uu.seUppsala University Publications
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Small Particles with Big Impact: Structural Studies of Viruses and Toxicological Studies of Nanodiamonds
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.ORCID iD: 0000-0002-5510-2245
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Description
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 [en]
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: urn:nbn:se:uu:diva-406705ISBN: 978-91-513-0933-0 (print)OAI: oai:DiVA.org:uu-406705DiVA, id: diva2:1421351
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
List of papers
1. Capsid structure of a marine algae virus of the order Picornavirales.
Open this publication in new window or tab >>Capsid structure of a marine algae virus of the order Picornavirales.
2020 (English)In: Journal of Virology, ISSN 0022-538X, E-ISSN 1098-5514, article id JVI.01855-19Article in journal (Refereed) Epub ahead of print
Abstract [en]

The order Picornavirales includes viruses that infect different kinds of eukaryotes and that share similar properties. The capsid proteins (CPs) of viruses in the order that infect unicellular organisms, such as algae, presumably possess certain characteristics that have changed little over the course of evolution, and thus these viruses may resemble the Picornavirales ancestor in some respects. Herein, we present the capsid structure of Chaetoceros tenuissimus RNA virus type II (CtenRNAV-II) determined using cryo-electron microscopy at a resolution of 3.1 Å, the first of an algae virus belonging to the family Marnaviridae of the order Picornavirales A structural comparison to related invertebrate and vertebrate viruses revealed a unique surface loop of the major CP VP1 that had not been observed previously, and further, that another VP1 loop obscures the so-called canyon, which is a host-receptor binding site for many of the mammalian Picornavirales viruses. VP2 has an N-terminal tail, which has previously been reported as a primordial feature of Picornavirales viruses. Based on the above-mentioned and other critical structural features, the acquired traits among Picornavirales viruses were categorized for profound discussions. The observations afford new insights on three long-standing theories among Picornavirales: the canyon hypothesis, the primordial VP2 domain swap, and the hypothesis that algae picorna-like viruses could share characteristics with the Picornavirales ancestor.ImportanceIdentifying the acquired structural traits in virus capsids is important for elucidating what functions are essential among viruses that infect different hosts. The Picornavirales viruses infect a broad spectrum of hosts, ranging from unicellular algae to insects and mammals, and include many human pathogens. Those viruses that infect unicellular protists, such as algae, are likely to have undergone fewer structural changes during the course of evolution compared to those viruses that infect multicellular eukaryotes, and thus still share some characteristics with the Picornavirales ancestor. This manuscript describes the first atomic capsid structure of an alga Marnavirus, CtenRNAV-II. A comparison to capsid structures of the related invertebrate and vertebrate viruses identified a number of structural traits that have been functionally acquired or lost during the course of evolution. These observations provide new insights on past theories on the viability and evolution of Picornavirales viruses.

National Category
Structural Biology
Research subject
Biology with specialization in Structural Biology
Identifiers
urn:nbn:se:uu:diva-406613 (URN)10.1128/JVI.01855-19 (DOI)32024776 (PubMedID)
Funder
Swedish Research Council, 2018-03387The Swedish Foundation for International Cooperation in Research and Higher Education (STINT), JA2014-5721Swedish Research Council Formas, 2018-00421The Royal Swedish Academy of Sciences, BS2018-0053
Available from: 2020-03-11 Created: 2020-03-11 Last updated: 2020-04-02Bibliographically approved
2. Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
Open this publication in new window or tab >>Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
Show others...
2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, p. 160064:1-12, article id 160064Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300203 (URN)10.1038/sdata.2016.64 (DOI)000390225700001 ()
Projects
eSSENCE
Available from: 2016-08-01 Created: 2016-08-05 Last updated: 2020-04-02Bibliographically approved
3. Detonation nanodiamond toxicity is core and surface dependent
Open this publication in new window or tab >>Detonation nanodiamond toxicity is core and surface dependent
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Detonation nanodiamonds are carbon-containing nanoparticles that because of their small size, reactive surface and fluorescent properties are proposed for many applications, including biomedical such as imaging and drug delivery. The detonation synthesis produces impure nanodiamonds with contaminants such as soot and metals that can be reduced to some extent through various purification procedures. Based on early studies, detonation nanodiamonds have nevertheless been generally considered biocompatible. Toxicity of nanodiamonds has however been reported in several publications the last couple of years. Meanwhile, the number of suggested applications for nanodiamonds is rapidly increasing, hence underlining the importance of continuing with toxicity evaluations. Here, toxicity studies were performed on two model organisms, Escherichia coli and Zebrafish (Danio rerio) embryos. A range of commercially available detonation nanodiamond products from different manufacturers and of various purity grades were tested. The results show that some nanodiamonds are toxic and that the effect is independent of purity from soot and metals, but depend on the chemical composition of both the nanodiamond exterior and interior. Nanodiamonds with positively charged polyelectrolytes attached have a strong effect on the viability of cells and embryos. Based on our results we also suggest that toxicity might be correlated with nitrogen species, originating from the nanodiamond synthesis. Additionally, there is a strong correlation between the bacterial and vertebrate tests, meaning that the effect is not exclusively bactericidal.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-406619 (URN)
Available from: 2020-03-26 Created: 2020-03-26 Last updated: 2020-04-13

Open Access in DiVA

fulltext(1712 kB)24 downloads
File information
File name FULLTEXT01.pdfFile size 1712 kBChecksum SHA-512
ee803f28c98d31f266f32baa334bb372e4bfe665e65c20615a68f5d494add9b405bec08965db67a14d232120dcbae83e2120983642d0d2ccd7032c63ebc4cffe
Type fulltextMimetype application/pdf

Authority records BETA

Munke, Anna

Search in DiVA

By author/editor
Munke, Anna
By organisation
Molecular biophysics
BiophysicsStructural Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 24 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 193 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf