Background: Heat-shock proteins of the 70 kDa family (Hsp70s) are essential chaperones required for key cellular functions. In eukaryotes, four subfamilies can be distinguished according to their function and localisation in different cellular compartments: cytosol, endoplasmic reticulum, mitochondria and chloroplasts. Generally, multiple cytosol-type Hsp70s can be found in metazoans that show either constitutive expression and/or stress-inducibility, arguing for the evolution of different tasks and functions. Information about the hsp70 copy number and diversity in microbial eukaryotes is, however, scarce, and detailed knowledge about the differential gene expression in most protists is lacking. Therefore, we have characterised the Hsp70 gene family of Paramecium caudatum to gain insight into the evolution and differential heat stress response of the distinct family members in protists and to investigate the diversification of eukaryotic hsp70s focusing on the evolution of heat-inducibility. Results: Eleven putative hsp70 genes could be detected in P. caudatum comprising homologs of three major Hsp70-subfamilies. Phylogenetic analyses revealed five evolutionarily distinct Hsp70-groups, each with a closer relationship to orthologous sequences of Paramecium tetraurelia than to another P. caudatum Hsp70-group. These highly diverse, paralogous groups resulted from duplications preceding Paramecium speciation, underwent divergent evolution and were subject to purifying selection. Heat-shock treatments were performed to test for differential expression patterns among the five Hsp70-groups as well as for a functional conservation within Paramecium. These treatments induced exceptionally high mRNA up-regulations in one cytosolic group with a low basal expression, indicative for the major heat inducible hsp70s. All other groups showed comparatively high basal expression levels and moderate heat-inducibility, signifying constitutively expressed genes. Comparative EST analyses for P. tetraurelia hsp70s unveiled a corresponding expression pattern, which supports a functionally conserved evolution of the Hsp70 gene family in Paramecium. Conclusions: Our analyses suggest an independent evolution of the heat-inducible cytosol-type hsp70s in Paramecium and in its close relative Tetrahymena, as well as within higher eukaryotes. This result indicates convergent evolution during hsp70 subfunctionalization and implies that heat-inducibility evolved several times during the course of eukaryotic evolution.

Les maladies cardiométaboliques sont les principales causes de décès dans le monde, et au Canada elles sont responsables d'environ 700 000 décès par année. Le diabète de type 2 et la maladie coronarienne sont les maladies cardiométaboliques les plus répandues. Malgré des avancées pharmacologiques, la prévalence de ces maladies demeure élevée, ce qui souligne l'importance des thérapies complémentaires qui améliorent le contrôle glycémique ainsi que la fonction vasculaire afin de prévenir les complications liées à ces maladies. Depuis quelques années, l’exposition à la chaleur reçoit une attention accrue pour son potentiel thérapeutique. En outre, des études scientifiques suggèrent que l’exposition à la chaleur pourrait diminuer la glycémie et améliorer la fonction vasculaire. Cependant, le potentiel thérapeutique de l'exposition à la chaleur demeure sous-étudié chez les personnes atteintes du diabète de type 2 ou de la maladie coronarienne. L’objectif général de cette thèse était d’évaluer les effets aigus de l’exposition à la chaleur sur des marqueurs de la fonction cardiométabolique auprès de gens ayant un diabète de type 2 ou une maladie coronarienne. L’article 1 a déterminé l’effet aigu d’une immersion en eau chaude sur la sensibilité à l’insuline, la fonction vasculaire, les concentrations des protéines de choc thermique plasmatique (eHSP70/90) et intracellulaire (iHSP70/90), les marqueurs inflammatoires (IL-6, IL1-RA, NFKB) ainsi que sur les médiateurs de l'action de l'insuline (IRS-1, GLP-1) comparativement à une immersion thermoneutre au sein d’une population ayant le diabète de type 2. Les résultats démontrent qu’une immersion en eau chaude n’améliore pas la sensibilité à l’insuline, ni la fonction vasculaire et elle n’affecte pas les concentrations de HSP70 / 90 et les marqueurs inflammatoires. L’article 2 a déterminé l’effet aigu d’une exposition dans un sauna Finlandais sur la fonction vasculaire, des marqueurs de dysfonction endothéliale (VCAM-1, ICAM-1) et des marqueurs inflammatoires (IL-6, IL-10, TNF-α, IL-1β, CRP) auprès de personnes ayant une maladie coronarienne. Les résultats démontrent qu’une séance de sauna Finlandais améliore la fonction endothéliale et augmente la concentration circulante d’IL-6 sans affecter d’autres marqueurs inflammatoires (IL-10, TNF-α, IL-1β, CRP) ainsi que des marqueurs de dysfonction endothéliale. Combinées, les deux études de cette thèse démontrent que l’exposition passive à la chaleur n’améliore pas de façon aiguë les marqueurs cardiométaboliques chez les personnes diabétiques de type 2. Par contre, la chaleur exerce un effet bénéfique sur la fonction endothéliale chez les personnes ayant une maladie coronarienne. / Cardiometabolic diseases are the leading cause of death globally, and in Canada they are responsible for approximately 700 000 deaths each year. Type 2 diabetes and coronary artery disease are the most prevalent cardiometabolic diseases. Despite advancements in pharmacological treatments, the prevalence of these diseases remains high which underlines the importance of complementary therapies to prevent complications related to these diseases. In recent years, heat exposure has received attention for its therapeutic potential. Studies have demonstrated that heat exposure could be an effective method to decrease glycemia and improve vascular function. However, the therapeutic potential of heat exposure remains understudied in people with type 2 diabetes or coronary artery disease. The general objective of this thesis was to evaluate the acute effects of heat exposure on cardiometabolic markers in people with type 2 diabetes and coronary artery disease. The first article of this thesis determined the acute effect of hot water immersion on insulin sensitivity, vascular function, plasma (eHSP70 / 90) and intracellular (iHSP70 / 90) heat shock protein concentrations, inflammatory markers (IL- 6, IL1-RA, NFKB) as well as mediators of insulin action (IRS-1, GLP-1) compared to thermoneutral water immersion in a population with type 2 diabetes. Findings from this study demonstrate that acute hot water immersion does not improve insulin sensitivity, vascular function or affect HSP70 / 90 concentrations and inflammatory markers. The second article of this thesis determined the acute effects of Finnish sauna bathing on vascular function, markers of endothelial dysfunction (VCAM-1, ICAM-1) and inflammatory markers (IL-6, IL-10, TNF- α, IL-1β, CRP) in older adults with coronary artery disease. Results from this study demonstrate that one bout of Finnish sauna bathing improves endothelial function and increases the circulating concentration of IL-6 without affecting other markers of inflammation (IL-10, TNF-α IL-1β, CRP) or endothelial dysfunction. Combined, these results show that acute heat exposure does not acutely improve cardiometabolic markers in people with type 2 diabetes. On the other hand, heat exposure has a beneficial effect on endothelial function in people with coronary artery disease.

Värmechockprotein 90 kDa (HSP90) bildar ett anmärkningsvärt komplicerat nätverk med en mängd olika cochaperones. Komplexet av FK506-bindande protein 51 kDa (FKBP51) och HSP90 förmedlar proteinveckning och funktion, främjar tau aggregation vid Alzheimers sjukdom och påverkar stressrelaterade störningar, fetma, typ två-diabetes, etc. I samarbete med den molekylära chaperonen HSP90, FKBP51 har nyligen föreslagits som ett lovande terapeutiskt mål för Alzheimers sjukdom (AD). Således skapades knock-in-musen med punktmutationer i tetratricopeptide repeat (TPR) domänen av FKBP51, vilket gör den oförmögen att interagera med HSP90, för att undersöka de potentiella terapeutiska målen för behandling av dessa sjukdomar. Glukokortikoidreceptorn (GR) fungerade traditionellt som utgångspunkten för de initiala studierna av FKBP51-funktion och mekanism som kan stimuleras av den syntetiska glukokortikoiden dexametason (Dexa). Det primära målet med projektet är att förstå den biologiska betydelsen av FKBP51-HSP90 interaktioner. Det är oklart hur FKBP51-mutation påverkar protein-protein-interaktionen och glukokortikoidsignalering. Här analyserades embryonala fibroblaster (MEF) isolerade från vildtyp och FKBP51 mutant mus med avseende på proteinlokalisering, proteinuttryck och genuttryck. Även om ingen säker skillnad mellan vildtyp och mutantmöss sågs i Dexa-medierad glukokortikoidsignalering, förekommer de posttranslationella modifieringarna (PTM) vid exponering för Dexa-behandling av FKBP51 i vildtypmöss i en signifikant högre utsträckning än i Fkbp51mute-möss.Fosforyleringsmodifieringen av FKBP51 antogs initialt och bekräftades av fosforyleringsanrikningsstrategier. Bekräftelse har dock ännu inte erhållits. / Heat shock protein 90 kDa (HSP90) forms a remarkably complicated network with a variety of cochaperones. The complex of FK506-binding protein 51 kDa (FKBP51) and HSP90 mediates protein folding and function, promoting tau aggregation in Alzheimer's disease and influencing stress-related disorders, obesity, type two diabetes, etc. In collaboration with the molecular chaperone HSP90, FKBP51 has recently been proposed as a promising therapeutic target for Alzheimer's disease (AD). Thus, the knock-in mouse harboring point mutations in the tetratricopeptide repeat (TPR) domain of FKBP51 rendering it unable to interact with HSP90 were created to investigate the potential therapeutic targets for the treatment of these diseases. Glucocorticoid receptor (GR) traditionally served as the starting point for the initial studies of FKBP51 function and mechanism which can be stimulated by the synthetic glucocorticoid, dexamethasone (Dexa). The primary goal of the project is to comprehend the biological significance of FKBP51-HSP90 interactions. It is unclear how FKBP51 mutation affects the protein-protein interaction and glucocorticoid signaling. Here, embryonic fibroblasts (MEFs) isolated from wildtype and FKBP51 mutant mouse were analyzed with respect to protein localization, protein expression, and gene expression. Although no certain difference between wildtype and mutant mice was seen in Dexa-mediated glucocorticoid signaling, the post-translational modifications (PTMs) in exposure to Dexa treatment of FKBP51 occur in wildtype mice to a significantly higher extent than in Fkbp51mute mice. The phosphorylation modification of FKBP51 was initially hypothesized and confirmed by phosphorylation enrichment strategies. However, confirmation has not yet been obtained.

Organisms are frequently exposed to fluctuating environmental conditions and might consequently experience stress. Environmental stress can damage cellular components, which can threaten especially single-celled organisms, such as yeast, as they cannot escape. To survive, cells mount protective stress responses, which serve to preserve cellular components and architecture. Recent findings in yeast show that the stress response upon energy depletion stress involves a gelation of the cytoplasm due to macromolecular protein assembly, characterized by drastic changes in cytoplasmic material properties. Remarkably, the stress-induced cytoplasmic gelation is protective, raising the question whether this could be a common strategy of cells to cope with severe stress. I hypothesized that protein aggregation induced by another common stress, severe heat shock, might cause a similar cytoplasmic gelation in yeast. Furthermore, I hypothesized that the reversibility of cytoplasmic gelation is provided by molecular chaperones, which are known regulators of protein aggregation. In this thesis, I therefore aimed to characterize the changes in the material properties of the cytoplasm upon severe heat shock as well as their underlying causes and how molecular chaperones affect these changes. To characterize heat-induced changes in the material properties of the cytoplasm, I monitored Schizosaccharomyces pombe cells during recovery from severe heat shock using a combination of cell mechanical assays, time-lapse microscopy and single-particle tracking. I found that the cells entered a prolonged growth arrested state upon stress, which coincided with significant cell stiffening and a long-range motion arrest of lipid droplets in the cytoplasm, while smaller cytoplasmic nanoparticles remained mostly mobile. At the same time, a significant fraction of proteins aggregated in the cytoplasm, forming insoluble inclusions such as heat shock granules. After stress cessation, the observed changes were reversed as stiffened cells softened and lipid droplets resumed long-range motion. Cell softening and lipid droplet motion recovery coincided with protein disaggregation. These processes could be delayed by impairing protein disaggregation through genetic perturbation of the molecular chaperone Hsp104, which functions as a protein disaggregase. In contrast, no influence on protein disaggregation or heat-induced cytoplasmic material property changes was detected for the small heat shock protein Hsp16. These results suggest that the cytoplasm gels upon severe heat shock due to protein aggregation and is refluidized during recovery with the help of Hsp104. Remarkably, cells resumed growth only after refluidization of the cytoplasm, suggesting that reversible cytoplasmic gelation may contribute to regulation of the heat-induced growth arrest. In addition, cytoplasmic gelation could potentially preserve cellular architecture during heat shock. Overall, the results from my thesis work indicate that reversible cytoplasmic gelation due to macromolecular protein assembly may be a universal cellular response to severe stress which is associated with a stress-protective growth arrest. A likely stress-specific part of this response is the chaperone-dependent refluidization of the cytoplasm, which might explain the prolonged growth arrest seen upon severe heat shock as compared to other stresses and might allow more time for the repair of heat-induced damage.:Abstract Zusammenfassung Table of contents Figure index List of abbreviations 1 Introduction 1.1 Heat shock affects cellular function and fitness 1.1.1 Cells respond to stress in phases 1.1.2 Heat shock threatens cellular homeostasis and structural integrity 1.1.3 Stress severity determines detrimental effects of heat shock 1.1.4 Heat stress causes protein aggregation 1.1.5 Heat shock granules are functional aggregates in yeast 1.2 The heat shock response protects cellular fitness 1.2.1 Cells change transcription to adapt to stress 1.2.2 Molecular chaperones are important in stress protection 1.2.3 Hsp104 is a protein disaggregase chaperone 1.2.4 Small heat shock proteins modulate protein aggregation 1.2.5 Stress severity determines modules of the heat shock response 1.3 Cytoplasmic material properties change during stress 1.3.1 Cells homeostatically adapt cytoplasmic material properties during stress 1.3.2 The cytoplasm is viscoelastic 1.3.3 Is the cytoplasm a gel? 1.3.4 Stress can induce cytoplasmic gelation 1.4 Research aims 2 Materials and Methods 2.1 S. pombe strains and growth conditions 2.1.1 Growth conditions 2.1.2 Construction of S. pombe strains 2.1.3 S. pombe transformation 2.1.4 S. pombe colony PCR 2.1.5 S. pombe strains used in this thesis 2.2 Plasmids and cloning 2.2.1 Plasmids used in this thesis 2.2.2 Construction of plasmid for fluorescent GEM nanoparticle expression 2.2.3 E. coli transformation 2.2.4 Plasmid purification from E. coli 2.3 S. pombe stress treatments 2.3.1 Heat shock treatment 2.3.2 Osmoadaptation 2.4 Cell biological methods 2.4.1 Viability assay 2.4.2 Growth assay 2.5 Cell bulk mechanical assays 2.5.1 Spheroplasting assay 2.5.2 Atomic force microscopy 2.5.3 Real-time deformability cytometry 2.5.4 RT-DC sample preparation 2.5.5 RT-DC setup and measurements 2.5.6 RT-DC data evaluation 2.6 Microscopy 2.6.1 Microscopy of GEM particles 2.6.2 Fluorescence microscopy of endogenously labeled Pabp-mCherry 2.6.3 Microscopy of µNS particles 2.7 Image analysis 2.7.1 Image analysis of Pabp-mCherry in vivo fluorescence microscopy 2.7.2 Differenced brightfield image analysis 2.7.3 Kymographs 2.8 Single-particle tracking analysis 2.8.1 Particle tracking 2.8.2 Mean squared displacement analysis 2.9 Optical diffraction tomography (ODT) 2.9.1 ODT sample preparation 2.9.2 ODT optical setup and measurements 2.9.3 ODT tomogram reconstruction and quantitative analysis 2.10 Lysis and sedimentation assay 2.10.1 Lysis buffer 2.10.2 S. pombe heat shock treatment and lysis 2.10.3 Sedimentation assay 2.10.4 Protein concentration measurement 2.10.5 SDS-PAGE 2.10.6 Coomassie staining 2.10.7 Western Blot 3 Results 3.1 Physical and chemical conditions affect heat shock survival and heat-induced growth arrest of S. pombe 3.1.1 S. pombe arrests growth during severe heat shock 3.1.2 Heat-induced growth arrest is dose-responsive 3.1.3 Heat-induced growth arrest depends on experimental conditions 3.1.4 Buffer pH and energy source have a strong impact on heat shock survival 3.1.5 Osmoadaptation protects cells during heat shock 3.2 Severe heat shock induces reversible cellular stiffening 3.2.1 Cellular rounding upon cell wall removal is delayed after heat shock 3.2.2 Elastic modulus of S. pombe cells is increased after heat shock 3.2.3 Recovery from heat-induced growth arrest is preceded by cell softening 3.3 Long-range particle dynamics in cytoplasm are abolished after heat shock 3.3.1 Small particle dynamics are largely independent of heat shock treatment 3.3.2 Lipid droplets are confined in space after heat shock 3.4 Cytoplasmic crowding increases during heat shock 3.5 Heat shock induces reversible protein aggregation 3.5.1 Insoluble protein fraction is increased after heat shock 3.5.2 Heat shock granules form reversibly during heat shock 3.5.3 HSG formation and dissolution are correlated with changes in cytoplasmic long-range dynamics 3.6 Molecular chaperones modulate cytoplasmic material property changes during heat stress recovery 3.6.1 Hsp104 but not Hsp16 is required for disaggregation of heat shock granules 3.6.2 Hsp104 but not Hsp16 is required for recovery from heat-induced growth arrest 3.6.3 Hsp104 but not Hsp16 is required for recovery of cytoplasmic long-range dynamics 3.6.4 Hsp104 but not Hsp16 is required for rapid reversal of cellular stiffening which coincides with growth recovery 4 Discussion 4.1 Summary and model 4.2 Which mechanism underlies cell stiffening upon heat shock? 4.2.1 Heat-induced protein aggregation might cause cell stiffening 4.2.2 Heat-induced protein aggregation might lead to cytoplasmic gelation 4.2.3 Many factors could contribute to protein aggregation and cytoplasmic gelation 4.3 The heat-induced growth arrest state is associated with reversible cytoplasmic gelation 4.3.1 Cytoplasmic material property changes mark the severe heat-induced growth arrest state 4.3.2 Is cytoplasmic gelation a common response to severe stress? 4.4 What are the biological consequences of cytoplasmic gelation? 4.4.1 Cytoplasmic gelation might obstruct processes that require motion of large structures 4.4.2 Is cytoplasmic gelation upon heat shock protective? 4.5 Heat shock recovery involves the chaperone-mediated refluidization of the cytoplasm 4.5.1 Cytoplasmic refluidization is required for growth recovery 4.5.2 Stress tolerance is marked by enhanced reversibility of cytoplasmic gelation 4.5.3 The protein disaggregase chaperone Hsp104 regulates the reversal of heat-induced cytoplasmic material property changes 4.6 Conclusion References Acknowledgements Publications and Contributions 5 Erklärung entsprechend §5.5 der Promotionsordnung

The development of shape in multicellular organisms has intrigued human minds for millenia. Empowered by modern genetic techniques, molecular biologists are now striving to not only dissect developmental processes, but to exploit their modularity for the design of custom living systems used in bioproduction, remediation, and regenerative medicine. Currently, our capacity to harness this potential is fundamentally limited by a lack of spatiotemporal control over gene expression in multicellular systems. While several synthetic genetic circuits for control of multicellular patterning have been reported, hierarchical induction of gene expression domains has received little attention from synthetic biologists, despite its fundamental role in biological self-organization. In this thesis, I introduce the first synthetic genetic system implementing population-based AND logic for programmed hierarchical patterning of bacterial populations of Escherichia coli, and address fundamental prerequisites for implementation of an analogous genetic circuit into the emergent multicellular plant model Marchantia polymorpha. In both model systems, I explore the use of bacteriophage T7 RNA polymerase as a gene expression engine to control synthetic patterning across populations of cells. In E. coli, I developed a ratiometric assay of bacteriophage T7 RNA polymerase activity, which I used to systematically characterize different intact and split enzyme variants. I utilized the best-performing variant to build a three-color patterning system responsive to two different homoserine lactones. I validated the AND gate-like behavior of this system both in cell suspension and in surface culture. Then, I used the synthetic circuit in a membrane-based spatial assay to demonstrate programmed hierarchical patterning of gene expression across bacterial populations. To prepare the adaption of bacteriophage T7 RNA polymerase-driven synthetic patterning from the prokaryote E. coli to the eukaryote M. polymorpha, I developed a toolbox of genetic elements for spatial gene expression control in the liverwort: I analyzed codon usage across the transcriptome of M. polymorpha, and used insights gained to design codon-optimized fluorescent reporters successfully expressed from its nuclear and chloroplast genomes. For targeting of bacteriophage T7 RNA polymerase to these cellular compartments, I functionally validated nuclear localization signals and chloroplast transit peptides. For spatiotemporal control of bacteriophage T7 RNA polymerase in M. polymorpha, I characterized spatially restricted and inducible promoters. For facilitated posttranscriptional processing of target transcripts, I functionally validated viral enhancer sequences in M. polymorpha. Taking advantage of this genetic toolbox, I introduced inducible nuclear-targeted bacteriophage T7 RNA polymerase into M. polymorpha. I showed implementation of the bacteriophage T7 RNA polymerase/PT7 expression system accompanied by hypermethylation of its target nuclear transgene. My observations suggest operation of efficient epigenetic gene silencing in M. polymorpha, and guide future efforts in chassis engineering of this multicellular plant model. Furthermore, my results encourage utilization of spatiotemporally controlled bacteriophage T7 RNA polymerase as a targeted silencing system for functional genomic studies and morphogenetic engineering in the liverwort. Taken together, the work presented enhances our capacity for spatiotemporal gene expression control in bacterial populations and plants, facilitating future efforts in synthetic morphogenesis for applications in synthetic biology and metabolic engineering.

Cette thèse présente les travaux de développement de formulations injectables capables de se solidifier in situ, formant ainsi un implant piégeant des microparticules magnétiques en vue du traitement de tumeurs par induction magnétique d'une hyperthermie locale modérée. Nous exposons tout d'abord le contexte physique, biologique et clinique de l'hyperthermie comme traitement anticancéreux, particulièrement des modalités électromagnétiques. Les performances in vitro et in vivo des matériaux et formulations sont alors présentées. L'objet du chapitre suivant est la caractérisation des propriétés physicochimiques, magnétiques, et chauffantes, dans un champ magnétique alternatif (115 kHz, 9 - 12 mT), des microparticules de silice renfermant des nanoparticules d'oxyde de fer superparamagnétiques (SPIONs) et de deux de leurs formulations: un hydrogel d'alginate de sodium et un organogel de poly(éthylène-co-alcool vinylique) dans le diméthylsulfoxide. Finalement, nous présentons le potentiel thérapeutique de 20 minutes d'hyperthermie locale induite après injection de l'organogel superparamagnétique dans un modèle murin sous-cutané de tumeurs nécrosantes de colocarcinome humain.