| 1. |
- Rundqvist, Louise, 1984-
(author)
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Thermodynamical and structural properties of proteins and their role in food allergy
- 2013
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Doctoral thesis (other academic/artistic)abstract
- Proteins are important building blocks of all living organisms. They are composed of a defined sequence of different amino acids, and fold into a specific three-dimensional, ordered structure. The three-dimensional structure largely determines the function of the protein, but protein function always requires motion. Small movements within the protein structure govern the functional properties, and this thesis aims to better understand these discrete protein movements. The motions within the protein structure are governed by thermodynamics, which therefore is useful to predict protein interactions.Nuclear magnetic resonance (NMR) is a powerful tool to study proteins at atomic resolution. Therefore, NMR is the primary method used within this thesis, along with other biophysical techniques such as Fluorescence spectroscopy, Circular Dichroism spectroscopy and in silico modeling.In paper I, NMR in combination with molecular engineering is used to show that the folding of the catalytical subdomains of the enzyme Adenylate kinase does not affect the core of the protein, and thus takes a first step to linking folding, thermodynamic stability and catalysis.In paper II, the structure of the primary allergen from Brazil nut, Ber e 1, is presented along with biophysical measurements that help explain the allergenic potential of the protein.Paper III describes the need for a specific Brazil nut lipid fraction needed to induce an allergenic response. NMR and fluorescence spectroscopy is used to show that there is a direct interaction between Ber e 1 and one or several components in the lipid fraction.
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| 2. |
- Johansson, Adam, 1984-
(author)
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Magnetic resonance imaging with ultrashort echo time as a substitute for X-ray computed tomography
- 2014
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Doctoral thesis (other academic/artistic)abstract
- Radiotherapy dose calculations have evolved from simple factor based methods performed with pen and paper, into computationally intensive simulations based on Monte Carlo theory and energy deposition kernel convolution.Similarly, in the field of positron emission tomography (PET), attenuation correction, which was originally omitted entirely, is now a crucial component of any PET reconstruction algorithm.Today, both of these applications – radiotherapy and PET – derive their needed in-tissue radiation attenuation coefficients from images acquired with X-ray computed tomography (CT). Since X-ray images are themselves acquired using ionizing radiation, the intensity at a point in an image will reflect the radiation interaction properties of the tissue located at that point.Magnetic resonance imaging (MRI), on the other hand, does not use ionizing radiation. Instead MRI make use of the net transverse magnetization resulting from the spin polarization of hydrogen nuclei. MR image contrast can be varied to a greater extent than CT and the soft tissue contrast is, for most MR sequences, superior to that of CT. Therefore, for many cases, MR images provide a considerable advantage over CT when identifying or delineating tumors or other diseased tissues.For this reason, there is an interest to replace CT with MRI for a great number of diagnostic and therapeutic workflows. Also, replacing CT with MRI would reduce the exposure to ionizing radiation experienced by patients and, by extension, reduce the associated risk to induce cancer.In part MRI has already replaced CT, but for radiotherapy dose calculations and PET attenuation correction, CT examinations are still necessary in clinical practice. One of the reasons is that the net transverse magnetization imaged in MRI cannot be converted into attenuation coefficients for ionizing radiation in a straightforward way. More specifically, regions with similar appearance in magnetic resonance (MR) images, such as bone and air pockets, are found at different ends of the spectrum of attenuation coefficients present in the human body. In a CT image, bone will appear bright white and air as black corresponding to high and no attenuation, respectively. In an MR image, bone and air both appear dark due to the lack of net transverse magnetization.The weak net transverse magnetization of bone is a result of low hydrogen density and rapid transverse relaxation. A particular category of MRI sequences with so-called ultrashort echo time (UTE) can sample the MRI signal from bone before it is lost due to transverse relaxation. Thus, UTE sequences permit bone to be imaged with MRI albeit with weak intensity and poor resolution.Imaging with UTE in combination with careful image analysis can permit ionizing-radiation attenuation-maps to be derived from MR images. This dissertation and appended articles present a procedure for this very purpose. However, as attenuation coefficients are radiation-quality dependent the output of the method is a Hounsfield unit map, i.e. a substitute for a CT image. It can be converted into an attenuation map using conventional clinical procedure.Obviating the use of CT would reduce the number of examinations that patients have to endure during preparation for radiotherapy. It would also permit PET attenuation correction to be performed on images from the new imaging modality that combines PET and MRI in one scanner – PET/MR.
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| 3. |
- Adhikari, Deepak, 1978-
(author)
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Signaling pathways in the development of female germ cells
- 2014
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Doctoral thesis (other academic/artistic)abstract
- Primordial follicles are the first small follicles to appear in the mammalian ovary. Women are born with a fixed number of primordial follicles in the ovaries. Once formed, the pool of primordial follicles serves as a source of developing follicles and oocytes. The first aim of this thesis was to investigate the functional role of the intra-oocyte signaling pathways, especially the phosphatidylinositol-3 kinase (PI3K) and mammalian target of rapamycin complex 1 (mTORC1) pathways in the regulation of primordial follicle activation and survival. We found that a primordial follicle remains dormant when the PI3K and mTORC1 signaling in its oocyte is activated to an appropriate level, which is just sufficient to maintain its survival, but not sufficient for its growth initiation. Hyperactivation of either of these signaling pathways causes global activation of the entire pool of primordial follicles leading to the exhaustion of all the follicles in young adulthood in mice. Mammalian oocytes, while growing within the follicles, remain arrested at prophase I of meiosis. Oocytes within the fully-grown antral follicles resume meiosis upon a preovulatory surge of leutinizing hormone (LH), which indicates that LH mediates the resumption of meiosis. The prophase I arrest in the follicle-enclosed oocyte is the result of low maturation promoting factor (MPF) activity, and resumption of meiosis upon the arrival of hormonal signals is mediated by activation of MPF. MPF is a complex of cyclin dependent kinase 1 (Cdk1) and cyclin B1, which is essential and sufficient for entry into mitosis. Although much of the mitotic cell cycle machinery is shared during meiosis, lack of Cdk2 in mice leads to a postnatal loss of all oocytes, indicating that Cdk2 is important for oocyte survival, and probably oocyte meiosis also. There have been conflicting results earlier about the role of Cdk2 in metaphase II arrest of Xenopus oocytes. Thus the second aim of the thesis was to identify the specific Cdk that is essential for mouse oocyte meiotic maturation. We generated mouse models with oocytespecific deletion of Cdk1 or Cdk2 and studied the specific requirements of Cdk1 and Cdk2 during resumption of oocyte meiosis. We found that only Cdk1 is essential and sufficient for the oocyte meiotic maturation. Cdk1 does not only phosphorylate the meiotic phosphoproteins during meiosis resumption but also phosphorylates and suppresses the downstream protein phosphatase 1, which is essential for protecting the Cdk1 substrates from dephosphorylation.
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| 4. |
- Andersson, Jonas, 1975-
(author)
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Ion recombination in liquid ionization chambers : development of an experimental method to quantify general recombination
- 2013
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Doctoral thesis (other academic/artistic)abstract
- An experimental method (the two-dose-rate method) for the correction of general recombination losses in liquid ionization chambers has been developed and employed in experiments with different liquids and radiation qualities. The method is based on a disassociation of initial and general recombination, since an ionized liquid is simultaneously affected by both of these processes.The two-dose-rate method has been compared to an existing method for general recombination correction for liquid ionization chambers, and has been found to be the most robust method presently available.The soundness of modelling general recombination in liquids on existing theory for gases has been evaluated, and experiments indicate that the process of general recombination is similar in a gas and a liquid. It is thus reasonable to employ theory for gases in the two-dose-rate method to achieve experimental corrections for general recombination in liquids. There are uncertainties in the disassociation of initial and general recombination in the two-dose-rate method for low applied voltages, where initial recombination has been found to cause deviating results for different liquids and radiation qualities.Sensitivity to ambient electric fields has been identified in the microLion liquid ionization chamber (PTW, Germany). Experimental data may thus be perturbed if measurements are conducted in the presence of ambient electric fields, and the sensitivity has been found to increase with an increase in the applied voltage. This can prove to be experimentally limiting since general recombination may be too severe for accurate corrections if the applied voltage is low.
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| 5. |
- Gustafsson, Dan, 1979-
(author)
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Adenovirus species B interactions with CD46
- 2012
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Doctoral thesis (other academic/artistic)abstract
- Adenoviruses (Ad) are double-stranded (ds) DNA, non-enveloped viruses. There are seven species (A-G) of human Ads with 52 knownserotypes to date. Human Ads cause a broad range of pathologies, ranging from upper respiratory tract infections to persistent urinary tract infections. The main determinant for Ads tropism in vitro is the protruding, antenna-like, fiber protein. The fiberknob is responsible for the main interaction with the attachment receptor of the host cell. Most Ad species use the coxsackie- adenovirus receptor (CAR) as their main attachment receptor. Most species B Ads, however use CD46. CD46 is a cell surface complement regulatory protein, which is expressed on all nucleated cells in humans. Species B Ads exhibit a low seroprevalenc in the human population, making these Ads promising vector candidates for gene therapy. We have studied human Ad species B members, serotypes 7 and 11 (Ad7 and Ad11), as well as their interaction with CD46. Our first experiments showed that all species B Ads use CD46 as their main attachment receptor, with the exception of Ad3 and Ad7. Second, we performed mutational studies of recombinant Ad11p fiberknobs. These studies showed that arginine 279 in the Ad 11 fiberknob is necessary for CD46 binding. Finally we studied the effect of Ad11 binding to CD46. The results indicate that CD46 is rapidly downregulated on the cell surface after Ad11 binding. These results may provide a further understanding of the basic biology and pathology of species B Ads and may also be useful in construction of gene therapy vectors based on species B Ads.
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| 6. |
- Johansson Söderberg, Jenny, 1983-
(author)
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The streptococcal IgG degrading enzyme IdeS : studies on host-pathogen interactions
- 2012
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Doctoral thesis (other academic/artistic)abstract
- The important human pathogen Streptococcus pyogenes causes both mild infections such as pharyngitis and impetigo but also severe life threatening invasive infections. Specific antibodies (IgG) recognize pathogens and are important mediators for pathogen clearance by the immune defence. S.ipyogenes expresses a highly effective and specific IgG endopeptidase called IdeS (immunoglobulin degrading enzyme of S.ipyogenes). IdeS rescues bacteria from opsonising IgG by cleavage of IgG generating two fragments F(ab´)2 and ½Fc. Moreover, IdeS block ROS production by neutrophils. In this thesis I have studied (i) allelic variants of IdeS and their biological potential, (ii) consequences of ½Fc production for host-pathogen interactions and (iii) IdeS processing by streptococcal and neutrophil proteases. When investigating the allelic variants of IdeS we could show that in respect to IgG degradation and inhibition of ROS production the allelic variants where indistinguishable, however the allelic variant of serotype M28 appears to be an unique exception as this protein was deficient in IgG cleavage but still inhibited ROS production. Further, the ½Fc fragments produced when IgG is cleaved by IdeS were shown to prime human neutrophils and under ex vivo experimental conditions this increased the bactericidal activity of the neutrophils. Finally, we made the interesting finding that IdeS is N-terminally processed by neutrophil proteases and by the streptococcal protease SpeB, but retain enzymatic activity and was less immunogenic compared to the full length protein.
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| 7. |
- Loh, Edmund, 1981-
(author)
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RNA-mediated virulence gene regulation in the human pathogen Listeria monocytogenes
- 2010
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Doctoral thesis (other academic/artistic)abstract
- The Gram-positive human pathogen Listeria monocytogenes uses a wide range of virulence factors for its pathogenesis. The majority of its virulence genes are encoded on a 9-kb pathogenicity island and are controlled by the transcriptional activator PrfA. Expression of these genes is maximal at 37°C and minimal at 30°C in a mechanism involving an RNA thermosensor. This thesis brings up different aspects of RNA-mediated regulation, including regulatory RNA structures within coding mRNA controlling expression to 5-untranslated RNA (5´-UTR) that controls downstream genes (cis-acting) as well as small non-coding RNAs (ncRNAs) that bind other target RNA (trans-acting).We investigated the importance of the coding region of the prfA-mRNA for its expression. Various lengths of prfA-mRNA were fused with reporter genes. Our finding suggested that the first 20 codons of prfA-mRNA were essential for efficient translation in Listeria monocytogenes. Translation of the shorter constructs was shown to be reduced. The expression level showed an inverse correlation with the RNA secondary structure stability in the beginning of the coding region. Riboswitches have previously been known to control expression of their downstream mRNA in a cis-acting manner. A trans-acting S-adenosylmethionine-binding riboswitch termed SreA was identified in Listeria monocytogenes. It was found to control the expression of the virulence regulator PrfA, by binding to the prfA-UTR and thereby affecting its translation. We examined the RNA locus encoding different virulence factors in Listeria monocytogenes. Several of them were preceded by 5´-UTRs of various lengths. We speculate that these 5´-UTRs could control expression of the downstream mRNA, provided they are of sufficient length. These findings prompted us to examine where and when Listeria monocytogenes switches on gene expression. Tiling array was used to compare RNAs isolated from wild-type and mutant bacteria grown at different growth conditions. Antisense RNAs covering parts of or whole open-reading frames as well as 29 new ncRNAs were identified. Several novel riboswitches possibly functioning as upstream terminators were also found.My thesis work compiles together a variety of novel RNA-mediated gene regulatory entities. A first coordinated transcriptional map of Listeria monocytogenes has been set up. My work has also revealed that the expression of the virulence regulator PrfA is controlled at several levels, indicating the importance of both the 5´-UTR and the coding RNA for regulated expression.
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| 8. |
- Pandit, Tanushree, 1984-
(author)
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Control of early development of the lens and the retina
- 2013
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Doctoral thesis (other academic/artistic)abstract
- The nervous system is composed of two separate compartments, the central and the peripheral nervous system. The peripheral nervous system (PNS) composed mainly of sensory organs transmits sensory information to the central nervous system (CNS) comprising the brain and the spinal cord. The CNS then processes this information and modifies the behaviour of the organism appropriately. To understand the functioning of these systems one has to understand how the different cell types belonging to these systems are generated during the course of embryonic development. Using the chick eye with the lens, which arises from the region that gives rise to components of PNS, and the retina, belonging to the CNS, as an embryonic model tissue the following questions were addressed: how do the BMP and the FGF signalling pathways affect developmental processes within the lens and retina? When do retinal cells get specified and how do the lens and the retina interact with each other during early development? These questions were addressed by using a combination of in vitro and in vivo assays in chick embryos. We show in chick that lens cells are committed to a lens identity, concomitant with the up-regulation of the lens specific marker, L-Maf. Before the onset of L-maf, or in the absence of ongoing BMP activity, lens cells switch to an olfactory fate. However, after cells have up-regulated L-Maf, they are no longer dependent upon BMP signaling for the next step of lens primary fiber differentiation, which is characterized by the onset of δ-crystallin. We provide evidence that the FGF signalling pathway is critical for regulating proliferation within the developing lens, while FGF and BMP signals cooperate with each other to regulate cell cycle exit. In addition we have characterized the expression of Equarin restricted to the differentiating population within the lens, and we show that this gene is subject to regulation by both FGF and BMP signalling. In the absence of FGF and BMP signals, Equarin expression is down-regulated similar to down-regulation of the cell cycle exit marker p27kip1. Over activation of BMP, but not FGF signals is sufficient to up-regulate Equarin expression within the lens. Concerning retinal cells, we provide evidence that retinal cells are not specified until stage 13 in chick. Prior to stage 13, retinal cells are initially specified as telencephalic cells. Our results indicate that prospective retinal cells require either BMP signals or lens tissue, to maintain a retinal identity and to promote further development of retinal cells.
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| 9. |
- Schmid, Martin Rudolf, 1979-
(author)
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Toll-mediated cellular immune response in Drosophila melanogaster
- 2014
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Doctoral thesis (other academic/artistic)abstract
- Insects are amongst the most abundant and diversified multi-cellular organisms on earth. As pollinators of the vast majority of our food crops their socio-economic value is hard to overestimate. Although many pest and pathogens of the honeybee have been known for decades, we still fail to explain the huge losses of honeybee colonies in recent years.At the beginning of my PhD studies, I investigated the effect that senescence and the age-related caste dimorphisms have on two basic parameters of the adult honeybee’s immune system, namely blood cell concentration and the activity of the phenoloxidase cascade. Realizing the limitations of working on an organism for which (at the time) no sequenced genome or molecular tools were available, I switched labs to work on Drosophila melanogaster. The fruit fly has proven to be a particularly useful model system to identify and study genes critical for both the innate immune response itself, as well as the signaling pathways regulating it. For the main part of my thesis, I used the tissue-specific expression of fluorescent markers to visualize segmentally aligned bands of sessile blood cells in the Drosophila larva. This phenotype is disturbed in larvae heterozygote for a gain-of-function mutation in the Toll pathway called Tl10b. In a genetic screen, I scored the ability of genomic mutations to modify the Tl10b loss of bands phenotype. I identified five genomic regions that suppressed the disturbed band pattern of sessile blood cells, and in three of these regions I mapped down this phenotype to single gene level. Two genes are involved in intracellular vesicle trafficking (Rab23 and ird1) and one is activated at the onset of metamorphosis (hdc). To confirm the experimental model, I tested the role of another negative regulator of the Toll pathway. I used tissue specific GAL4 fly lines to express RNAi silencing constructs targeting Gprk2 expression in vivo. This led to an unexpected and novel discovery. Even though blood cells give rise to the most apparent phenotypes in the Tl10b larva, the main source for the immune signal is the fat body. This indicates that besides the humoral response, also in cell based immunity this organ plays a major role. Based on this finding, I could show that the modification of Tl10b blood cell phenotypes caused by loss of ird1 expression are due the role this gene plays in autophagy cell motility. The improved understanding of these basic and evolutionary highly conserved mechanisms will undoubtedly help in fending off infectious disease in both man and honeybees in the future.
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| 10. |
- Sundström, Mia, 1980-
(author)
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B cell deviations and type 1 diabetes in the NOD mouse
- 2012
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Doctoral thesis (other academic/artistic)abstract
- Type 1 diabetes (T1D) is a chronic autoimmune disease in which the insulin producing β-cells in the pancreatic islets of Langerhans are selectively attacked by the immune system. The β-cells are destroyed resulting in a reduced or eliminated insulin production, which in turn lead to a high blood glucose level. The non-obese diabetic (NOD) mouse is the most commonly used animal model for human T1D. NOD mice develop diabetes spontaneously through a process that closely resembles the human pathogenesis. In both humans and the NOD mouse, disease is caused by a combination of genetic and environmental factors. In the NOD mouse, more than 30 insulin-dependent diabetes (Idd) loci on 15 chromosomes have been linked to disease susceptibility, however, most of the Idd-regions lack identification of a disease associated gene. B cells are required for T1D development, although the underlying mechanisms are not fully revealed. The aim of this thesis was to dissect B cell-related immune deviations in the NOD mouse, including the underlying genetics of these traits. The TACI receptor binds two ligands, i.e. the cytokines BAFF and APRIL.TACI ligation by APRIL mediates class switch, drives plasma cell differentiation and increases immunoglobulin production. In Paper I, a novel NOD-specific B cell-related trait was identified, i.e. the increased percentage of TACIhigh-expressing splenic B cells, by comparing NOD mice with non-autoimmune disease prone C57BL/6 mice. To investigate if the described TACI trait was controlled by genes linked to any Idd-region, an Idd-focused linkage analysis was performed. The TACI-trait mapped to regions on chromosome 1 and 8, more specifically to the vicinity of the Idd5.4 and Idd22. Interestingly, the linkage to Idd22 was explained by mice ≥61 days of age, suggesting a temporal genetic regulation of TACI expression possibly influenced by the ongoing autoimmune process. In Paper II, the linkage of the TACI trait to chromosome 1 and 8 was confirmed by analyzing the percentage of TACIhigh-expressing B cells in congenic NOD.C1/Idd22 mice. Moreover, the functional consequence of TACI upregulation was investigated, with the focus on plasma cell development and immunoglobulin production. NOD splenic B cells stimulated with APRIL displayed increased numbers of plasma cells and produced higher amounts of IgG and IgA compared to B cells from C57BL/6 mice. Thus, the TACI upregulation on NOD B cells possibly contribute to a B cell compartment which is more disposed to plasma cell differentiation and isotype switch. NOD mice display enhanced and prolonged immune response towards several antigens, including non-self immunoglobulins. In Paper III, the genetic factor(s) controlling the altered immune response against a BALB/c derived monoclonal antibody were dissected. Significant linkage to the Idd1/Idd24, Idd12, and Idd18.1 regions as well as to a proximal region on chromosome 2 (33.5 Mb) was detected. The linkage to Idd1/24 was verified by analyzing a set of H2-congenic NOD and C57BL/6 mice, and the linked region was narrowed down to ~8 Mb. Candidate gene analysis revealed a significant difference in the transcription of the H2-O/DO molecule. This suggests that multiple mechanisms contribute to the loss of immune response control, including an altered MHC class II peptide loading on NOD B cells. In Paper IV, a novel B cell intrinsic receptor for IgM and IgG was revealed. The receptor appeared to be more abundant in NOD mice compared to C57BL/6 mice, as the level of extramembranous IgG monomers and IgM pentamers on peripheral blood B cells from NOD mice was significantly higher compared to C57BL/6 mice. In addition, analysis of immune complex binding using IgG- or IgM-opsonized bacterial particles revealed a higher degree of binding in NOD mice compared with C57BL/6 mice. The enhanced capture of immunoglobulins and immune complexes could thus contribute to the development of T1D by altering normal B cell functions such as activation and immune complex transportation.
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