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Skeletal muscle injury results in functional deficits that can take several weeks to fully recover. Ultimate recovery of function is dependent on the muscle’s ability to regenerate, a highly coordinated process that involves transient muscle inflammation and the replacement of damaged myofibers. Instrumental in the inflammatory response, is the pro-inflammatory cytokine TNF-α. Expression of TNF-α is thought to be regulated, in part, by the stress sensing 70 kDa heat shock protein (Hsp70). However, it remains unclear how Hsp70 alters TNF-α following injury, and if so, how these changes affect skeletal muscle repair. Therefore, we up-regulated Hsp70 expression using 17-allylamino-17-demethoxygeldanamycin (17-AAG) prior to and following BaCl2-induced injury, and assessed TNF-α and myogenin content. Regenerating fiber cross-sectional area (CSA) and in vivo isometric torque were also analyzed in the weeks following the injury. Treatment of 17-AAG resulted in a ~5 fold increase in Hsp70 of the uninjured muscle, but did not affect any other biochemical, morphological or functional variables compared to controls. In the days following the injury, TNF-α and myogenin were elevated and directly correlated. At these earlier time points (≤7 days), treatment of 17-AAG increased TNF-α above that of the injured controls and resulted in a sustained increase in myogenin. However, no differences were observed in regenerating fiber CSA or in vivo torque production between the groups. Together, these data suggest that Hsp70 induction increases TNF-α and myogenin content following BaCl2-induced injury, but does not appear to alter skeletal muscle regeneration or attenuate functional deficits in otherwise healthy young mice.

This is a text about a work of art, “The Room”, and about the process that brought it about. The process includes experiments in clay bodies, mixing different elements with the base clay in search of a material both suitable to work with in terms of texture and color, but also rich in less tangible qualities, as I mix in elements which carry a set of values of cultural identity. The text follows the path towards development of the final piece during the two-year course of the master program at Konstfack. During these two years, external factors such as dealing with the issues of culture shock, and searching for a place to live, interfere with my way of thinking, leading to unexpected turns in the direction of my artistic process. Searching for an apartment finds me standing in strangers' apartments as they sell their homes, their ways of life and their house rules. These sometimes awkward meetings provide a good starting point in my research of people's habits and habitats. In trying to understand some elements of Swedish culture, I become aware of the fact of my own culture and start thinking about it from an outside perspective. Eventually, the central question of the essay crystallizes: Who will carry on the traditional craft techniques of my home country? Romania is the rare place in Europe where crafts are still being practiced as they have been for hundreds of years, in the villages by crafts persons leading traditional lives. As the villages are emptied of young people, moving into cities, and as Romania as a whole is drained of a large part of its young and ambitious generation, moving to other European countries for jobs and education, a trend that I am of course part of, the traditions that I have taken for granted, growing up with my grandmother in a traditional village, become threatened. The answer to the question is a simple as it is demanding: I have to be part of the future of Romanian crafts. To document them, understand them, and incorporate them in my art. For this purpose, I undertake an investigative research trip. The text presents my findings about the crafts, and about the people working to document and preserve the traditions. The research trip is also presented in the movie “Six days in Romania”, which I include as an appendix to the essay. Over the course of two years, several short-term art projects have been completed within the master program. They are presented in the form of an interview with myself. Looking back at these projects, they become explained as necessary steps in preparation for the final piece, a viewpoint very different from the utter confusion that was the dominating feeling of at least the first year of the course. The interview tries to give insight into the non-linear process that is the creative work. Finally, in a poetic description of the final piece, I let my art speak for itself in a very literal way. In giving voice to the piece, I try to access truths hidden even to myself, in an effort to be as transparent as possible about the value of my efforts.

Numerical simulations of Mach shock reflections have shown that the Mach stem can bifurcate as a result of the slip line jetting forward. Numerical simulations were conducted in this study which determined that these bifurcations occur when the Mach number is high, the ramp angle is high, and specific heat ratio is low. It was clarified that the bifurcation is a result of a sufficiently large velocity difference across the slip line which drives the jet. This bifurcation phenomenon has also been observed after triple point collisions in detonation simulations. A triple point reflection was modelled as an inert shock reflecting off a wedge, and the accuracy of the model at early times after reflection indicates that bifurcations in detonations are a result of the shock reflection process. Further investigations revealed that bifurcations likely contribute to the irregular structure observed in certain detonations.

Lipopolysaccharide (LPS), one of the main components of Gram-negative bacterial cell walls, is a potent endotoxin. Structures of the unique protective monoclonal antibody (mAb) WN1 222-5 in complex with Escherichia coli R2 and R4 LPS core regions show that recognition occurs in a manner similar to the innate immune receptor Toll-like receptor 4 (TLR4). Inner core LPS is shown to exist in a conserved epitope with multiple intramolecular interactions that allows the conserved epitope to bind strongly to mAb WN1 222-5. The structure of mAb FDP4, directed against truncated E. coli J-5 LPS, shows a deep pocket combining site specific for a terminal epitope that does not allow room for wild type (wt) LPS. Research into these anti-LPS binding mAbs opens up new avenues for potential septic shock therapy. The explosion of new techniques and bright x-ray sources in the 80’s and 90’s led to rapid advancement of protein x-ray crystallography; however, structure determination on some of the most important problems is now stalled due to the general inability to grow crystals of sufficient size. Recent advances in electron microscopy (EM) technology has led to improved beam characteristics, which has allowed the initiation of research to develop EM as a viable alternative to x-ray crystallography. In this research, method development using standard equipment to explore potential avenues for analysing three-dimensional protein crystals via EM has been explored. / Graduate / 0982 / 0487 / 0537 / kgomery@uvic.ca

A system for recording the trajectories of non-planar shocks and particle tracers within a shock tube flow has been developed. The optics consists of a double-pass schlieren system with a multiply pulsed ruby laser as light source. The laser is synchronized with a high speed framing camera. A grid of ammonium chloride tracers is injected into the flow field, and the motion of the tracers behind the Mach reflection of intermediate strength shocks has been recorded. Analysis of the trajectories has yielded the space and time variation of the physical properties within the flow field. / Graduate / 0605

Heat shock proteins (Hsps) are increasingly being seen as having roles other than those of intracellular molecular chaperones, particularly with regard to their potential to act as cytokines, and to stimulate the innate immune system. Hsps have also been found to promote bone resorption and osteoclast formation in vitro, although the mechanism has not been previously identified. The overall aims of this thesis were to determine whether Hsps could stimulate bone resorption by affecting the RANKL/OPG pathway, and to address the hypothesis that Hsps can act as a danger signal to the innate immune system. In order for Hsps to affect either the RANKL/OPG system of bone resorption or act as danger signals they would need to be actively released from cells, ideally in a controlled manner following exposure to the source of stress. Hsp60 and Hsp70 were found to be released from a range of immune cells including the cell lines Jurkat and U937, and also PBMCs, T-cells and B-cells. This release was not due to cell damage. The release of Hsp60 and Hsp70 were downregulated by inhibitors of protein secretion, in particular Hsp70 release was reduced by compounds that inhibited lysosomal pathways and Hsp60 release by classical secretion inhibitors. Hsp60, Hsp70, GroEL and LPS all affected the RANKL/OPG system of bone regulation; OPG production and release was down-regulated in the MG63 and GCT osteoblast-like cell lines following treatment with Hsp60, Hsp70 and LPS, and RANKL expression was upregulated following treatment with Hsp60, Hsp70, GroEL and LPS. This effect on the RANKL/OPG system was found to translate into an effect on osteoclast formation when conditioned media from treated osteoblasts was added to osteoclast precursors in the presence of M-CSF. A range of different factors that affected Hsp release were identified; PHA activation of PBMCs was found to upregulate Hsp60 release from PBMCs. GroEL and LPS caused an upregulation in Hsp70 release from PBMCs and GCT osteoblast like cells, and Hsp70 was found to stimulate Hsp60 release from PBMCs and GCT cells. These responses of Hsp release were used to form a theory of a cascade-like danger signal that may occur when cells are exposed to bacterial infection and which would result in activation of antigen presenting cells via previously identified receptors for Hsps such as CD14/TLR4 or by unidentified pathways. The elevated release of Hsps in response to GroEL and LPS was also identified as a mechanism that could stimulate bone loss during infection or autoimmuniry by affecting the RANKL/OPG system. hi conclusion, Hsp60 and Hsp70 can be released from immune cells under normal conditions, and from both immune and osteoblast-like cells following stimulation with LPS and other Hsps. The observed release responses provide a mechanism through which Hsps can act as danger signals to the innate immune system, and also as promoters of bone resorption via the RANKL/OPG system.

The heat shock response (HSR) is a highly conserved mechanism that enables organisms to survive environmental and pathophysiological stress. In Drosophila, the HSR is regulated by a single transcription factor, heat shock factor (HSF). During stress, HSF trimerizes and binds to over 200 loci on Drosophila polytene chromosomes with only nine mapping to major heat shock (HS) inducible gene loci. The function of HSF binding to the other sites in the genome is currently unknown. Some of these sites may contain yet unidentified “minor” HS genes. Interestingly, the binding of HSF also coincides with puff regression at some sites. Two such sites contain the major developmentally regulated genes Eip74 and Eip75: key regulators in the response to 20-hydroxyecdysone (20E), the main hormone responsible for the temporal co-ordination of post-embryonic development in Drosophila. Previous work in our and other labs indicates that the regression of non-HS puffs during the HSR is dependent on the presence of functional HSF. Using chromatin immunoprecipitation (ChIP) followed by hybridization to genome tiling arrays (Chip), I have identified 434 regions in the Drosophila Kc cell genome that are bound by HSF during HS, and have determined that 57% of these sites are located within the transcribed regions of genes. By examining the transcriptional response to HS in Kc cells and third instar larvae using expression microarrays, I found that only about 10% of all genes within 1250 bp of an HSF binding site are transcriptionally regulated by HS and many genes whose transcript levels change during HS do not appear to be near an HSF binding site. Furthermore, genes with an HSF binding site within their introns are significantly enriched (modified Fisher Exact p-value between 2.0x10-3 and 1.5x10-6) in gene ontology terms related to developmental processes and reproduction. Using expression microarray technology, I characterized the transcriptional response to 20E and its structural analog ponasterone A. I have identified multiple HSF binding sites within Eip74 and Eip75, and show that induction of the HSR correlates with repression of these genes and all other 20E-inducible genes. Taken together, this work provides a basis for further investigation into the role of HSF binding to sites not associated with HS genes and its possible function as a repressor of gene transcription during conditions of stress and as a regulator of developmental genes under stress and non-stress conditions.

Hsp104 and ClpB are hexameric ATPases that resolubilize aggregated proteins in collaboration with the Hsp70 chaperone system. Hsp104/ClpB functionally interact only with their respective Hsp70 system and this specificity is mapped to the Hsp104/ClpB coiled-coil domain (CCD). We hypothesize that the interaction between Hsp70 and Hsp104/ClpB CCD stimulates nucleotide exchange and release of substrate from Hsp70. In the current study, the CCDs of E. coli ClpB and S. cerevisiae Hsp104 have been purified. Isolated domains are monomeric and well folded. They inhibit refolding of aggregated firefly luciferase in a species-specific manner. We found that the ATPase activity of E. coli DnaK is stimulated at low concentrations of the E. coli ClpB CCD but not by yeast Hsp104 CCD. However, in another bacterial system (Thermus thermophilus) we found that the ClpB CCD inhibits The ATPase activity of DnaK suggesting that the interaction may have different consequences in distinct chaperone networks.