New and innovative technologies to improve the techniques that are already being used are constantly developing. This project was about evaluating if containers could be something for the IT company Tieto to use on their products in telecommunications. Container are portable, standalone, executable lightweight packages of software that also contains all it needs to run the software. Containers are a very hot topic right now and are a fast-growing technology. Tieto wanted an investigation of the technology and it would be carried out with certain requirements where the main requirement was to have a working and executable protocol stack in a container environment. In the investigation, a proof of concept was developed, proof of concept is a realization of a certain method or idea in order to demonstrate its feasibility. The proof of concept led to Tieto wanting additional experiments carried out on containers. The experiments investigated if equal performance could be achieved with containers compared to the method with virtual machine used by Tieto today. The experiment observed a small performance reduction of efficiency, but it also showed benefits such as higher flexibility. Further development of the container method could provide a just as good and equitable solution. The project can therefore be seen as successful whereas the proof of concept developed, and experiments carried out both points to that this new technology will be part of Tieto's product development in the future.

Nano-sized materials are being used to address some of humanities greatest challenges— cancer therapy, food and water security, and environmental remediation. While extremely promising for these applications, the production, use, and disposal of nanomaterials have resulted in their release into environmental compartments. One major concern of any novel contaminant is how it interacts with bacteria. Bacteria play essential roles in human health, engineered systems, and ecological functioning. Bacteria are capable of macro-scale influence because they have evolved communication systems that enable coordinated behaviors. Communication among cells involves chemical signals that enter the environment, where they are subjected to its biogeochemistry, which now includes novel nanomaterials. The overall goal of this thesis was to improve understanding of the relationship between nanoparticles and cell-to-cell signaling behavior in bacteria focusing on two population-level behaviors: autolysis and quorum sensing. Specifically, this project sought to: (1) improve our understanding of how metal-oxide nanoparticles affect the autolytic process in Bacillus subtilis, by elucidating the biological response of the interactions between titanium dioxide nanoparticles and biomolecules; (2) reveal the interactions between quorum sensing signaling molecules and metal cations commonly used in antimicrobial nanomaterials, silver and copper; and (3) demonstrate the potential of quorum sensing-regulated cyanide production to affect oxidation and dissolution of gold nanoparticles in an environmentally relevant system. By addressing these objectives, the work demonstrated that: 1. TiO2 nanoparticles disrupt the autolytic process by delaying the onset of autolysis, and intercepting released autolytic enzymes, preventing the enzymes from degrading peptidoglycan in neighboring cells. 2. Quorum sensing signaling molecules form complexes with Ag+ and Cu2+, removing the most bioavailable form (free HHL, Ag+, and Cu2+) from the cells’ environment. 3. Quorum sensing-regulated cyanide production induces oxidative dissolution in Au nanoparticles, which were previously assumed to be inert in environmental systems. Taken together, this body of work highlights the relationship between nanoparticles and population-level behavior in bacteria. The presence of nanoparticles can have significant effects on population-level behaviors, and the activity of population-level behaviors can have significant effects on nanoparticles behavior. This inter-connected relationship, where the nanoparticles are both acted on and act upon their environment, must be considered in nanoparticle-based studies and applications.

abstract: Given the process of tumorigenesis, biological signaling pathways have become of interest in the field of oncology. Many of the regulatory mechanisms that are altered in cancer are directly related to signal transduction and cellular communication. Thus, identifying signaling pathways that have become deregulated may provide useful information to better understanding altered regulatory mechanisms within cancer. Many methods that have been created to measure the distinct activity of signaling pathways have relied strictly upon transcription profiles. With advancements in comparative genomic hybridization techniques, copy number data has become extremely useful in providing valuable information pertaining to the genomic landscape of cancer. The purpose of this thesis is to develop a methodology that incorporates both gene expression and copy number data to identify signaling pathways that have become deregulated in cancer. The central idea is that copy number data may significantly assist in identifying signaling pathway deregulation by justifying the aberrant activity being measured in gene expression profiles. This method was then applied to four different subtypes of breast cancer resulting in the identification of signaling pathways associated with distinct functionalities for each of the breast cancer subtypes. / Dissertation/Thesis / M.S. Computer Science 2011

L’autophagie est un processus d’autodigestion qui se produit dans toutes les cellules eucaryotes et conduit à la dégradation d’éléments du cytoplasme (organites, macromolécules) par le lysosome. Elle peut se produire au hasard dans le cytoplasme où elle peut être sélective, par exemple d’un organite intracellulaire. Lorsque les mitochondries sont sélectivement dégradées par autophagie, on parle de mitophagie. L’autophagie et la mitophagie sont impliquées dans diverses pathologies comme les maladies neurodégénératives et le cancer car leur dérégulation peut grandement perturber l’homéostasie cellulaire.Mon projet de thèse porte sur le rôle de la protéine co-chaperonne BAG6 dans la régulation de la mitophagie.BAG6 est une protéine de 150 kDa, également appelée BAT3 ou Scythe, dont la fonction majeure réside dans le contrôle qualité du cytoplasme mais BAG6 est également impliquée dans l’immunité, l’apoptose ou l’autophagie. Nous montrons que son mécanisme d’action passe, tout d’abord, par la régulation de la morphologie mitochondriale en induisant la fission des mitochondries. Ensuite, la protéine BAG6 induit la mitophagie : les protéines impliquées dans la mitophagie (PINK1 et PARKIN) s’accumulent à la mitochondrie alors que les protéines de la mitochondrie (TOM20, TFAM et TIM23) voient leur expression diminuée. BAG6 diminue également la masse mitochondriale par un mécanisme dépendant de l’autophagie. L’analyse de la séquence de BAG6 montre qu’elle est composée de nombreux domaines protéiques incluant les domaines UBL et deux domaines LIR (LC3-Interacting Region) et nous avons montré que BAG6 interagit avec LC3 grâce à son domaine LIR2. Ces caractéristiques identifient la protéine BAG6 comme un nouveau récepteur potentiel de la mitophagie. / Autophagy, literally meaning self-eating, is a highly evolutionary conserved process in eukaryotes where elements of the cytoplasm (organelles, macromolecules) are degraded by lysosomes. Autophagy can occur randomly in the cytoplasm or can be selective of a specific organelle. Among other, the specific degradation of mitochondria is called mitophagy. Autophagy and mitophagy have been implicated in several physiopathologies such as neurodegenerative diseases or cancer. Deregulations of autophagy/mitophagy may profoundly affect homeostasis.The aim of my thesis is to characterize the role of the co-chaperonne protein BAG6 in the regulation of mitophagy.BAG6 is a 150kDa protein, also known as BAT3 or Scythe, which functions in the quality control of the cytoplasm. Moreover BAG6 is also involved in immunity, apoptosis or autophagy. Our work showed that it is implicated in the regulation of mitochondrial morphology by inducing mitochondrial fission. Also, BAG6 induces mitophagy: in presence of BAG6, mitophagy markers such as PINK1 and PARKIN are more localized at the mitochondria whereas the expression of mitochondrial specific protein’s (TOM20, TFAM and TIM23) decreases. After its sequence analysis, we discovered that BAG6 is composed of many domains such as the UBL domains and two LIR domains (LC3- Interacting Region) and that BAG6 interacts with LC3 through its LIR2 domain. These features lead to identify BAG6 as a new potential receptor of mitophagy.

Our laboratory has identified two secreted proteins, Wnt7a and Sonic hedgehog (Shh), that regulate satellite cell (SC) fate, during muscle differentiation. While Wnt7a stimulates symmetric SC division through the planar cell polarity (PCP) pathway, Shh activates Myf5 expression in the committed SC following asymmetric division through cilia-mediated Hedgehog (Hh) signaling. Crosstalk between these pathways has been well characterized during development, and is likely to be conserved in muscle regeneration. Indeed, accumulating evidence suggests the PCP pathway influences primary cilia formation, an organelle required for proper Hh signal transduction. Here we show that Wnt7a treatment in primary myoblasts increases the presence of primary cilia. Additionally, using myofiber culture, we demonstrate that Wnt7a increases myogenin (MyoG) expression. Removal of primary cilia through a small interfering RNA (siRNA) targeted towards IFT88 impedes Wnt7a mediated MyoG expression, suggesting crosstalk between the PCP and Hh pathways facilitates muscle differentiation. Furthermore, through siRNA knockdown we have identified the downstream PCP effectors, Inturned and Fuzzy as the main candidates responsible for this crosstalk. Knockdown of either Inturned or Fuzzy impedes Wnt7a-mediated MyoG expression. Taken together our data demonstrates crosstalk between the PCP pathway and Hh signaling regulates the differentiation of SCs.

Substantial research has examined how linguistic structures are realized in the visual/spatial modality. However, we know less about linguistic pragmatics in signed languages, particularly the functioning of referring expressions (REs). Recent research has explored how REs are deployed in signed languages, but much remains to be learned. Study 1 explores the inventory and workings of REs in American Sign Language by seeking to replicate and build upon Frederiksen & Mayberry (2016). Following Ariel, F&M propose an inventory of REs in ASL ranked according to the typical accessibility of the referents each RE type signals. Study 1 reproduced their results using more complex narratives and including a wider range of REs in various syntactic roles. Using Toole’s (1997) accessibility rating protocol, we calculated average accessibility ratings for each RE type, thus making possible statistical analyses that show more precisely which REs differ significantly in average accessibility. Further, several RE types that F&M had collapsed are shown to be distinct. Finally, we find general similarities between allocations of REs in ASL and in spoken English, based on 6 matched narratives produced by native English speakers. Study 2 explores a previously unexamined set of questions about concurrently occurring REs: collections of REs produced simultaneously. It compares isolated REs that occur in a linear fashion, similar to spoken language grammars, with co-occurring REs, signaling multiple referents simultaneously (termed here constellations). This study asks whether REs in constellations have pragmatic properties different from those of isolated/linear REs. Statistical evidence is presented that some categories of REs do differ significantly in the average accessibility values of their referents, when compared across linear versus concurrent configurations. Study 3 examines whether the proportions of various RE categories used by native ASL signers vary according to the recipient’s familiarity with the narrative. Do ASL narratives designed to be maximally explicit because of low recipient familiarity demonstrate distinct RE allocations? In this sample of 34 narratives, there is no statistically significant difference in RE use attributable to recipient familiarity. These findings have important implications for understanding the impact of modality on accessibility, the use of REs in ASL, and visual processing.

abstract: Postnatal skeletal muscle repair is dependent on the tight regulation of an adult stem cell population known as satellite cells. In response to injury, these quiescent cells are activated, proliferate and express skeletal muscle-specific genes. The majority of satellite cells will fuse to damaged fibers or form new muscle fibers, while a subset will return to a quiescent state, where they are available for future rounds of repair. Robust muscle repair is dependent on the signals that regulate the mutually exclusive decisions of differentiation and self-renewal. A likely candidate for regulating this process is NUMB, an inhibitor of Notch signaling pathway that has been shown to asymmetrically localize in daughter cells undergoing cell fate decisions. In order to study the role of this protein in muscle repair, an inducible knockout of Numb was made in mice. Numb deficient muscle had a defective repair response to acute induced damage as characterized by smaller myofibers, increased collagen deposition and infiltration of fibrotic cells. Satellite cells isolated from Numb-deficient mice show decreased proliferation rates. Subsequent analyses of gene expression demonstrated that these cells had an aberrantly up-regulated Myostatin (Mstn), an inhibitor of myoblast proliferation. Further, this defect could be rescued with Mstn specific siRNAs. These data indicate that NUMB is necessary for postnatal muscle repair and early proliferative expansion of satellite cells. We used an evolutionary compatible to examine processes controlling satellite cell fate decisions, primary satellite cell lines were generated from Anolis carolinensis. This green anole lizard is evolutionarily the closet animal to mammals that forms de novo muscle tissue while undergoing tail regeneration. The mechanism of regeneration in anoles and the sources of stem cells for skeletal muscle, cartilage and nerves are poorly understood. Thus, satellite cells were isolated from A. carolinensis and analyzed for their plasticity. Anole satellite cells show increased plasticity as compared to mouse as determined by expression of key markers specific for bone and cartilage without administration of exogenous morphogens. These novel data suggest that satellite cells might contribute to more than muscle in tail regeneration of A. carolinensis. / Dissertation/Thesis / Ph.D. Molecular and Cellular Biology 2012

Adipokinetic hormones (AKHs) are neuropeptides from the arthropod AKH/RPCH (adipokinetic hormone/ red pigment concentrating hormone) family. The typical AKH is an octa-, nona- or decamer that is synthesized, stored and released by the neurosecretory cells of the corpora cardiaca (CC) connected to the brain and primarily involved in the mobilization of energy reserves from the fat body in insects. In addition to its well established role in energy metabolism, AKH has also been implicated to be involved in stress responses specifically to oxidative stress. Oxidative stress induced elevation of AKH levels as well as a modulation of biomarkers of oxidative damage following exogenous application of AKH have been demonstrated. However, the discrete steps involved in the mode of action of AKH in triggering an anti-oxidative response is far from clear. Given the role of AKH as a neuroendocrine factor that mediates a response to oxidative stress, the mode of action of AKH at the sub-cellular level was investigated. Using isolated central nervous system (brain) as an in vitro model, we establish that AKH can potentiate an anti-oxidative response to oxidative stress. Further, we also demonstrate that AKH uses a conserved signal transduction mechanism involving both protein kinase C (PKC) and cyclic adenosine monophosphate (cAMP) and by mobilizing both intra as well as extra-cellular Ca2+ stores to elaborate its anti-oxidative response. Finally, using the genetically tractable fruit fly Drosophila melanogaster, we demonstrate through RNAi mediated knockdown of AKH synthesis as well as overexpression of AKH using the GAL4/UAS system, that the fork-head box transcription factor (dFoXO) might function downstream of AKH signaling in its stress responsive role. These results implicate AKH as a stress hormone while offering possibilities to further identify specific regulatory mechanisms and downstream effector molecules. Since stress signaling pathways are conserved, insights obtained from such studies on insects will offer some unique avenues for understanding stress responses and related pathologies in vertebrates including humans.

Base Teórica O sistema purinérgico é um sistema de sinalização extracelular que influencia processos fisiológicos e patológicos. O exercício físico promove adaptações moleculares e teciduais sendo sugerido como uma conduta terapêutica em algumas patologias crônicas. Dados apontam uma possível influência do exercício físico sobre o sistema purinérgico, no entanto as bases bioquímicas desse processo ainda não estão muito bem compreendida. Objetivos Analisar a hidrólise extracelular dos nucleotídeos da adenina e quantificar os níveis dos nucleotídeos, nucleosídeos e resíduos metabólicos no soro sanguíneo de indivíduos adultos sedentários do sexo masculinos submetidos a uma sessão aguda de exercício aeróbico moderado. Métodos Indivíduos adultos sedentários do sexo masculino, sem patologia prévia, foram selecionados de acordo com critérios clínicos pré-definidos. Os sujeitos foram avaliados, responderam ao questionário PAR-Q (Instrumental Physical Activity Questionaire) e submetidos a um teste do consumo máximo de oxigênio. Sete dias após a avaliação, os indivíduos realizaram 30 minutos de exercício aeróbico moderado. Amostras de sangue foram coletadas pré e pós-exercício. Ao fim da coleta, o soro sanguíneo foi separado e a atividade enzimática foi avaliada pela liberação de fosfato inorgânico (Pi). Os nucleotídeos da adenina, nucleosídeo e resíduos metabólicos foram quantificados por cromatografia líquida de alta performace (HPLC). Os níveis de creatina quinase (CK), creatinina (CR), colesterol total (CT), triglicerídeos (TG), lipoproteína de alta densidade (HDL) e lipoproteína baixa densidade (LDL) foram avaliados por meio de kits específicos conforme instruções do fabricante. Resultados A hidrólise da adenosina 5’-trifosfato (ATP), adenosina 5’-difosfato (ADP), adenosina 5’-monofosfato (AMP) e p-nitrofenil 5’-timinidina monofosfato (p-Nph-5’-TMP) se mostrou aumentada após a realização do exercício aeróbico agudo. O nível de ATP extracelular diminuiu após a realização da sessão de exercício. As concentrações de adenosina (ADO), inosina (INO) e ácido úrico apresentaram-se aumentadas. Conclusão Nossos resultados demonstram uma modificação no perfil da atividade ectonucleotidásica e nos níveis dos nucleotídeos da adenina, nucleosídeos e metabólitos do ATP após a realização do exercício aeróbico agudo em intensidade moderado no soro sanguíneo de indivíduos sedentários, sugerindo uma possível atuação do exercício físico como modulador da sinalização purinérgica. Mais estudos são necessários para melhor compreensão das ações do exercício físico na sinalização purinérgica, e de como ocorre está interação. / Background The purinergic system is an extracellular signaling system, which affect physiological and pathological processes. Physical exercise promotes molecular and tissue adaptations, being suggested as therapeutic approach in some chronic diseases. Data indicate a possible influence of exercise on purinergic system, however the biochemical basis are not well understood. Objectives Analyze extracellular hydrolysis of adenine nucleotides and quantify nucleotides, nucleosides and metabolic residues levels in blood serum of male sedentary individuals submitted an acute session of moderate aerobic exercise. Methods Male sedentary adults, without previous disease, were selected according predefined clinical criteria. Subjects were evalauated, answered to PAR-Q questionnaire (Instrumental Physical Activity Questionaire) and performed maximum intake oxygen test. Seven days after evaluation, individuals conducted 30 minutes of aerobic moderate exercise. Blood samples was collected pre and post exercise. At the end of collection, blood serum separated and enzymatic activity measured by inorganic phosphate (Pi) release. Adenine nucleotides, nucleoside and metabolics residue were quantified using high performance liquid chromatography (HPLC). Creatine kinase (CK), creatinine (CR), total cholesterol (TC), triglycerides (TG), high density lipoprotein (HDL) and low density lipoprotein (LDL) levels were evaluated by particular kit according manufacturer´s instructions. Results Adenosine 5’-triphosphate (ATP), adenosine 5’-diphosphate (ADP), adenosine 5’-monophosphate (AMP) and p-nitrophenyl 5’-thymidine monophosphate (p-Nph-5’-TMP) hydrolysis increased after acute session of aerobic exercise. ATP extracellular levels decreased after acute exercise. ADO, inosine (INO) and uric acid concentrations increased. Conclusion Our results demonstrate modifications in ectonucleotidasic activity profile and levels of adenine nucleotides, nucleoside and ATP metabolites after performing acute aerobic exercise of moderate intensity in blood serum of sedentary male individuals, suggesting a possibly modulation of purinergic signaling from exercise. Additional studies are necessary for better understanding physical exercise actions in purinergic signaling, and how these interactions occur.

The present study revealed that FOXO1 is present in the nuclei of non-dividing pituitary cells and in a subset of differentiated cells with highest level of expression in somatotrophs, followed by corticotrophs, thyrotrophs and gonadotrophs throughout development and in adulthood stage. A significant difference in Foxo1 transcript between age-matched males and females at 8-9 weeks of age was demonstrated in the anterior pituitary for the first time. IHC data demonstrating (i) FOXO1 co-localization with p27kip1 (ii) an increase in FOXO1 immunopositive cells within anterior pituitary in p27KO embryos compared to WT (iii) absence of FOXO1 in the nucleus of BrdU positive cells suggested that in absence of p27Kip1 FOXO1 might be important for preventing unbridled cell proliferation. Data suggested that FOXO1 might not be important for initiating pituitary cell differentiation but might be involved with p27kip1 in maintaining pituitary cell quiescence. Increase in nuclear localization of FOXO1 in the pituitary of Foxp3 mutant (lacking insulin signaling) suggested that it might be a down-stream target of insulin/PI3K/PKB pathway in the pituitary as it is in several other tissues.