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Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, p. 160064:1-12, article id 160064Article in journal (Refereed) Published
Resource type
Text
Place, publisher, year, edition, pages
2016. Vol. 3, p. 160064:1-12, article id 160064
National Category
Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-300203DOI: 10.1038/sdata.2016.64ISI: 000390225700001OAI: oai:DiVA.org:uu-300203DiVA, id: diva2:951095
Projects
eSSENCEAvailable from: 2016-08-01 Created: 2016-08-05 Last updated: 2020-04-02Bibliographically approved
In thesis
1. Structural studies of small viruses using an X-ray Free Electron Laser
Open this publication in new window or tab >>Structural studies of small viruses using an X-ray Free Electron Laser
2016 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

X-ray crystallography has since its introduction been the most successful technique for solving protein structures. Viruses however, often possess structural components such as fibrils, tails and envelopes that make them difficult or impossible to crystallize. To explore virus structures and the structural changes they undergo during host entry and infection, instrumental developments are required. X-ray Free Electron Lasers posses some advantages compared to conventional synchrotron sources, which enable experiments that previously were impossible. The femtosecond pulses and peak brilliance that exceeds synchrotrons by 109 facilitate recording of diffraction from nano/microcrystals and single particles before radiation damage takes place. The challenges for XFELs to reach its true potential in structural biology are nevertheless still many. During the technical and computational developments, using well-characterized reference samples is advantageous. In this thesis, the Rice Dwarf virus and MS2 bacteriophage have been used for single particle imaging and crystallography experiments using XFELs. These viruses are two of the smallest biological samples so far studied as single particles using this technique and the crystallography data of MS2 presented might serve as basis for solving the first high-resolution genome structure.

Nanodiamonds, having a similar elemental composition as biological samples, could potentially serve as reference samples in XFEL studies. However, the biomedical field also has an interest in nanodiamonds, for drug delivery and as implant coating for example. Toxicity and biocompatibility is therefore a legitimate concern. Here, results from toxicity experiments of nanodiamonds on bacterial and zebrafish model organisms are presented.

Place, publisher, year, edition, pages
Uppsala: Uppsala Universitet, 2016. p. 30
National Category
Structural Biology
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-303623 (URN)
Presentation
2016-10-13, C8:305, Biomedicinskt centrum, Husargatan 3, Uppsala, 10:15 (English)
Opponent
Supervisors
Available from: 2016-09-26 Created: 2016-09-21 Last updated: 2016-09-26
2. Small Particles with Big Impact: Structural Studies of Viruses and Toxicological Studies of Nanodiamonds
Open this publication in new window or tab >>Small Particles with Big Impact: Structural Studies of Viruses and Toxicological Studies of Nanodiamonds
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Nanoparticles (NPs) can be found everywhere and their existence has both beneficial and harmful consequences for the environment and living beings. The investigations on which this thesis is based upon have contributed to an increased understanding of some of these particles and to the development of a method that could be used to study their structure.

Three different NPs have been studied by different means. In the first study, I describe how single-particle cryo-electron microscopy was used to determine the atomic structure of an algal virus; Chaetoceros tenuissimus RNA virus type II. This virus is taxonomically classified in the order Picornavirales, which includes viruses that infect a wide range of organisms, including humans, plants and insects. By comparing the algal virus structure to structures of related viruses in the order, we could identify a number of traits that were likely acquired or lost among these viruses during the course of evolution. In the second study, rice dwarf virus was utilised as a test sample to develop a new structural biology method, single-particle coherent diffractive imaging (CDI). The method aims to study macromolecules in a single-particle fashion at room temperature with the help of an X-ray free-electron laser, thus enabling studies of fast dynamics without the need to crystallize or freeze the sample. The study was the first of several within a large international collaboration and the first single-particle CDI experiment reported using femtosecond hard X-ray pulses. Despite several advances by the team, many challenges remain for the method to reach its full potential. In the third study, I describe in vitro and in vivo toxicological studies of detonation nanodiamonds (DNDs). I could demonstrate that some DNDs are toxic and that the toxicity is dependent both on the core and surface of the particles. DNDs are suggested for numerous different biomedical applications that alternately utilise their toxic properties or require biocompatibility. The results presented show that these contrasting properties can be exhibited by similar DNDs and that thorough characterisation and close control of the manufacturing process is essential for biomedical applications.

This thesis explores how studies of some of nature’s nanoparticles - viruses - can lead to biological insight, how virus NPs can play a role in developing new technologies that may enable an even deeper understanding and explores issues that need to be considered for NPs to reach their potential in biomedical applications.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2020. p. 93
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1929
Keywords
Chaetenuissarnavirus II, cryo-EM, CtenRNAV-II, Escherichia coli, Danio rerio, flash X-ray imaging, Marnaviridae, single-particle analysis, single-particle imaging, Sogarnavirus, virus evolution, virus structure, XFEL, zebrafish embryo
National Category
Biophysics Structural Biology
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-406705 (URN)978-91-513-0933-0 (ISBN)
Public defence
2020-05-27, Room B8, Biomedicinskt centrum, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2020-05-06 Created: 2020-04-02 Last updated: 2020-05-06

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Munke, AnnaAndreasson, JakobBielecki, JohanDaurer, Benedikt J.Hajdu, JanosHantke, Max F.Reddy, Hemanth K. N.Larsson, Daniel S. D.Maia, Filipe R. N. C.Mühlig, KerstinNettelblad, CarlOkamoto, Kentavan der Schot, GijsSeibert, M. MarvinSvenda, MartinTimneanu, NicusorWestphal, Daniel

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Munke, AnnaAndreasson, JakobBielecki, JohanDaurer, Benedikt J.Hajdu, JanosHantke, Max F.Reddy, Hemanth K. N.Larsson, Daniel S. D.Maia, Filipe R. N. C.Mühlig, KerstinNettelblad, CarlOkamoto, Kentavan der Schot, GijsSeibert, M. MarvinSvenda, MartinTimneanu, NicusorWestphal, Daniel
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