Time-resolved cryo-EM has already provided ground-breaking discoveries in various fields, including structural biology, biochemistry, and drug development. Compared to traditional structural biology methods where mostly stabilized conformations are reconstructed, the main advantage of time-resolved cryo-EM is its ability to capture dynamic processes in biological samples at near-atomic resolution, which allows for studying biological structures as they change and interact in real-time. In this project, I focused on the expression and purification of the individual proteins of two dynamic molecular complexes – Staphylococcus aureus (S. aureus) DNA gyrase and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) replication-transcription complex – and attempted to assemble them into their functional forms for cryo-EM imaging.  Both of these complexes are interesting drug targets as they play an essential role in nucleic acid replication. The function of DNA gyrase is to modulate DNA supercoiling, facilitate DNA replication, and resolve intertwined DNA molecules. The replication-transcription complex of SARS-CoV-2 comprises, among other proteins, the RNA-dependent RNA polymerase, which, together with non-structural proteins 7 and 8, is responsible for the replication of the viral genome. There are still many questions about the underlying mechanisms of these key processes, and time-resolved cryo-EM studies will provide valuable information to advance our understanding of them. Here I present expression and purification protocols for S. aureus DNA gyrase subunits A and B and SARS-CoV-2 non-structural proteins 7, 8 and 12. DNA gyrase subunits A and B were expressed in Escherichia coli (E. coli) and purified in several steps, including affinity chromatography (His-Trap), ion exchange chromatography (IEX) and size exclusion chromatography (SEC). Despite many challenges with gyrase A precipitation, I obtained enough of both subunits for the intended cryo-EM. Different strategies to assemble them into a functional tetramer were tested but did not result in the expected outcome. The gained knowledge about the behaviour of the subunits in solution will serve as a basis for further optimization of the protocols before the assembly of the complex can be attempted again. Non-structural proteins 7 and 8 were expressed in E. coli as a polyprotein and successfully purified using His-Trap and SEC. I obtained a great amount of the polyprotein and established a protocol for its cleavage. Nsp12 was expressed using the baculovirus-insect cell expression system. The immunofluorescence assay data showed that the tested lipofection protocol works, and nsp12 is being produced in sufficient quantities. This result provides a solid base for further experiments to establish a purification method and assemble the nsp12-nsp7-nsp8 complex for cryo-EM imaging.

Argonautes are conserved RNA-binding proteins that can regulate gene expression post transcriptionally through a process known as RNA interference (RNAi). This is done through the use of small RNAs, e.g. sRNAs that act as a guide for the argonautes, allowing for sequence-specific binding to the target site. This interaction has been studied in many organisms, one of which is the model organism Dictyostelium discoideum. D. discoideum is an amoeba that has been used extensively in genetic experiments due to its unique lifestyle, and ease of use. Being a eukaryotic, unicellular organism, it proves to be a great tool for the study of regulatory systems in eukaryotes, allowing us to study this argonaute-sRNA interaction in detail. By analysing which RNAs bind to the argonautes, we can better understand which genes these proteins regulate and what role RNAi has in the organisms as a whole.  In this study, I investigate three of the five argonautes found in D. discoideum, namely agnA, agnC and agnE. By transforming FLAG-tagged versions of these genes into the amoeba, I successfully express two of these modified proteins in D. discoideum and verified expression by using antibodies designed specifically to recognise the FLAG-tags. This opens up the possibility for the characterisation of the argonaute proteins to better understand their role and function in the regulation of genes. / <p>The Biology Education Centre (IBG) is the responsible department. </p><p></p><p>Presentation has been made through Zoom. </p>

Amyloidosis are diseases caused by misfolded proteins that have transformed into extracellular insoluble amyloid fibrils. One type of amyloidosis is AA amyloidosis caused by AA amyloid and diseases connected are Rheumatoid arthritis and Tuberculosis. C. Elegans is a nematode used as a model organism and in this experiment. They are transgenic and express GFP (green fluorescent protein), a probe that mark the body-wall muscle cells in order to be visible in fluorescence microscopes.  Worms expressing AA45 and AA76 as well as a GFP control were fed with E. Coli OP50 and amyloid AA896 or Lin100. One control group was only fed with OP50. Three different aspects were researched: the size of the worms, their movements and a confocal microscope was used to detect amyloid. Neither the size of the worms nor the movements seemed to be linked to AA amyloid formation. However, amyloid were detected in worms expressing AA45 and AA76 but not in the GFP control when studied through a confocal microscope.  In this research it is shown that worms fed with amyloid fibrils and expressing AA45 or AA76 start forming amyloid in the body-wall muscle. This can be of much help in future research in order to make simpler diagnostical methods which can reduce the time for patients to start treatment and improve chances of survival or living with the disease with less complications.

<p>  G Protein Coupled Receptor (GPCR) signaling plays a key role in intercellular communication and regulates many physiological processes relevant to disease. Approximately 30-40% of all FDA approved drugs target GPCR pathways, but limitations and off-target side effects remain obstacles. Regulator of G protein Signaling (RGS) proteins negatively modulate GPCR signaling by accelerating deactivation of the Gα subunit and thus represent a novel alternative to current approaches. While research on RGS proteins and how they are regulated has expanded rapidly, there are still gaps in knowledge for some members of the RGS family. One example is RGS2, which is selective for Gαq signaling. Lowered RGS2 levels are implicated in numerous diseases, and while the E3 ligase responsible for facilitating degradation of RGS2 has been identified more work needs to be done to viably drug it to enhance RGS2 protein levels. In this thesis, I explore how FBXO44, an E3 ligase substrate recognition component responsible for RGS2 degradation, interacts with RGS2 to explore approaches to inhibit degradation.</p> <p><br></p> <p>While the FBXO44-RGS2 interaction has been demonstrated previously, the degron sequence of RGS2 remained unknown. We hypothesized that FBXO44 binds RGS2 at its Nterminus and investigated this using N-terminally truncated RGS2 constructs. Our results indicated that FBXO44 binds between residues 5 and 16 of RGS2, as removal of these stabilized RGS2 against proteasomal degradation. Based on these results we designed a peptide microarray to identify important residues and properties for FBXO44 in vitro and found that Cys13 is essential for FBXO44 binding.</p> <p><br></p> <p>We also developed and optimized a high-throughput split luciferase screen to identify potential inhibitors of the FBXO44-RGS2 interaction. After forming a cell-line stably expressing tagged FBXO44 and RGS2 and optimizing assay condition, we achieved a robust assay for screening as determined by Z’-factor. <br>  </p>

<p>Sea urchins are fascinating marine creatures belonging to the phylum Echinodermata that serve as an essential ecological component and hold promise as a prospective source of therapeutics. However, sudden environmental changes, such as global warming and marine pollution, are placing significant stress on these organisms. To maintain natural resources and exploit sea urchins commercially, researchers are investigating aquaculture as a solution.</p> <p>This investigation discloses the physiological and immunological effects of physical and chemical stressors on one of the most common edible species of sea urchin, <em>Arbacia punctulata</em>. The study employed an elevated temperature as a physical stressor (1°C/day), lipopolysaccharides (LPS) inoculation as a chemical stressor (4µg/ml/day), and a combination of both LPS and elevated temperature as combined stressors. The results demonstrated a significant alteration in the total and differential coelomocyte count in the LPS-stressed group (p<0.05) and combined stressed group (p<0.05) followed by abnormal behavioral activity compared to those of control. Additionally, exposure to acute LPS exposure (at day 1 and day 3) and combined stressors led to an increase in phagocytic capacity (p<0.05) and lysozyme activity (p<0.05). Chronic exposure to LPS and combined stressors resulted in a decrease in gonadosomatic index (p<0.05, at day 10) and lysozyme activity (at day 7). A significant increase in coelomic fluid (CF) protein (p<0.05)was observed in the temperature-stressed group on days 5 and 10, while the combined stressed group had significantly more CF protein on days 1, 5, 7, and 10. An upregulation of Nf-kB gene expression was also observed (p>0.05) in temperature stressed group.  </p> <p>The study also revealed that sea urchins contain bioactive compounds that protect against external and internal injury, cell death, and body wall extract of sea urchin exhibited high antioxidant activity(p<0.05). Furthermore, it confirmed the antibacterial activity (p<0.05) of sea urchin (<em>Arbacia punctulata </em>and<em> Lytechinus variegatus</em>) body wall and coelomic fluid (cell-free plasma) extracts against ten pathogenic bacteria. The ethyl acetate body wall extract of both sea urchin species demonstrated higher inhibitory activity against the pathogenic bacteria tested. Overall sea urchin has potentials to meet the demand of food and medicine. </p>

Mitochondria are dynamic organelles that function in a complex interconnected network within the cell. Neurons are sensitive and highly energy demanding cells in the brain which require a functioning mitochondrial network that is able to provide ATP and modulate calcium. Mitochondrial networks have yet to be explored which gives rise to the need for specific and efficient molecular tools. In this project, I designed and produced adeno-associated virus vectors carrying a fluorescent reporter gene for imaging mitochondrial networks under human synapsin 1 promoter to target neurons specifically. The design of each vector was conducted with careful consideration of the different components in the plasmid design that are important for optimal expression, which resulted in two constructs; one self-complementary adeno-associated virus vector that marks the mitochondria and one single-stranded that marks mitochondria and the membrane of neurons.  The modularity of viral vectors allows the usage of different serotypes which adapt the vector to the cell type and the model. For this project I chose the serotypes 1 for neurons in vitro and PHP.eB which suits in vivo models since it has better permeability to the blood brain barrier. The production was conducted in human embryonic kidney cells using the triple-plasmid transfection method, followed by extraction and purification. The existence of viral particles was verified through transmission electron microscopy and the DNA titer of the vector through quantitative polymerase chain reaction. The produced adeno-associated virus vectors were delivered into young brain organoids which were not able to express the reporter gene, probably due to not fully developed neurons. The fluorescent protein expression targeting specifically mitochondria and the membrane was however verified in the human embryonic kidney cells during the packaging stages.

Hepatocellular carcinoma (HCC) is the most common liver malignancy that usually develops in patients suffering from chronic liver diseases. One of the major problems faced in the treatment of HCC is severe chemoresistance. Endoplasmic reticulum (ER) stress and hepatic stellate cells play an important role in tumour survival and growth as well as fibrosis. This study further investigates the crosstalk between ER-stress and hepatic stellate cells in HCC resistant cells as well as their relation to chemoresistance markers expression. Mice with chemically induced HCC were divided in 3 different treatment group; one was only treated with doxorubicin, one only with pharmacological ER-stress inhibitor 4μ8C, and one was treated with a combination of doxorubicin and 4μ8C. Tumour burden, fibrosis and cell proliferation were assessed through histological analysis and ImageJ processing. Chemoresistance markers expression was evaluated through mRNAs determination using real-time qPCR. While the combined treatment consisting of doxorubicin and pharmacological ER-stress inhibitor (4μ8C) has shown to positively reduce tumour progression, ferroptosis and collagen deposition, consequently decreasing fibrosis, drug resistance markers’ expression, on the other hand, seems to be more intricate, thus indicating that further investigations are probably needed. / Hepatocellulärt karcinom (HCC) är den vanligaste maligniteten i levern som vanligtvis utvecklas hos patienter som lider av kroniska leversjukdomar. Ett av de största problemen vid behandling av HCC är svår kemoresistens. Stress i endoplasmatiska retikulum (ER) och hepatiska stellatceller spelar en viktig roll för tumörernas överlevnad och tillväxt samt för fibros. I denna studie undersöks vidare samspelet mellan ER-stress och hepatiska stellatceller i HCC-resistenta celler samt deras relation till uttryck av kemoresistensmarkörer. Möss med kemiskt inducerad HCC delades in i tre olika behandlingsgrupper; en behandlades enbart med doxorubicin, en enbart med den farmakologiska ER-stresshämmaren 4μ8C och en behandlades med en kombination av doxorubicin och 4μ8C. Tumörbörda, fibros och cellproliferation bedömdes genom histologisk analys och ImageJ-bearbetning. Kemoresistensmarkörernas uttryck utvärderades genom bestämning av mRNA med hjälp av qPCR i realtid. Medan kombinationsbehandlingen bestående av doxorubicin och farmakologisk ER-stresshämmare (4μ8C) har visat sig minska tumörprogressionen, ferroptos och kollagenavlagring och därmed minska fibros, verkar uttrycket av läkemedelsresistensmarkörer å andra sidan vara mer invecklat, vilket tyder på att det troligen behövs ytterligare undersökningar.

Bakgrund: Akne är en av de vanligaste dermatologiska sjukdomarna och drabbar nästan alla människor under puberteten. Sjukdomen kan även fortsätta eller utvecklas i vuxen ålder där prevalensen av akne är högre bland kvinnor. Vid måttlig till svår akne förekommer inflammatoriska lesioner i ansikte och på övre bål som ofta lämnar ärr vid läkning. Isotretinoin (Iso) är det mest effektiva läkemedlet mot akne men kommer med många besvärliga och allvarliga biverkningar. Utifrån två fallpresentationer verkar Iso kunna påverka kroppens folatstatus negativt. Folat är ett essentiellt vitamin som har en viktig roll i DNA-syntesen och metabolismen av aminosyror. Syfte: Syftet med litteraturstudien var att undersöka om behandling med Iso har negativ effekt på kroppens folatstatus. Vid undersökning av detta söktes följande frågor att besvaras: Sänker Iso kroppens folatstatus? Ökar Iso homocysteinnivåerna i plasma? Sänker Iso kroppens B12-status? Metod: Arbetet har utförts genom systematisk litteratursökning i Pubmed och Scopus under januari och februari 2021. I båda databaserna har fyra olika fritextsökningar genomförts med isotretinoin som bestående sökord vidare tillsammans med folic acid, folate, homocysteine och vitamin B12. Elva artiklar har inkluderats för analys. Resultat: Effekten av Iso på kroppens folatstatus undersöktes i tio studier och i sex av dessa studier observerades signifikant minskade serumfolatnivåer. Homocysteinnivåer undersöktes i tio studier och i åtta av dessa observerades ökade homocysteinnivåer efter behandling med Iso. Åtta studier undersökte förändringar i serumkoncentrationen av B12 vid behandling med Iso och i tre av dessa studier observerades signifikant minskande B12-nivåer. Slutsats: Utifrån resultatet går det att tolka att omsättningen av folat och B12 kan ha ökat vid stigande homocysteinnivåer. Tillskott av folsyra och B12 kan vara att rekommendera till patienter med akne som behandlas med Iso och där homocysteinnivåerna i plasma stiger. Studier med längre behandlingsperiod bör utföras för att kunna avgöra hur en fullständig behandling med Iso påverkar vitaminstatusen för folat och B12. / Background: Acne is one of the most common dermatological diseases generally affecting people going through puberty. The prevalence of adult acne is increasing and especially among women. Clinical symptoms of acne in moderate and severe cases are inflammatory lesions located in the face and upper body that can often cause scarring. Isotretinoin (Iso) is the most effective therapeutic drug against acne but has many side-effects. Iso appears to adversely affect the body's folate status according to two case presentations. Folate is an essential vitamin and has an important role in DNA synthesis and amino acid metabolism. Aim: The aim of the literature study was to examine if treatment with Iso has a negative effect on the body's folate status. Following questions were searched to be answered: Does Iso lower the body's folate status? Dose Iso increase plasma homocysteine levels? Does Iso lower the body's vitamin B12 status?Method: Eleven articles examining the effect of Iso treatment on folate status, homocysteine and B12 levels were collected from a literature search in Pubmed and Scopus during January and February 2021. Four different free text searches were carried out with isotretinoin as the consisting key word together with folic acid, folate, homocysteine ​​and vitamin B12. Results: The effect of Iso on the body's folate status was examined by ten studies and in six of these studies significantly reduced serum folate levels were observed. Homocysteine levels were examined in ten studies and in eight of these were increased homocysteine levels observed after treatment with Iso. Eight studies examined changes in the serum concentration of B12 and in three of these studies significantly decreased B12 levels were observed after treatment with Iso. Conclusion: The results give an indication that the turnover of folate and B12 may have increased with rising homocysteine plasma levels. Supplements of folic acid and B12 may be recommended for patients undergoing treatment with Iso if plasma homocysteine levels are rising during treatment. Studies with a longer treatment period with Iso need to be done to determine how a complete treatment with Iso affects folate and B12 status.

<p dir="ltr">The actin cytoskeleton is a dynamic structure that regulates various important cellular processes, such as cell protrusion, migration, transport, and cell shape changes. Cells employ different actin architectures best suited for each of these functions. We have employed an agent-based model to illuminate how the actin cytoskeleton plays such functions in animal and plant cells, via dynamic interactions between molecular players.</p><p dir="ltr">Lamellipodia found in animal cells are two-dimensional actin protrusion formed on the leading edge of cells, playing an important role in sensing surrounding mechanical environments via focal adhesions. Various molecular players, architecture, and dynamics of the lamellipodia have been investigated extensively during recent decades. Nevertheless, it still remains elusive how each component in the lamellipodia mechanically interacts with each other to attain a stable, dynamic steady state characterized by a retrograde flow emerging in the branched actin network. Using the agent-based model, we investigated how the balance between different subcellular processes is achieved for the dynamic steady state. We simulated a branched network found in the lamellipodia, consisting of actin filament (F-actin), myosin motor, Arp2/3 complex, and actin crosslinking protein. We found the importance of a balance between F-actin assembly at the leading edge of cells and F-actin disassembly at the rear end of the lamellipodia. We also found that F-actin severing is crucial to allow for the proper disassembly of an actin bundle formed via network contraction induced by motor activity. In addition, it was found that various dynamic steady states can exist.</p><p dir="ltr">The actin cytoskeleton in plant cells plays a crucial role in intracellular transport and cytoplasmic streaming, and its structure is very different from the actin cytoskeleton in animal cells. The plant actin cytoskeleton is known to show distinct dynamic behaviors with homeostasis. We used the agent-based model to simulate the plant actin cytoskeleton with the consideration of the key governing mechanisms, including F-actin polymerization/depolymerization, different types of F-actin nucleation events, severing, and capping. We succeeded in reproducing experimental observations in terms of F-actin density, length, nucleation frequency, and rates of severing, polymerization, and depolymerization. We found that the removal of nucleators results in lower F-actin density in the network, which supports recent experimental findings.</p>

Breast cancer is the most common form of cancer in women worldwide and the second leading cause of cancer death. It is a heterogeneous disease and is subdivided into different subtypes, all with different treatment responses and survival outcomes. Luminal breast cancers are characterised by the expression of oestrogen receptor and generally have a good prognosis. More aggressive tumours are marked by the presence of growth stimulating receptor tyrosine kinase HER2 (HER2-like breast cancer) or the absence of oestrogen receptor, progesterone receptor, and HER2 (triple-negative breast cancer,TNBC). The latter is the most aggressive form and is difficult to treat due to lack of treatment targets. This thesis aimed to explore possible prognostic and predictive biomarkers in different subtypes and study their role in breast cancer. To this aid, breast cancer tumours of pre- and post-menopausal patients enrolled in two cohorts were analysed for gene copy numbers and expression of proteins involved in cell proliferation. Gene copy numbers of receptor tyrosine kinases MET and EGFR, Met’s ligand HGF, and protein tyrosine phosphatase PTPN2 were determined by droplet digital PCR or quantitative PCR in both cohorts. Met, phosphorylated Met (pMet), HGF, and PTPN2 protein expression levels were analysed with immunohistochemical staining in the pre-menopausal cohort. Moreover,the role of the aforementioned proteins was investigated in breast cancer cell lines. Amplification of MET, HGF, and EGFR in breast tissues was found to be low (5-8%). These three genes, all located on chromosome 7, were found to be strongly correlated with eachother and to be associated with shortened distant recurrence-free survival. High protein expression of Met, pMet, and HGF was found in 33%, 53%, and 49% of the breast tumours. MET and EGFR were found to be more often amplified in TNBC disease, correlating with worse survival. Moreover, stromal expression of HGF was associated with shorter survival in TNBC. EGF stimulation in TNBC cell line MDA-MB-468 led to inhibited cell proliferation and migration. Partial knockdown of EGFR caused TNBC cells to proliferate and migrate more upon EGF treatment, mirroring EGFR inhibitor resistance. Knockdown of Met had in part the opposite effects, indicating that Met inhibitors might be useful in the treatment of TNBC. The increase in proliferation and migration upon EGFR depletion could be counteracted with simultaneous knockdown of EGFR and Met, indicating that dual inhibition of these proteins might be a future treatment option in TNBC. Copy loss of PTPN2 was reported in 15% of the cases in both pre- and post-menopausal cohorts. Low cytoplasmic PTPN2 protein expression was found in half of the cases. Loss of PTPN2 gene or protein was associated with a shorter distant recurrence-free survival in Luminal A and HER2-positive tumours, not in TNBC, suggesting a subtype-related prognostic value of PTPN2. Subtype relevance of PTPN2 was further implied by in vitro analyses. Whereas PTPN2 knockdown had no observed effect on TNBC cell lines, knockdown in the Luminal A cell line MCF7 inhibited Met phosphorylation and promoted phosphorylation of Akt, a key regulator of cellular proliferation and survival. The cell growth and survival regulating RAS/MAPK pathway remained unaffected. Knockdown in the HER2-positive cell line SKBR3 led to increased Met phosphorylation and decreased RAS/MAPK-related Erk phosphorylation as well as EGF-mediated transcription factor STAT3 phosphorylation. These results indicate that the role of PTPN2 in breast cancer is subtype-related and needs to be further investigated for future treatment options.