| 1. |
- Perland, Emelie, 1988-
(författare)
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Atypical Solute Carriers : Identification, evolutionary conservation, structure and histology of novel membrane-bound transporters
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Solute carriers (SLCs) constitute the largest family of membrane-bound transporter proteins in humans, and they convey transport of nutrients, ions, drugs and waste over cellular membranes via facilitative diffusion, co-transport or exchange. Several SLCs are associated with diseases and their location in membranes and specific substrate transport makes them excellent as drug targets. However, as 30 % of the 430 identified SLCs are still orphans, there are yet numerous opportunities to explain diseases and discover potential drug targets. Among the novel proteins are 29 atypical SLCs of major facilitator superfamily (MFS) type. These share evolutionary history with the remaining SLCs, but are orphans regarding expression, structure and/or function. They are not classified into any of the existing 52 SLC families. The overall aim in this thesis was to study the atypical SLCs with a focus on their phylogenetic clustering, evolutionary conservation, structure, protein expression in mouse brains and if and how their gene expressions were affected upon changed food intake. In Papers I-III, the focus was on specific proteins, MFSD5 and MFSD11 (Paper I), MFSD1 and MFSD3 (Paper II), and MFSD4A and MFSD9 (Paper III). They all shared neuronal expression, and their transcription levels were altered in several brain areas after subjecting mice to food deprivation or a high-fat diet. In Paper IV, the 29 atypical SLCs of MFS type were examined. They were divided into 15 families, based on phylogenetic analyses and sequence identities, to facilitate functional studies. Their sequence relationships with other SLCs were also established. Some of the proteins were found to be well conserved with orthologues down to nematodes and insects, whereas others emerged at first in vertebrates. The atypical SLCs of MFS type were predicted to have the common MFS structure, composed of 12 transmembrane segments. With single-cell RNA sequencing and in situ proximity ligation assay, co-expression of atypical SLCs was analysed to get a comprehensive understanding of how membrane-bound transporters interact. In conclusion, the atypical SLCs of MFS type are suggested to be novel SLC transporters, involved in maintaining nutrient homeostasis through substrate transport.
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| 2. |
- Klar, Robert
(författare)
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Digital twinning for ports : from characterization to operations’ modelling
- 2024
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Ports are actively pursuing greater operational efficiency to effectively handle the increasing global flow of goods, while striving to improve the energy efficiency of their operations to comply with new environmental regulations. As a result, innovation-leading ports have begun to recognize the potential of digital twins to overview, coordinate and optimize port processes, resulting in energy savings, and reductions of costs and of CO2 emissions. While digital twins have gained momentum in other domains such as smart manufacturing and aerospace, their adoption in ports has been comparatively slow. This can be explained, among other things, by the multi-stakeholder nature of the port and the high complexity of the often interconnected port processes. Thus, this thesis, grounded in the context of ports, discusses what constitutes a digital twin, proposes characteristics to assess the maturity of existing digital twins, and introduces and evaluates mathematical models to support a key port process, which can be used as components of a digital twin for the port.
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| 3. |
- Nilsson, Anna, 1984-
(författare)
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Mechanisms Behind Illness-Induced Anorexia
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Loss of appetite is together with fever and malaise hallmarks of infection. Loosing appetite during an acute infection such as influenza does not result in any longlasting effects, but loosing appetite during chronic diseases such as cancer or AIDS constitutes a risk factor for mortality. Food intake regulation during inflammation is orchestrated by the brain in response to peripheral inflammatory signals. It is known that expression of the prostaglandin synthesizing enzyme cyclooxygenase 2 (COX-2) is crucial for the mechanisms underlying inflammation-induced anorexia, and that prostaglandin E2 (PGE2) is involved in anorexia induced by interleukin-1 beta (IL-1β). In this thesis I examined the prostaglandin-pathways proposed to be involved in anorexia. We show that acute anorexia is dependent on COX-2 expression, while cancer-induced anorexia is mediated by cyclooxygenase 1 (COX-1), at least in the initial stages, suggesting that the signaling pathways for chronic- and acute anorexia are distinct. We were able to demonstrate that the pathway underlying acute anorexia is distinct from that of fever, and that taste aversion is prostaglandin independent. We could also show that both acute and chronic anorexia-cachexia is dependent on expression of myeloid differentiation primary response gene (MyD88) in hematopoietic/myeloid cells.In summary, the findings presented in this thesis suggest that anorexia is a result of many different signaling pathways, as opposed to what is the case for several other inflammatory symptoms such as fever and malaise, where the pathways have been shown to be very exclusive. This provides new insight into the diversity of the pathways underlying inflammatory symptoms, which is fundamental for the ability to present potential, symptom-specific drug targets.
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| 4. |
- Sreedharan, Smitha, 1981-
(författare)
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Functional Characterization of Centrally Expressed Solute Carriers and G Protein-Coupled Receptors
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Transmembrane proteins are gatekeepers of the cells; controlling the transport of substrates as well as communicating signals among cells and between the organelles and cytosol. Solute carriers (SLC) and G protein-coupled receptors (GPCR) are the largest family of membrane transporters and membrane receptors respectively. The overall aim of this thesis was to provide a basic understanding of some of the novel SLCs and GPCRs with emphasis on expression, transport property, evolution and probable function. The first part of the thesis directs towards the study of some novel solute carriers. In an initial study, we provided an overall picture of the sequence relationship and tissue expression of 14 diverse atypical SLCs confirming some of their evolutionary conservation and highly specific expression pattern. The focus then was on the SLC17 family (mainly vesicular proteins) and a novel member named Slc17a9. This study revealed that SLC17 family could be divided into four main phylogenetic clades which were all present before the divergence of the insect lineage with Slc17a9 having the most restricted evolutionary history. Detailed expression study of Slc17a9 in the mouse brain suggests that it is also expressed in some regions important for purinergic neurotransmission. Further, we deorphanised an aminoacid transporter Slc38a7 which was expressed in a majority of neurons in the CNS and showed that it preferably mediate transport of L–glutamine and L–histidine. The second part of the thesis focuses on the study of two GPCRs belonging to the Rhodopsin superfamily, Gpr162 and Gpr153. A phylogenetic analysis revealed that both Gpr153 and Gpr162 originated from a common ancestor before the radiation of the mammalian lineage. Expression study revealed that Gpr162 had a predominant expression in the CNS and relatively lower expression in the other tissue tested whereas Gpr153 had a more widespread and similar expression pattern in both CNS and peripheral tissues. The functional studies of the two GPCRs were done using the antisense oligodeoxynucleotide knockdown rat model. These studies provided evidence linking the orphan Gpr162 gene with the regulation of food intake– related behaviour whereas Gpr153 gene caused only a slight reduction in food intake.
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| 5. |
- Syk, Mikaela, 1990-
(författare)
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Immunometabolic patterns in psychiatric disease
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Many forms of immune system dysregulation are linked to psychiatric disorders. This thesis examines specific types of immune dysregulation in broad cohorts with psychiatric disease. The first section focuses on adipokines and other immunometabolic biomarkers and their interaction with state vs. trait symptoms. Direct-acting autoantibodies are an increasingly recognized mechanism for causing psychosis and obsessive-compulsive disorder, but it is unclear how prevalent this patient group is. To identify which patients to investigate more extensively, superior methods are needed. Therefore, the second section addresses the value of clinical red flags in predicting elevated central nervous system (CNS) damage biomarkers and other CNS pathology.In paper I-III, a psychiatric cohort of young adults was examined for plasma immunometabolic biomarkers, depressive symptom severity, bulimia nervosa and neurotic traits. Psychiatric diagnoses were based on diagnostic interviews while depressive symptom severity was assessed with the self-rating version of the Montgomery-Åsberg Depression Rating Scale. Personality traits were evaluated using the Swedish universities Scales of Personality. Young adults with higher leptin levels self-reported more severe depressive symptoms (paper I) and leptin levels were independently linked to neuroticism (paper III). Neuroticism was also linked to other immunometabolic alterations. Women with bulimia nervosa had elevated plasma adiponectin levels that remained stable over time (paper II), suggesting long-term metabolic changes.In paper IV, a psychiatric patient cohort enriched for clinical signs of suspected autoimmune psychiatric disease was investigated for psychiatric symptoms, neurological findings and signs of CNS pathology in radiological, neurophysiological, blood and CSF analyses. In this cohort, 27% had CSF signs of CNS tissue damage and 21% had CSF signs of neuroinflammation or blood-brain barrier dysfunction. Six percent had known anti-neuronal autoantibodies in serum and 2% in CSF. CNS damage biomarkers in CSF were also linked to red flags and specific psychiatric features.In summary, the thesis confirms different patterns of immunometabolic biomarkers and associations with trait and state symptoms in a psychiatric patient cohort that may have important implications for the future health of young adults with psychiatric morbidity. The final study supports clinical red flags in previous guidelines, indicating that a more comprehensive inclusion of patients with diverse psychiatric symptoms (not restricted to purely psychosis) is necessary to find all psychiatric patients requiring further investigation for immune system involvement.
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| 6. |
- Cedernaes, Jonathan
(författare)
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Intestinal Gene Expression Profiling and Fatty Acid Responses to a High-fat Diet
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The gastrointestinal tract (GIT) regulates nutrient uptake, secretes hormones and has a crucial gut flora and enteric nervous system. Of relevance for these functions are the G protein-coupled receptors (GPCRs) and the solute carriers (SLCs). The Adhesion GPCR subfamily is known to mediate neural development and immune system functioning, whereas SLCs transport e.g. amino acids, fatty acids (FAs) and drugs over membranes. We aimed to comprehensively characterize Adhesion GPCR and SLC gene expression along the rat GIT. Using qPCR we measured expression of 78 SLCs as well as all 30 Adhesion GPCRs in a twelve-segment GIT model. 21 of the Adhesion GPCRs had a widespread (≥5 segments) or ubiquitous (≥11 segments) expression. Restricted expression patterns were characteristic for most group VII members. Of the SLCs, we found the majority (56 %) of these transcripts to be expressed in all GIT segments. SLCs were predominantly found in the absorption-responsible gut regions. Both Adhesion GPCRs and SLCs were widely expressed in the rat GIT, suggesting important roles. The distribution of Adhesion GPCRs defines them as a potential pharmacological target.FAs constitute an important energy source and have been implicated in the worldwide obesity increase. FAs and their ratios – indices for activities of e.g. the desaturase enzymes SCD-1 (SCD-16, 16:1n-7/16:0), D6D (18:3n-6/18:2n-6) and D5D (20:4n-6/20:3n-6) – have been associated with e.g. overall mortality and BMI. We examined whether differences in FAs and their indices in five lipid fractions contributed to obesity susceptibility in rats fed a high fat diet (HFD), and the associations of desaturase indices between lipid fractions in animals on different diets. We found that on a HFD, obesity-prone (OP) rats had a higher SCD-16 index and a lower linoleic acid (LA) proportions in subcutaneous adipose tissue (SAT) than obesity-resistant rats. Desaturase indices were significantly correlated between many of the lipid fractions. The higher SCD-16 may indicate higher SCD-1 activity in SAT in OP rats, and combined with lower LA proportions may provide novel insights into HFD-induced obesity. The associations between desaturase indices show that plasma measurements can serve as proxies for some lipid fractions, but the correlations seem to be affected by diet and weight gain.
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| 7. |
- Chatzikyriakidou, Yurie, 1991-
(författare)
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Determining Ligand- and Lipid- Interactions of SLC Transporters
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Solute carrier transporters (SLCs) mediate the inter- and intra- cellular trafficking of a plethora of substrates and are essential to cell homeostasis. Despite their importance to human physiology and their potential as therapeutic targets, many SLCs are considered orphans as the physiological substrate has not been experimentally determined. Furthermore, SLCs remain understudied and underutilized, partly due to the inherent difficulties in working with SLC transporters. In this thesis, I present the development of the GFP-based thermostability assay (GFP-TS), which enables the detection of ligand-SLC interactions using un-purified material, but with the same high-throughput screening capability as dye-based thermal-shift assays. We highlight how GFP-TS is an excellent complement to native mass spectrometry approaches for analyzing lipid-protein interactions, by demonstrating how specific lipids modulate oligomerization in Na+/H+ exchangers. GFP-TS was combined with other biochemical approaches to show that not all SLC35 members transport nucleotide-sugars, as currently believed. Specifically, we unequivocally demonstrate that SLC35B1 is a strict ADP/ATP exchanger, which is critical for cell homeostasis, as it supplies the endoplasmic reticulum (ER) with ATP. Finally, I outline the progress towards elucidating the function of the synaptic vesicle protein 2A (SV2A), an enigmatic brain SLC transporter that is the receptor for clinically-used anti-epileptic drugs. In summary, my research contributes to the growing body of knowledge of SLC function, and outlines how a simple thermal stability can be utilised for determining ligand- and lipid-interactions of SLC transporters.
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| 8. |
- Haitina, Tatjana, 1981-
(författare)
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Function, Pharmacology, Evolution and Anatomical Localization of G Protein-Coupled Receptors and Solute Carriers
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The G protein-coupled receptors (GPCRs) and solute carriers (SLC) are two large families of membrane-bound proteins. The aim of this study was to characterize these two families in terms of evolution and function. The melanocortin (MC) receptors belong to the Rhodopsin family of GPCRs and we cloned the MC4 and MC5 receptors from the rainbow trout, MC3 and MC5 from the spiny dogfish and MCa and MCb from the river lamprey. Pharmacological characterization of the cloned MC receptors demonstrated higher affinity for adrenocorticotropic hormone (ACTH) compared to melanocyte stimulating hormone (MSH) peptides (alpha-, beta- and gamma-MSH). We performed expression analysis with reverse transcription PCR, which showed that the MC4 and MC5 receptors in the rainbow trout are expressed centrally as well as in peripheral tissues. The dogfish MC3 and MC5 receptors were expressed in the brain, while the lamprey MCa and MCb receptors were expressed in the periphery. An extensive tissue localization analysis was performed for the entire family of Adhesion GPCRs in the rat and mouse. Using quantitative real-time PCR (qRT-PCR) we discovered that the majority of GPCRs were expressed either specifically in the CNS or ubiquitously in the CNS and peripheral tissues. We identified all non-olfactory GPCRs in the dog and classified them into Adhesion, Frizzled, Glutamate, Rhodopsin and Secretin families. The dog GPCR repertoire seemed to be more similar to the human repertoire than to the repertoires in rodents. Solute carrier family 25 includes mitochondrial membrane transporters. Using bioinformatics techniques we identified 14 novel members of the SLC25 family, which now has 46 members. We identified orthologs of the novel SLC25 family members in yeast and performed expression analysis of 9 of them with qRT-PCR on a panel containing 30 central and peripheral tissues from the rat. To conclude, this study has expanded our knowledge of the repertoire of genes coding for membrane-bound proteins and provided information about their functional roles.
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| 9. |
- Hellsten, Sofie Victoria, 1985-
(författare)
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Characterization of Amino Acid Transporters : Transporters expressed in the central nervous system belonging to the Solute Carrier family SLC38
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In cells and organelles transporters are responsible for translocation of amino acids, sugars and nucleotides among others. In the central nervous system (CNS), amino acid transporters can function as neurotransmitter transporters and nutrient sensors. The Solute carrier (SLC) superfamily is the largest family of transporters with 395 members divided in 52 families. The system A and system N amino acid transporter family, SLC38, consists of 11 members, SNAT1-11 (SLC38A1-11). The members are expressed in the brain, exclusively in neurons or astrocytes and some in both. Amino acid signaling is mainly regulated via two pathways, the amino acid responsive (AAR) pathway and the mechanistic/mammalian target of rapamycin complex 1 (mTORC1) pathway. These pathways regulate the protein synthesis in opposite directions depending on the amino acid availability. SLC38 members along with other SLCs have been identified to participate in these pathways.In paper I, the regulation of SLC genes after complete amino acid starvation in mouse hypothalamic cells have been studied with microarray and we found that 47 SLC genes were significantly altered at five hours of starvation. Interestingly, we found that Slc38a1 and Slc38a7 were upregulated along with the known starvation responding gene, Slc38a2. A complementary starvation study for the SLC38 genes was performed using primary mouse embryonic cortex cells. We found that Slc38a1, Slc38a2, Slc38a5, Slc38a6 and Slc38a8 were upregulated while Slc38a3, Slc38a7 and Slc38a11 were downregulated.Three members from the SLC38 family, SNAT8 (paper IV), SNAT9 (paper III) and SNAT10 (paper II) have been histologically characterized in mouse brain and all these transporters are exclusively neuronal. SNAT8 and SNAT10 were also functionally characterized and shown to be transporters for alanine and glutamine among others. SNAT8 was shown to mediate sodium dependent transport and was classified to system A. SNAT10 was shown to be a sodium independent bidirectional transporter and displayed characteristics for system A and N. SNAT9 is a lysosomal component of the Ragulator-Rag complex which senses amino acid availability and activates mTORC1. In paper III we also found that Slc38a9 gene expression was upregulated following starvation and downregulated following high-fat diet in mouse brain.
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| 10. |
- Höglund, Pär J., 1980-
(författare)
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Identification, Characterization and Evolution of Membrane-bound Proteins
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Membrane proteins constitute approximately 30% of all genes in the human genome and two large families of membrane proteins are G protein-coupled receptors (GPCRs) and Solute Carriers (SLCs) with about 800 and 380 human genes, respectively.In Papers I, II and IV, we report 16 novel human Adhesion GPCRs found by searches in NCBI and Celera databases. In Paper I, we report eight novel human GPCRs, and six in Paper II. We identified two new human Adhesion GPCRs and 17 mouse orthologs in Paper IV. Phylogenetic analysis demonstrates that the 16 novel human genes are additional members of the Adhesion GPCR family and can be divided into eight phylogenetic groups. EST expression charts for the entire repertoire of Adhesions in human and mouse were established, showing widespread distribution in both central and peripheral tissues. Different domains were found in their N-terminus, some, such as pentraxin in GPR112, indicates that they take part in immunological processes.In Paper III, we discovered seven new human Rhodopsin GPCRs.In Paper V, we present the identification of two new human genes, termed SLC6A17 and SLC6A18 from the Solute Carriers family 6 (SLC6). We also identified the corresponding orthologs and additional genes from the mouse and rat genomes. We analysed, in total, 430 unique SLC6 proteins from 10 animal, one plant, two fungi and 196 bacterial genomes.In Paper VI, we provide the first systematic analysis of the evolutionary history of the different SLC families in Eukaryotes. In all, we analysed 2403 sequences in eight species and we delineate the evolutionary history of each of the 46 SLC families.
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