design a robust, generally applicable tool for the analysis of RNA-protein interactions. Finally, our analysis did not detect any strong periodicities in the interaction patterns between the MS2 RNA and coat protein going beyond randomized controls

Ribeiro, Alice Cristina Gomes - One of the best experts on this subject based on the ideXlab platform.

  • Development of methods to determine the antiviral activity in several substrates
    2013
    Co-Authors: Ribeiro, Alice Cristina Gomes
    Abstract:

    Dissertação de mestrado integrado em Engenharia Biológica (área de especialização em Tecnologia Ambiental)Recentemente, vários grupos de investigação têm vindo a desenvolver estratégias de funcionalização de superfícies sólidas para que estas exibam características antivíricas, para além das antimicrobianas, face à capacidade dos vírus se aderirem às mesmas. Contudo, a principal dificuldade está relacionada com a limitação dos métodos existentes para determinar a sua eficácia, ou seja, a sua atividade antivírica. O objetivo fundamental do presente projeto consistiu no desenvolvimento de um método para determinar a atividade antivírica de substratos sólidos e foi proposto pelo Centro de Nanotecnologia e Materiais Técnicos, Funcionais e Inteligentes (CeNTI). Numa primeira fase, funcionalizou-se um substrato sólido rígido (aglomerado revestido com papéis melamínicos) com diferentes concentrações de agentes antivíricos comerciais, nomeadamente um zeólito de prata X (agente X), um composto orgânico Y (agente Y), e um substrato flexível (tecido de algodão) com uma proteína Z de origem natural (agente Z). Após a funcionalização, as superfícies sólidas foram caracterizadas física e quimicamente através das técnicas qualitativas de Espetroscopia de Infravermelho com Transformadas de Fourier com Refletância Total Atenuada (FTIRATR), Espetroscopia de Fotoelectrões de Raios- X (XPS) e Microscopia Eletrónica de Varrimento com Espetrometria de Dispersão de Energia (SEM- EDS). Os resultados indicaram a presença dos agentes X e Y nos laminados, porém não foi possível detetar a presença da proteína Z no tecido têxtil. Numa fase posterior, desenvolveu-se um método para a determinação da atividade antivírica dos agentes na sua forma livre e adsorvidos aos substratos sólidos, utilizando para o efeito o bacteriófago MS2 de Enterobacteria (MS2). Os resultados demonstraram que, na sua forma livre, os agentes possuem uma atividade antivírica ligeira, a partir das 6 h de ensaio. Verificouse igualmente que o agente Y foi o que demonstrou a maior atividade contra o fago MS2 ao final de 24 h. Nos ensaios com os substratos sólidos, os laminados com os agentes X e Y e o tecido têxtil com o agente Z revelaram não ter qualquer atividade antivírica contra o bacteriófago MS2. Porém, nos ensaios observaram-se desvios elevados, pelo que os resultados foram pouco conclusivos e requerem confirmação com mais ensaios laboratoriais. Conclui-se que o método desenvolvido neste trabalho, apesar de preliminar e de necessitar de alguns ajustes, pode ser importante para o desenvolvimento futuro de superfícies sólidas antivíricas.Recently, several research groups have developed strategies for the functionalization of surfaces so that they can exhibit antiviral characteristics, in addition to the antimicrobial ones. However, the main difficulty associated with the development of these surfaces is related to the limitation of existing methods to determine their antiviral activity. This project aimed to develop a method to determine the antiviral activity of functionalized solid substrates and was proposed by the Center for Nanotechnology and Smart Materials (CeNTI). Initially, a rigid substrate (agglomerate coated with melamine paper) was functionalized with different concentrations of commercial antiviral agents, particularly a silver zeolite X (agent X) and an organic compound Y (agent Y), and a flexible substrate (cotton fabric) with a protein Z of natural origin (agent Z). After functionalization, the solid surfaces were characterized physically and chemically through qualitative techniques that included Fourier Transform Infrared Spectroscopy with Attenuated Total Reflectance (FTIR- ATR), X-ray Photoelectron Spectroscopy (XPS) and Scanning Electron Microscopy with Energy Dispersion Spectrometry (SEM-EDS). The results indicated the presence of agent X and Y in the laminates, but it was not possible to detect the presence of the protein in the textile. A method was later developed to determine the activity of the antiviral agents in their free form, as well as adsorbed to the solid substrates, using for this purpose the Enterobacteria Phage MS2 (MS2). The results showed that the agents, in their free form, have a slight antiviral activity after 6 h. It was also found that agent Z showed the greatest activity against Phage MS2 after 24 h. In the tests with solid substrates, laminates with agents X and Y and textile with agent Z revealed no antiviral activity against the bacterioPhage MS2. However, in these assays, high deviations were observed, indicating that the results were not conclusive and require confirmation with more laboratory tests. In conclusion, the method developed in this project, although preliminary and requiring some adjustments, may be important for the future development of antiviral solid surfaces