Phosphoinositide-dependent protein kinase-1 (PDK1) plays an integral role in signaling cellular growth and proliferation, one that's dependent on its ability to autophosphorylate Ser-241 in its T-loop. This process appears to have a strict requirement for its C-terminal pleckstrin homology (PH) domain. Thus, the overall objective of this work was to determine the mechanism by which the PH domain induces an active kinase conformation in unphosphorylated PDK1, capable of Ser-241 autophosphorylation. First, computational modeling and protein cross linking studies were combined with site-directed mutagenesis and kinetic assays in order to provide initial assessment of how the PH domain scaffolds Ser-241 autophosphorylation. A significant number of contacts were identified between the enigmatic "N-bud" region of the PH domain and the kinase domain. Specifically, these studies implicated Glu-432 and Glu-453 of the N-bud region of the PH domain that bind and serve as mimics of the phosphorylated Ser-241 in the T-loop and the phosphorylated C-terminal tail of PDK1 substrates, respectively. Next, a novel method for protein trans-splicing of the regulatory and catalytic kinase domains of PDK1 was developed. The method utilizes the N- and C-terminal split inteins of the gene dnaE from Nostoc punctiforme [(N)NpuDnaE] and Synechocystis sp. strain PCC6803 [(C)SspDnaE], respectively. The cross-reacting KINASE(AEY)-(N)NpuDnaE-His6 and GST-His6-(C)SspDnaE-(CMN)PH fusion constructs generated full length spliced-PDK1 with kobs = (2.8 +- 0.3) x 10-5 s-1. Finally, NMR was used to further characterize the structural and dynamical properties of the PH domain in both its isolated form and in full length PDK1. Whereas, it was not possible to obtain chemical shift assignments of any backbone or side chain nuclear resonances, methods were optimized for 2H,13C,15N-isotopic labeling of the recombinant PH domain. Furthermore, the protein trans-splicing method was significantly improved and utilized for segmental isotopic labeling of the PH domain in full length PDK1. These new findings and developments may provide specific insight and technological improvements towards future studies aimed to better understand and target autoinhibited conformations of PDK1 for translational purposes.

Plusieurs études ont démontré que les agonistes du PPARgamma, dont la pioglitazone (PGZ), améliorent les paramètres métaboliques et histologiques de la stéatohépatite non-alcoolique (NASH) chez l'homme et la souris, et qu’ils ont des effets bénéfiques sur la fibrose hépatique chez le rat. Les mécanismes d’action sont mal connus. La NASH, caractérisée par de la stéatose, des lésions hépatocytaires, de l’inflammation et une fibrose variable, est considérée comme une complication hépatique du syndrome métabolique. L'obésité, un des facteurs de risque pour le développement de la NASH, est caractérisée par de faibles taux d'adiponectine sérique. Cette adipocytokine, dont l'expression génique est régulée par le PPARgamma, possède des propriétés anti-stéatosique et anti-fibrotique chez la souris. L'activité intracellulaire de l'adiponectine est médiée via ses récepteurs spécifiques qui activent la protéine kinase AMPK et/ou le PPARalpha. Une fois activée, l’AMPK induit les voies cataboliques de production d’énergie (telles que l'oxydation des acide gras) et inhibe les voies consommant de l’ATP (telles que la lipogenèse). L'activation du PPARalpha augmente l'oxydation des acides gras et inhibe la réponse inflammatoire. Le but de notre travail est d’évaluer l'implication de la voie PGZ–adiponectine–AMPK et/ou PPARalpha dans la prévention de la NASH et de la fibrose hépatique. Nous avons tout d’abord évalué l'effet de la PGZ sur la fibrose hépatique chez la souris. Nos observations montrent que, contrairement aux résultats observés chez le rat, la PGZ n’inhibe pas le développement de la fibrose hépatique chez la souris in vivo. Ces résultats ont été confirmés par des études sur les cellules stellaires hépatiques (HSCs), les cellules effectrices de la fibrose, in vitro. Dans une seconde étude, nous avons évalué l'impact de l’AMPK sur la fibrose hépatique in vivo et sur l’activation des HSCs in vitro. Nous avons constaté que l’AMPK jouait un rôle dans le contrôle de la trans-différentiation des HSCs in vitro mais pas dans le développement de la fibrose hépatique chez la souris in vivo. Finalement, nous avons évalué l'hypothèse que l'effet bénéfique de la PGZ sur la NASH résulte de la stimulation de l'AMPK et/ou du PPARalpha par l’adiponectine. Nos résultats ont montrés que cet effet de la PGZ était strictement dépendant de l’adiponectine mais ne semblait pas impliquer l'AMPK ni le PPARalpha. Nous avons également identifié SREBP-1c, régulant la lipogenèse de novo, comme cible thérapeutique potentielle pour le développement de la NASH. Les résultats obtenus dans le cadre de ce travail de thèse fournissent une meilleure compréhension de l’axe PPARgamma–adiponectine–AMPK dans le contrôle du développement de la NASH et de la fibrose hépatique chez la souris. / Several studies have demonstrated that peroxisome proliferator-activated receptor gamma (PPARg) agonists, such as pioglitazone (PGZ), improve metabolic parameters and histology of nonalcoholic steatohepatitis (NASH) development in humans and mice, and have beneficial effects on liver fibrosis in rats. NASH, characterized by steatosis, hepatocellular damage, inflammation and variable fibrosis, is recognised as the hepatic complication of the metabolic syndrome. Obesity, one of the risk factors for NASH development, is characterized by low serum adiponectin levels. This adipocytokine, of which gene expression is regulated by PPARg, demonstrates anti-steatotic and anti-fibrotic properties in mice. Intracellular activity of adiponectin is mediated through its specific receptors which activate AMP-activated protein kinase (AMPK) and PPARalpha. Once activated, AMPK switches on catabolic pathways (such as fatty acid oxidation and glycolysis) and switches off ATP-consuming pathways (such as lipogenesis). Activation of PPARalpha increases fatty acid oxidation and reduces inflammatory reaction. The aim of the present work is to analyse the activation of the axis PGZ-adiponectin-AMPK and/or PPARalpha as a way to control NASH and hepatic fibrosis development. We first evaluated the effect of PGZ on hepatic fibrosis in mice. We observed that, by contrast with results in rats, PGZ did not prevent hepatic fibrosis development in vivo in mice. These results were confirmed by in vitro studies on the key effector cells of fibrogenesis, the hepatic stellate cells (HSCs). We then assessed the impact of AMPK on hepatic fibrosis in vivo and on HSC trans-differentiation/activation phenomenon in vitro. We found that AMPK played a role in the control of HSC trans-differentiation in vitro but was not implicated in the wound-healing fibrosis in vivo in mice. Finally, we tested the hypothesis that the beneficial effect of PGZ on steatohepatitis results from the adiponectin-dependent stimulation of AMPK and/or PPARalpha. We found that this preventive effect was clearly dependent of adiponectin but did not involve AMPK or PPARalpha activation. We have also identified SREBP-1c, implicated in the regulation of de novo lipogenesis, as a potential therapeutic target for the control of the development of NASH. The present thesis provides a better understanding of the axis PPARg–adiponectin–AMPK in the control of NASH and hepatic fibrosis development in mouse.

Ribosomes stalled on problematic mRNAs can be rescued by a mechanism called trans-translation. This mechanism employs a dual transfer-messenger RNA molecule (tmRNA) together with a helper protein (SmpB). In this work we have used an in vitro translation system with pure components to further clarify the roles of tmRNA and SmpB in trans-translation. We found that SmpB binds ribosomes in vivo and in vitro independently of tmRNA presence and is essential for tmRNA binding and trans-peptidation. We show that two SmpB molecules can bind per ribosome, that SmpB does not leave the ribosome after trans-peptidation and that SmpB pre-bound to the ribosome can trigger trans-translation. We demonstrated that the rate of trans-transfer of a peptide from the P-site tRNA to Ala-tmRNA and the efficiency by which Ala-tmRNA competes with peptide release factors decrease with increasing the mRNA length downstream from the P site of the ribosome. We showed that trans-translation is strongly stimulated by RelE cleavage of A-site mRNA. We concluded that tmRNA action in vivo must always be preceded by mRNA truncation. We showed that rapid release of truncated mRNAs from the ribosome requires translocation of the peptidyl-tmRNA into the ribosomal P site, which is strictly EF-G dependent. mRNA release is slowed down by strong Shine and Dalgarno like sequences upstream the A site and by long 3’-extensions downstream from the P-site codon. Footprinting was used to monitor SmpB binding to tmRNA, ribosomes and subunits and to study tmRNA interactions with the ribosome at distinct trans-translation stages. We confirmed that two SmpB molecules bind per ribosome and interact with nucleotides below the L7/L12-stalk on the 50S subunit and near the subunit interface on the 30S. We showed that tmRNA is mostly in complex with SmpB in vivo and during trans-translation. Specific cleavage patterns of tmRNA were observed at different stages of trans-translation, but the overall tmRNA conformation seems to be maintained during the whole process.

Biogeographers have long searched for common processes responsible for driving diversification in the Holarctic region. Although terrestrial flora and fauna have been well studied, much of the marine biogeographic work addresses patterns and processes occurring over a relatively recent timescale. A prerequisite to comparative biogeographic analysis requires well-resolved phylogenies of similarly distributed taxa that diverged over a similar timeframe. The overall aim of my Ph.D. thesis was to address fundamental questions in the systematics and biogeography of a family of Holarctic fish (Osmeridae) and place these results in a broad comparative biogeographic framework. With eight conflicting morphological hypotheses, the northern hemisphere smelts have long been the subjects of systematic disagreement. In addition to the uncertainty in the interrelationships within this family, the relationship of the Osmeridae to several other families remains unclear. Using DNA sequence data from three mitochondrial and three nuclear genes from multiple individuals per species, I reconstructed the phylogenetic relationships among the 6 genera and 15 osmerid species. Phylogenetic reconstruction and divergence dating yielded a well-resolved phylogeny of the osmerid genera and revealed several interesting evolutionary patterns within the family: (1) Hypomesus chishimaensis and H. nipponensis individuals are not reciprocally monophyletic, suggesting that they are conspecific and H. chishimaensis is a recently evolved freshwater ecotype that invaded the Kuril Islands following the last glaciation, (2) The trans-Pacific sister relationships in Hypomesus based on lateral line scale counts are not supported, implying that this phenotype evolved in parallel on each side of the North Pacific Ocean, (3) The Plecoglossidae are the Osmeridae sister group, (4) Over half of the characters from previous studies show evidence of parallel evolution; however, 27 traits reflect ancestral relationships, (5) Multiple divergences within the Osmeridae date to both the mid-Miocene cooling period and the Pliocene Bering Seaway opening, suggesting these events were important in the evolution of these fishes, and (6) Divergences in many marine taxa for which dated phylogenies are available are also correlated with these time periods. Future research should target additional Holarctic marine taxa for further comparative analysis.

This thesis aims to analyze the Turkish policy of being an energy hub. Within this context Turkey, as it is geographically very close to the two thirds of the world&#039 / s proven oil and natural gas reserves, has a very big advantage to manage its location and the purpose of this study is to discuss the measures taken to utilize this advantage. Therefore relative weakness of Turkey in comparison to the other actors like Russia, the USA or the EU and the strengths of the Turkish policy like the geopolitical advantage, the ethnic link between Turkey and the newly independent states of the Caspian and the already existing infrastructure for the transportation of oil and natural gas like Kirkuk-Yumurtalik Pipeline, Baku Tblisi Ceyhan Oil Pipeline, Ceyhan Terminal, and Baku Tblisi Erzurum Natural Gas Pipeline are discussed. With this respect, this study argues that, as a result of the existing and planned projects, Ceyhan&#039 / s claim to become a hub is a realistic objective and in addition to BTC and Kirkuk-Yumurtalik Pipeline, the realization of Samsun-Ceyhan Pipeline will increase Ceyhan&#039 / s potential as an energy hub.

Over the past four decades, obesity in the United States has risen to record levels. Co-morbid conditions such as heart disease, diabetes, and stroke will impose over twenty trillion dollars of economic burden over the next two decades. More than half that sum will be direct medical expenses. Under current entitlement programs, governments, and ultimately taxpayers, will be responsible for about 43 percent of that. Even with all this spending, millions of lives will be cut short. Dietary factors are largely to blame. This thesis explores how policy interventions to encourage healthy diet and discourage healthy diet can be projected to affect future healthcare spending. It assesses six dietary factors to determine whether there is sufficient research to determine how much economic disease burden they will impose. Among those for which such research exists, the thesis estimates the cost-effectiveness of interventions such as education, subsidies, taxes and legislative bans.

During inflation quantum fluctuations of the field driving inflation, known as inflaton, were stretched by inflationary expansion to galactic size scales or even larger. A possible implication of inflation -- if it is correct -- is that our observable universe was once of sub-Planckian size. Thus inflation could act as a magnifier to probe the short distance structure of space-time. General arguments about the quantum theory of gravity suggest that the short distance structure of space-time can be modeled as arising from some corrections to the well-known uncertainty relation between the position and momentum operators. Such modifications have been predicted by more fundamental theories such as string theory. This modified commutation relation has been implemented at the first quantized level to the theory of cosmological perturbations. In this thesis, we will show that the aforementioned scenario of implementing the minimal length to the action has an ambiguity: total time derivatives that in continuous space-time could be neglected and do not contribute to the equations of motion, cease to remain total time derivatives as we implement minimal length. Such an ambiguity opens up the possibility for trans-Planckian physics to leave an imprint on the ratio of tensor to scalar fluctuations. In near de-Sitter space, we obtain the explicit dependence of the tensor/scalar on the minimal length. Also the first consistency relation is examined in a power-law background, where it is found that despite the ambiguity that exists in choosing the action, Planck scale physics modifies the consistency relation considerably as it leads to large oscillations in the scalar spectral index in the observable range of scales. In the second part of the thesis, I demonstrate how the assumption of existence of invariant minimal length can assist us to explain the origin of cosmic magnetic fields. The third part of the thesis is dedicated to the study of signatures of M-theory Cascade inflation.

During inflation quantum fluctuations of the field driving inflation, known as inflaton, were stretched by inflationary expansion to galactic size scales or even larger. A possible implication of inflation -- if it is correct -- is that our observable universe was once of sub-Planckian size. Thus inflation could act as a magnifier to probe the short distance structure of space-time. General arguments about the quantum theory of gravity suggest that the short distance structure of space-time can be modeled as arising from some corrections to the well-known uncertainty relation between the position and momentum operators. Such modifications have been predicted by more fundamental theories such as string theory. This modified commutation relation has been implemented at the first quantized level to the theory of cosmological perturbations. In this thesis, we will show that the aforementioned scenario of implementing the minimal length to the action has an ambiguity: total time derivatives that in continuous space-time could be neglected and do not contribute to the equations of motion, cease to remain total time derivatives as we implement minimal length. Such an ambiguity opens up the possibility for trans-Planckian physics to leave an imprint on the ratio of tensor to scalar fluctuations. In near de-Sitter space, we obtain the explicit dependence of the tensor/scalar on the minimal length. Also the first consistency relation is examined in a power-law background, where it is found that despite the ambiguity that exists in choosing the action, Planck scale physics modifies the consistency relation considerably as it leads to large oscillations in the scalar spectral index in the observable range of scales. In the second part of the thesis, I demonstrate how the assumption of existence of invariant minimal length can assist us to explain the origin of cosmic magnetic fields. The third part of the thesis is dedicated to the study of signatures of M-theory Cascade inflation.

Two experimental seismic surveys were collected in the 1991 LITHOPROBE Trans-Hudson Orogen (THO) data acquisition program. The purpose of the coincident dynamite and vibroseis reflection surveys was to compare crustal images obtained using high-fold low-energy and low-fold high-energy sources. On single-fold field records, signal amplitudes from explosive sources are consistently 50 dB higher than on the corresponding vibroseis records. The vibroseis final stack exhibits better defined upper-crustal reflectivity due primarily to the higher fold. However, at lower-crustal and Moho levels, the dynamite data provides images which are equal or superior to those obtained from the vibroseis data. The dynamite source not only allowed deeper signal penetration but also succeeded in mapping of a number of subcrustal reflections not identified in previous vibroseis data. These new seismic images indicate that the crustal root is not simple depression on the upper-mantle as was inferred initially but a broad (3 s) zone of reflectivity that dips west and extends more than 10 km below the younger regional Moho. Moreover, the dynamite data also indicates that diffraction patterns, detected at lower crustal and Moho depths, have large apertures which permitted proper migration of these lower crustal events. Four vibroseis expanding spread profiles (ESP) were also acquired during the data acquisition program to obtain more detailed and accurate velocity structure. These profiles, with a maximum offset of 18 km, were centered on areas where prominent crustal reflectivity was detected by the regional vibroseis survey. The small source stepout distance (100 m) generated high-fold ($>$30) data. Extensive modeling was carried out to estimate the offset range within which each traveltime approximation and velocity analysis technique may be implemented. The results reveal that velocity estimation becomes more robust and accurate when crustal seismic surveys utilize longer offsets than commonly used. These larger source-receiver separations, however, must be generally limited to offset/depth ratios not exceeding 1.5 when conventional velocity analysis techniques, based on the hyperbolic moveout assumptions, are implemented. Besides the semblance method two velocity estimators adapted to crustal studies, namely the covariance and the $\tau$ - p techniques, were tried. The former yielded the highest resolution followed by the semblance and the $\tau$ - p methods. Resolution of the semblance estimator for a maximum offset of 36 km is equal to that of the covariance method with a corresponding offset of 18 km for mid-crustal reflectors. The advantages provided by the long-offset data acquisition include increased S/N ratio and a greater number of traces with sufficiently large moveouts whichimproved velocity resolution, especially below mid-crustal depths. To achieve similar advantages in a regional crustal reflection survey would require the adoption of longer spread lengths than those presently implemented in standard data acquisition procedures.

Recently, with advances in CMOS process, the RF receiver which is integrated into the SOC chip can effectively reduce production costs. When designing the wireless receiver, one of the most important technologies is to design channel-selection filter. Typically, the design of the channel-selection filter in multi-standard high-frequency will take up a large chip area and higher power consumption. Therefore, in order to reduce the area and power consumption, this thesis designed a low-power OTA and low-pass filter. This thesis presents a multi-mode wireless communication application in the receiver channel selection filter. This filter is designed to use the fifth-order Butterworth low pass filter, the filter range can be used in Bluetooth, cdma2000, wideband CDMA, and IEEE 802.11a/b/g/n wireless LAN. Using floating transistor architecture in the input stage of OTA can effectively increase the THD performance. Using MOS transistors operating in triode region and combined with current multiplier can achieve the voltage-to-current conversion. Using the trans-linear loop can reach a wide tunable range, and the OTA operating in weak inversion region can significantly reduce the transconductance. Implementation is to use the TSMC 0.18£gm CMOS process. Simulation results show that the successful operation of this filter can be between 650 kHz ~ 22MHz frequency range. The filter may have compatibility in different wireless communication applications. 14.5mW to 17.5mW, respectively, is the smallest to the largest power consumption. The supply voltage is 1.2 volts.