| 1. |
- Munke, Anna
(författare)
-
Small Particles with Big Impact : Structural Studies of Viruses and Toxicological Studies of Nanodiamonds
- 2020
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
|
|
| 2. |
- Andersson, Britt-Inger
(författare)
-
Förstudie Del A Underlag till en FoU-strategi : inspel till myndighetens strategiska plan 2021-2023
- 2019
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Syftet med förstudien är att ta fram ett underlag till en FoU-strategi för myndigheten. Den ska användas som inspel till myndighetens kommande strategiska plan 2021– 2023. Myndigheten saknar en FoU-strategi som omfattar hela verksamheten. Idag utförs en liten del egen forskningsverksamhet främst runforskning och en större del annan FoU-verksamhet. I stort sett all FoU utförs i samarbete och/eller samverkan med externa parter exempelvis museer, universitet och högskolor. I rapporten har sex kategorier av FoU-verksamhet identifierats. De flesta avdelningar utför FoU-verksamhet främst Kulturvårdsavdelningen, men även Arkiv och bibliotek samt Informationsavdelningen. Kulturmiljöavdelningen arbetar främst operativt med FoU-anslaget och det tillhörande externa FoU-programmet. Staben arbetar strategiskt med FoU-frågor i Sverige och inom EU samt ansvarar strategiskt för det externa FoU-programmet.
|
|
| 3. |
|
|
| 4. |
- Locmelis, Roland, 1984-
(författare)
-
Structural biology studies of thylakoid lumen proteins required for photosystem II assembly and function
- 2018
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Little is known about the structures and functions of thylakoid lumen proteins. However, some of these proteins have an essential role in photosynthesis. Photosystem II (PSII) complexes are embedded in the thylakoid membrane of oxygenic photosynthetic organisms and one of the central subunits, the D1 protein, is damaged by light during the light driven water – splitting reaction and must be replaced frequently. One of the thylakoid lumen proteins that is essential for assembly and renewal of PSII complexes is the High Chlorophyll Fluorescence 136 (HCF136) protein. Another important protein for the PSII complex assembly is the Low PSII Accumulation Protein 19 (LPA19). Both proteins, HCF136 and LPA19, were shown to bind to the core subunits of the PSII complex from the lumenal side and LPA19 has been shown to explicitly interact with the soluble C-terminus of the D1 protein, one of the core PSII complex proteins. Prior to the replacement of the damaged D1 protein, the PSII complex needs to be disassembled, which is done with the help of the Maintenance of Photosystem II under High light 2 (MPH2) protein. MPH2, also called TL16, is required during the repair cycle of the PSII complex particularly under increased and fluctuating light conditions.In this work I have determined the three-dimensional X-ray structures of the HCF136 protein at 1.6 Å resolution and the LPA19 protein at 1.2 Å resolution and have also biochemically analyzed possible interactions of HCF136 with the C-termini of D1 protein. In addition, we have determined the NMR structure of the MPH2 protein.The protein structures of HCF136, LPA19, and MPH2 determined from A. thaliana provide us with a starting point for further studies to improve our understanding of their functional roles in the assembly, maintenance, disassembly and renewal of the PSII complex. The structures are revealing the molecular details that are particularly important during the design of mutations to study protein-protein interactions and the binding of co-factors.Furthermore, I have contributed to the characterization of AnPrx6, the 1-Cyx peroxiredoxin from Anabaena sp. 7120. Peroxiredoxins are important caretakers of reactive oxygen species and a homolog PrxQ in A.thaliana is found in the thylakoid lumen. The dimeric AnPrx6 protein revealed different active site residues conformations in each of the dimers, which is probably coupled to its enzymatic activity. Unexpectedly, the protein acted also as a chaperone and showed chaperone activity in its dimeric state, which is a novelty for Prx proteins.
|
|
| 5. |
- Munke, Anna, et al.
(författare)
-
Coherent diffraction of single Rice Dwarf Virus particles using soft X-rays at the Linac Coherent Light Source
- 2018
-
Ingår i: Nature Scientific Data.
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Single particle imaging using X-ray Free Electron Lasers has recently made major advancements that have facilitated experiments on smaller samples compared to the earliest reported works on giant viruses and cells. Here, the technique was used to image the 70 nm Rice dwarf virus, for which the generated dataset is described here. The virus particles were aerosolized and injected into the X-ray beam of the Linac Coherent Light Source. A total number of 36534 diffraction patterns were recorded, of which approximately 10 % were classified as ‘single hits’ by the RedFlamingo software. With the anticipation to advance method development, the dataset along with usage instructions are deposited in the Coherent X-ray imaging data bank, free to access and analyze.
|
|
| 6. |
- Munke, Anna
(författare)
-
Structural studies of small viruses using an X-ray Free Electron Laser
- 2016
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
|
|
| 7. |
|
|
| 8. |
- Andersson, Inger, 1964
(författare)
-
Health-related quality of life after stem cell transplantation - The firs year
- 2010
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Health-related quality of life after stem cell transplantation – The first year Inger Andersson Institute of Health and Care Sciences at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden Abstract High-Dose Chemotherapy (HDC) followed by Stem Cell Transplantation (SCT) has been proven to be beneficial for a variety of haematological diseases, solid tumours and immune disorders. Despite improved care and treatment, SCT continues to produce significant long-term complications with impaired functioning and distressing symptoms. In this thesis the overall aim was to improve our knowledge about how SCT patients experience different types of transplantations and the effect it may have on their Health-Related Quality of Life (HRQoL) during the first year after SCT. Semi structured interviews were performed and two questionnaires, the European Organization for Research and Treatment of Cancer Quality of Life questionnaire (EORTC QLQ-C30) and the module, High-Dose-Chemotherapy (HDC-19), were administered. Health-related quality of life after allogeneic SCT following Reduced Intensity Conditioning (RIC) and MyeloAblative Conditioning (MAC) were compared. Both groups showed a similar pattern of development over time in functioning and symptoms, albeit more severe in the MAC group. One year after SCT there were no significant differences between the groups in global Quality of Life (QoL). However, RIC patients improved in global QoL back to baseline earlier compared to MAC patients. When allogeneic and autologous patients were compared, RIC patients seemed to recover in the same way as autologous patients and these two groups were closer in their scoring compared to MAC patients. The results emphasize the need to separate the two allogeneic groups when evaluating HRQoL after SCT. Symptoms related to the digestive system like; dry mouth, sore mouth, appetite loss and change of taste together with fatigue were among the most frequent reported symptoms throughout the SCT period for all three groups. In the MAC group, symptoms of dry mouth and change of taste even increased, and one year after SCT these symptoms were more pronounced compared to baseline. Four themes emerged from the data analysis of the interviews and illustrate how the participants described their life from discharge until one year after SCT; obstacles on the road to normality, to be part of a normal life, the chance to be cured overshadow everything and new values in life. The patients described that they felt restricted in life and had problems to manage the response from family and friends. Stem cell transplantation had changed their opportunities in life, meaning that plans for the future had to be altered, sometimes in a negative way. Stem cell transplantation is a demanding procedure that affects the patients HRQoL over a long period of time. Alleviation and management of distressing symptoms and impaired functioning are some of the most important tasks for the health care providers in order to contribute to a better health and life situation for SCT survivors.
|
|
| 9. |
- Forsgren, Nina, 1979-
(författare)
-
Structural studies of the surface adhesin SspB from Streptococcus gordonii
- 2010
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Surface proteins on microorganisms that build up the oral biofilm are key players in the formation of the biofilm. Antigen I/II proteins are surface adhesins found on virtually all oral streptococci and share a conserved multi-domain architecture. These adhesins bind surface components on other bacteria and on host cells. Thus, they are crucial for the development of the biofilm. The objective of this thesis work is the structural characterization of the large multi-domain Antigen I/II protein SspB from the primary colonizing commensal bacterium Streptococcus gordonii. The crystal structure of the variable domain of SspB was determined to 2.3 Å resolution. The domain comprises a β-supersandwich and a putative binding cleft stabilized by a calcium ion. Despite high similarity in the overall structure, the cleft within SspB is significantly smaller than the cleft within the homologous protein from Streptococcus mutans, indicating that different substrates may bind in the clefts. A screen for carbohydrate binding resulted in no hits for interaction with the SspB variable domain suggesting that the cleft may not be suitable for binding sugars. This thesis also presents the high resolution 1.5 Å structure of a truncated C-terminal domain of SspB, the first of an Antigen I/II C-domain. The structure contains two structurally related domains, each containing one calcium ion and one intramolecular isopeptide bond. The SspB protein shares the feature of intramoleular isopeptide bonds with other surface proteins from Gram positive bacteria, such as pili from Streptococcus pyogenes and Corynebacterium diphtheriae. Intramolecular isopeptide bonds are suggested to be a common feature for retaining stability in a harsh environment. The SspB adherence region, shown to be the recognition motif for Porphyromonas gingivalis attachment to S. gordonii, protrudes from the core protein as a handle available for recognition. In conclusion, this thesis work has provided new knowledge about the SspB protein and increased the understanding of the common structure of AgI/II proteins.
|
|
| 10. |
- Wikström Hultdin, Ulrika, 1977-
(författare)
-
Structural studies of FocB and Transthyretin
- 2010
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The molecular structure of a protein decides its function, its way to interact with other molecules. Using X-ray crystallography methods, a 3-dimensional, atomic model of a macromolecule can be determined. In this thesis work, the X-ray structures of two different proteins involved in human diseases were studied: FocB, which is associated with urinary tract infections, and transthyretin, which is the causative of hereditary systemic transthyretin amyloidosis. FocB is a 12 kDa protein which binds DNA in an oligomeric fashion. It is involved in the regulation of the expression of bacterial surface organelles (fimbriae), responsible for the adhesion to specific receptors in host tissue. Specifically, FocB regulates the expression of one fimbrial type found in uropathogenic E. coli (UPEC): F1C. Our FocB structure revealed it to be an all-alpha helical protein with an atypical helix-turn-helix (HTH) motif. Residues previously found important for DNA-binding in the FocB homologue PapB, were not located in the putative “recognition helix” of the HTH-motif. FocB was also found to bind to the minor groove of the DNA. Together with homology searches showing that the DNA-interactions possible for FocB are greatly diversified, these findings indicated a DNA-interaction different from the typical DNA-interaction of a HTH-protein. Transthyretin (TTR) is a plasma protein involved in transport of thyroxin (T4) and retinol. Mutated TTR is also the cause of the neurodegenerative disease hereditary systemic transthyretin amyloidosis, which is characterized by systemic deposition of TTR amyloid fibrils. The amyloid occurs through a process of TTR tetramer destabilization and partial unfolding. A common way to inhibit amyloid formation is to design small molecules that bind unoccupied thyroxin binding sites and stabilize the tetrameric form of the protein. The structural characterization of the binding of chloride and iodide ions to TTR revealed that two of three previously identified halogen binding pockets in the T4-binding site were just as optimal for halide binding. In addition, a third halide-binding site, bridging two TTR subunits, was found. In biochemical experiments, chloride and iodide ions were shown to stabilize the TTR structure and inhibit the TTR aggregation and/or amyloid formation, with iodide ions doing so more efficiently than the chloride ions. In the search for new TTR amyloid-inhibiting drugs, the identified halide-binding sites in the T4-binding pocket are possible starting points for structure-based drug design.
|
|
