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Asymmetrical Flow Field-Flow Fractionation In YEB Recent Publications in this Series LAMPI MIRKA 10/2018 Silviya Korpilo An Integrative Perspective on Visitor Spatial Behaviour in Urban Green Spaces: Linking Movement, Motivations, Values and Biodiversity for Participatory Planning and Management 11/2018 Hui Zhang Responses of Arctic Permafrost Peatlands to Climate Changes over the Past Millennia PURIFICATION IN VIRUS FRACTIONATION FIELD-FLOW FLOW ASYMMETRICAL 12/2018 Minna Santalahti Fungal Communities in Boreal Forest Soils: The Effect of Disturbances, Seasons and Soil DISSERTATIONES SCHOLA DOCTORALIS SCIENTIAE CIRCUMIECTALIS, ALIMENTARIAE, Horizons BIOLOGICAE. UNIVERSITATIS HELSINKIENSIS 13/2018 Marika Tossavainen Microalgae – Platform for Conversion of Waste to High Value Products 14/2018 Outi-Maaria Sietiö The Role of Plant-Fungal Interaction for the Soil Organic Matter Degradation in Boreal Forest Ecosystem 15/2018 Nanbing Qin Effects of Dietary Management on the Energy Metabolism of Periparturient Dairy Cows: Regulation of Lipidome and Transcriptome MIRKA LAMPI 16/2018 Anu Humisto Antifungal and Antileukemic Compounds from Cyanobacteria: Bioactivity, Biosynthesis, and Mechanism of Action ASYMMETRICAL FLOW FIELD-FLOW FRACTIONATION 17/2018 Vilma Sandström IN VIRUS PURIFICATION Telecouplings in a Globalizing World: Linking Food Consumption to Outsourced Resource Use and Displaced Environmental Impacts 1/2019 Yafei Zhao Evolution of Asteraceae Inflorescence Development and CYC/TB1-Like Gene Functions 2/2019 Swarnalok De Interactions of Potyviral Protein HCPro with Host Methionine Cycle Enzymes and Scaffolding Protein VARICOSE in Potato Virus A Infection 3/2019 Anirudra Parajuli The Effect of Living Environment and Environmental Exposure on the Composition of Microbial Community in Soil, on Human Skin and in the Gut 4/2019 Jaakko Leppänen Cladocera as Sentinels of Aquatic Mine Pollution 5/2019 Marjukka Lamminen Potential of Microalgae to Replace Conventional Protein Feeds for Sustainable Dairy Cow Nutrition 6/2019 Maisa Nevalainen Preparing for the Unprecedented – Moving Towards Quantitative Understanding of Oil Spill Impacts on Arctic Marine Biota 7/2019 Zhen Zeng Genome, Transcriptome, and Methylome in the Conifer Pathogen Heterobasidion parviporum 8/2019 Elina Felin Towards Risk-Based Meat Inspection ― Prerequisites of Risk-Based Meat Inspection of Pigs in Finland 9/2019 Maria Kalliola MOLECULAR AND INTEGRATIVE BIOSCIENCES RESEARCH PROGRAMME Phytohormone-Related Crosstalk in Pathogen and Stomatal Responses in Arabidopsis thaliana FACULTY OF BIOLOGICAL AND ENVIRONMENTAL SCIENCES 10/2019 Friederike Gehrmann DOCTORAL PROGRAMME IN MICROBIOLOGY AND BIOTECHNOLOGY Effects of Microclimatic Variation of Snowmelt and Temperature on Subarctic-Alpine and Arctic Plants UNIVERSITY OF HELSINKI 11/2019 Helsinki 2019 ISSN 2342-5423 ISBN 978-951-51-5252-7 Asymmetrical flow field-flow fractionation in virus purification Mirka Lampi Molecular and Integrative Biosciences Research Programme Faculty of Biological and Environmental Sciences and Doctoral programme in Microbiology and Biotechnology University of Helsinki ACADEMIC DISSERTATION To be presented for public discussion with the permission of the Faculty of Biological and Environmental Sciences of the University of Helsinki, in Auditorium 1401a of Biocenter 1, Viikinkaari 9, Helsinki on May 17th, 2019 at 12 o’clock noon. Helsinki 2019 Supervisors Associate professor Vesa Hytönen Docent Minna Poranen Faculty of Medicine and Health Molecular and Integrative Biosciences Technology Research Programme, Tampere University Faculty of Biological and Finland Environmental Sciences University of Helsinki Opponent Finland Adjunct professor Kari Airenne Head of vector development, Docent Katri Eskelin Kuopio Center for Gene and Cell Molecular and Integrative Biosciences Therapy, KCT Research Programme, Finland Faculty of Biological and Environmental Sciences Custos University of Helsinki Professor Sarah Butcher Finland Molecular and Integrative Biosciences Research Programme, Reviewers Faculty of Biological and Associate professor Lars Nilsson Environmental Sciences Department of Food technology, and Engineering and Nutrition, Institute of Biotechnology, Faculty of Engineering LTH Helsinki Institute of Life Sciences Lund University (HiLIFE) Sweden University of Helsinki Finland ISBN 978-951-51-5252-7 (paperback) ISBN 978-951-51-5253-4 (PDF) ISSN 2342-5423 (print) ISSN 2342-5431 (Online) Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae Hansaprint Helsinki 2019 No. Try not. Do.. or do not. There is no try. Grand Master of the Jedi Order, Yoda LIST OF ORIGINAL PUBLICATIONS This thesis is based on the following articles, which are referred to in the text by their Roman numerals: I Eskelin K, Lampi M, Meier F, Moldenhauer E, Bamford DH, and Oksanen HM (2016). Asymmetric flow field flow fractionation methods for virus purification. Journal of Chromatography A 1469, 108-119. II Eskelin K, Lampi M, Meier F, Moldenhauer E, Bamford DH, and Oksanen HM (2017). Halophilic viruses with varying biochemical and biophysical properties are amenable to purification with asymmetrical flow field-flow fractionation. Extremophiles 21, 1119-1132. III Lampi M, Oksanen HM, Meier F, Moldenhauer E, Poranen MM, Bamford DH, and Eskelin K (2018). Asymmetrical flow field-flow fractionation in purification of an enveloped bacteriophage ࡏ6. Journal of Chromatography B 1095, 251-257. The doctoral candidate’s contribution to the articles included in this thesis: I The doctoral candidate ML performed the life cycle measurements of PRD1 with AF4. ML participated in analysis of the data obtained from AF4 purification of different PRD1 input samples. ML participated in the preparation of virus samples used in the study. ML participated in the writing of the manuscript and preparation of the figures. II The doctoral candidate ML performed AF4 experiments conducted with HVTV1 and HRPV1, except for the light scattering measurements, and performed the life cycle measurements of His1. The doctoral candidate ML participated in the preparation of virus samples and analysis of the experimental data obtained for all four studied halophilic viruses. ML also performed the analysis on the effect of ionic strength on elution of proteins and PRD1. ML participated in the writing of the manuscript and preparation of figures. III ML participated in the planning of the research and the experiments, prepared virus samples used in the study, performed all AF4 experiments except for the light scattering measurements, analysed the data, and wrote the manuscript, on which all authors commented. i ABBREVIATIONS 1×virus input virus material purified from culture supernatant through PEG-NaCl precipitation and ultracentrifugation AF4 asymmetrical flow field-flow fractionation CRISPR clustered regularly interspaced short palindromic repeats CsCl cesium chloride DLS dynamic light scattering DNA deoxyribonucleic acid EM electron microscopy His1 Haloarcula hispanica virus 1 HRPV1 Halorubrum pleomorphic virus 1 HVTV1 Haloarcula vallismortis tailed virus 1 ICTV International Committee on Taxonomy of Viruses MALS multi-angle light scattering MWCO molecular weight cut off value NCIB National Centre of Biotechnology Information PEG polyethylene glycol PEG-virus input virus material precipitated from the culture supernatant with PEG and NaCl PFU plaque forming unit RC regenerated cellulose RNA ribonucleic acid SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis SEC size exclusion chromatography TEM transmission electron microscopy VLP virus-like particle WHO World Health Organization ii SUMMARY Viruses are the most abundant entities in the biosphere, the estimated amount of viruses is more than 1030. The number is incomprehensible and exceeds the amount of host cells at least by one order of magnitude. Viruses are extremely diverse entities by means of morphologies, sizes, genomes and biochemical and biophysical properties. As obligate parasites, viruses can only be propagated in living cells. This sets challenges for the virus purification, since the starting material contains host and growth media derived impurities. Medical applications such as phage therapy, vaccine development, and gene therapy require large amounts of highly purified viruses and virus-like particles (VLPs). Nanotechnology utilizes viruses and VLPs as building blocks for nanoscale materials and devices and also requires virus purification methods which maintain the biophysical and biochemical properties of the particles. Viruses are often purified with combinations of different methods. The most common ones are precipitation and ultracentrifugation. Precipitation does not lead into high purities and is generally applied as a pre-step for purification. Ultracentrifugation leads to high purity but it exposes viruses to high shear forces possibly leading to losses of infectivity. The large size of many viruses may restrict utilization of traditional chromatography. However, monolithic matrices are applicable for virus purification. In this work asymmetrical flow field-flow fractionationation (AF4) method was developed for virus purification. AF4 is a highly versatile size-based separation method applicable for samples with sizes ranging between ~1വ500 nm. The separation in AF4 is conducted with the aid of liquid flows. Solid stationary phase is not applied at all, thus no strong interactions during the separation occur making the method gentle. Several parameters in the AF4 system are adjustable,
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