Novel insights into the mechanisms of regulation of tyrosine kinase receptors by Ras Interference 1

Receptor-tyrosine kinases (RTKs) are membrane bound receptors characterized by their intrinsic kinase activity. RTK activities play an essential role in several human diseases, including cancer, diabetes and neurodegenerative diseases. RTK activities have been regulated by the expression or silencing of several genes as well as by the utilization of small molecules. Ras Interference 1 (Rin1) is a multifunctional protein that becomes associated with activated RTKs upon ligand stimulation. Rin1 plays a key role in receptor internalization and in signal transduction via activation of Rab5 and association with active form of Ras. This study has two main objectives: (1) It determines the role of Rin1 in the regulation of several RTKs focusing on insulin receptor. This was accomplished by studying the Rin1-insulin receptor interaction using a variety of biochemical and morphological assays. This study shows a novel interaction between the insulin receptor and Rin1 through the Vps9 domain. Two more RTKs (epidermal growth factor receptor and nerve growth factor receptor) also interacted with the SH2 domain of Rin1. The effect of the Rin1-RTK interaction on the activation of both Rab5 and Ras was also studied during receptor internalization and intracellular signaling. Finally, the role of Rin1 was examined in two differentiation processes (adipogenesis and neurogenesis). Rin1 showed a strong inhibitory effect on 3T3-L1 preadipocyte differentiation but it seems to show a modest effect in PC12 neurite outgrowth. These data indicate a selective function and specific interaction of Rin1 toward RTKs. (2) It examines the role of the small molecule Dehydroleucodine (DhL) on several key signaling molecules during adipogenesis. This was accomplished by studying the differentiation of 3T3-L1 preadipocytes exposed to different concentrations of DhL in different days of the adipocyte formation process. The results indicate that DhL selectively blocked adipocyte formation, as well as the expression of PPARγ, and C/EBP&agr;. However, DhL treatment did not affect Rin1 or Rab5 expression and their activities. Taken together, the data indicate a potential molecular mechanism by which proteins or small molecules regulate selective and specific RTK intracellular membrane trafficking and signaling during cell growth and differentiation in normal and pathological conditions.

Mechanisms governing the eyewall replacement cycle in numerical simulations of tropical cyclones

Eyewall replacement cycle (ERC) is frequently observed during the evolution of intensifying Tropical Cyclones (TCs). Although intensely studied in recent years, the underlying mechanisms of ERC are still poorly understood, and the forecast of ERC remains a great challenge. To advance our understanding of ERC and provide insights in improvement of numerical forecast of ERC, a series of numerical simulations is performed to investigate ERCs in TC-like vortices on a f-plane. The simulated ERCs possess key features similar to those observed in real TCs including the formation of a secondary tangential wind maximum associated with the outer eyewall. The Sawyer-Eliassen equation and tangential momentum budget analyses are performed to diagnose the mechanisms underlying the secondary eyewall formation (SEF) and ERC. Our diagnoses reveal crucial roles of outer rainband heating in governing the formation and development of the secondary tangential wind maximum and demonstrate that the outer rainband convection must reach a critical strength relative to the eyewall before SEF and the subsequent ERC can occur. A positive feedback among low-level convection, acceleration of tangential winds in the boundary layer, and surface evaporation that leads to the development of ERC and a mechanism for the demise of inner eyewall that involves interaction between the transverse circulations induced by eyewall and outer rainband convection are proposed. The tangential momentum budget indicates that the net tendency of tangential wind is a small residual resultant from a large cancellation between tendencies induced by the resolved and sub-grid scale (SGS) processes. The large SGS contribution to the tangential wind budget explains different characteristics of ERC shown in previous numerical studies and poses a great challenge for a timely correct forecast of ERC. The sensitivity experiments show that ERCs are strongly subjected to model physics, vortex radial structure and background wind. The impact of model physics on ERC can be well understood with the interaction among eyewall/outer rainband heating, radilal inflow in the boundary layer, surface layer turbulent processes, and shallow convection in the moat. However, further investigations are needed to fully understand the exhibited sensitivities of ERC to vortex radial structure and background wind.

Mechanisms of Arsenic Detoxification and Resistance

Arsenic is a ubiquitous environmental toxic substance. As a consequence of continual exposure to arsenic, nearly every organism, from Escherichia coli to humans have evolved arsenic detoxification pathways. One of the pathways is extrusion of arsenic from inside the cells, thereby conferring resistance. The R773 arsRDABC operon in E. coli encodes an ArsAB efflux pump that confers resistance to arsenite. ArsA is the catalytic subunit of the pump, while ArsB forms the oxyanion conducting pathway. ArsD is an arsenite metallochaperone that binds arsenite and transfers it to ArsA. The interaction of ArsA and ArsD allows for resistance to As(III) at environmental concentrations. The interaction between ArsA ATPase and ArsD metallochaperone was examined. A quadruple mutant in the arsD gene encoding a K2A/K37A/K62A/K104A ArsD is unable to interact with ArsA. An error-prone mutagenesis approach was used to generate random mutations in the arsA gene that restored interaction with the quadruple arsD mutant in yeast two-hybrid assays. Three such mutants encoding Q56R, F120I and D137V ArsA were able to restore interaction with the quadruple ArsD mutant. Structural models generated by in silico docking suggest that an electrostatic interface favors reversible interaction between ArsA and ArsD. Mutations in ArsA that propagate changes in hydrogen bonding and salt bridges to the ArsA-ArsD interface also affect their interactions. The second objective was to examine the mechanism of arsenite resistance through methylation and subsequent volatilization. Microbial ArsM (As(III) S-adenosylmethyltransferase) catalyzes the formation of trimethylarsine as the volatile end product. The net result is loss of arsenic from cells. The gene for CrArsM from the eukaryotic green alga Chlamydomonas reinhardtii was chemically synthesized and expressed in E. coli. The purified protein catalyzed the methylation of arsenite into methyl-, dimethyl- and trimethyl products. Synthetic purified CrArsM was crystallized in an unliganded form. Biochemical and biophysical studies conducted on CrArsM sheds new light on the pathways of biomethylation. While in microbes ArsM detoxifies arsenic, the human homolog, hAS3MT, converts inorganic arsenic into more toxic and carcinogenic forms. An understanding of the enzymatic mechanism of ArsM will be critical in deciphering its parallel roles in arsenic detoxification and carcinogenesis.

Fault-controlled and stratabound dolostones in the Late Aptian-earliest Albian Benassal Formation (Maestrat Basin, E Spain) : petrology and geochemistry constrains

This study was developed under the ExxonMobil FC2 Alliance (Fundamental Controls on Flow in Carbonates). The authors wish to thank ExxonMobil Production Company and ExxonMobil Upstream Research Company for providing funding. The views in this article by Sherry L. Stafford are her own and not necessarily those of ExxonMobil. This research was supported by the Sedimentary Geology Research Group of the Generalitat de Catalunya (2014SGR251). We would like to thank Andrea Ceriani and Paola Ronchi for their critical and valuable reviews, and Associated Editor Piero Gianolla for the editorial work.

Expectation Modulates Episodic Memory Formation via Dopaminergic Circuitry

Episodic memory formation is shaped by expectation. Events that generate expectations have the capacity to influence memory. Additionally, whether subsequent events meet or violate expectations has consequences for memory. However, clarification is still required to illuminate the circumstances and direction of memory modulation. In the brain, the mechanisms by which expectation modulates memory formation also require consideration. The dopamine system has been implicated in signaling events associated with different states of expectancy; it has also been shown to modulate episodic memory formation in the hippocampus. Thus, the studies included in this dissertation utilized both functional magnetic resonance imaging (fMRI) and behavioral testing to examine when and how the dopaminergic system supports the modulation of memory by expectation. The work aimed to characterize the activation of dopaminergic circuitry in response to cues that generate expectancy, during periods of anticipation, and in response to outcomes that resolve expectancy. The studies also examined how each of these event types influenced episodic memory formation. The present findings demonstrated that novelty and expectancy violation both drive dopaminergic circuitry capable of contributing to memory formation. Consistent with elevated dopaminergic midbrain and hippocampus activation for each, expected versus expectancy violating novelty did not differentially affect memory success. We also showed that high curiosity expectancy states drive memory formation. This was supported by activation in dopaminergic circuitry that was greater for subsequently remembered information only in the high curiosity state. Finally, we showed that cues that generate high expected reward value versus high reward uncertainty differentially modulate memory formation during reward anticipation. This behavioral result was consistent with distinct temporal profiles of dopaminergic action having differential downstream effects on episodic memory formation. Integrating the present studies with previous research suggests that dopaminergic circuitry signals events that are unpredicted, whether cuing or resolving expectations. It also suggests that contextual differences change the contribution of the dopaminergic system during anticipation, depending on the nature of the expectation. And finally, this work is consistent with a model in which dopamine elevation in response to expectancy events positively modulates episodic memory formation.

Experimental and Theoretical Models to Probe Mechanisms of Biological Charge Flow

Nature is challenged to move charge efficiently over many length scales. From sub-nm to μm distances, electron-transfer proteins orchestrate energy conversion, storage, and release both inside and outside the cell. Uncovering the detailed mechanisms of biological electron-transfer reactions, which are often coupled to bond-breaking and bond-making events, is essential to designing durable, artificial energy conversion systems that mimic the specificity and efficiency of their natural counterparts. Here, we use theoretical modeling of long-distance charge hopping (Chapter 3), synthetic donor-bridge-acceptor molecules (Chapters 4, 5, and 6), and de novo protein design (Chapters 5 and 6) to investigate general principles that govern light-driven and electrochemically driven electron-transfer reactions in biology. We show that fast, μm-distance charge hopping along bacterial nanowires requires closely packed charge carriers with low reorganization energies (Chapter 3); singlet excited-state electronic polarization of supermolecular electron donors can attenuate intersystem crossing yields to lower-energy, oppositely polarized, donor triplet states (Chapter 4); the effective static dielectric constant of a small (~100 residue) de novo designed 4-helical protein bundle can change upon phototriggering an electron transfer event in the protein interior, providing a means to slow the charge-recombination reaction (Chapter 5); and a tightly-packed de novo designed 4-helix protein bundle can drastically alter charge-transfer driving forces of photo-induced amino acid radical formation in the bundle interior, effectively turning off a light-driven oxidation reaction that occurs in organic solvent (Chapter 6). This work leverages unique insights gleaned from proteins designed from scratch that bind synthetic donor-bridge-acceptor molecules that can also be studied in organic solvents, opening new avenues of exploration into the factors critical for protein control of charge flow in biology.

NOX-driven ROS formation in cell transformation of FLT3-ITD positive AML

In different types of myeloid leukemia, increased formation of reactive oxygen species (ROS) has been noted and associated with aspects of cell transformation including the promotion of leukemic cell proliferation and migration, as well as DNA-damage and accumulation of mutations. Work reviewed in this article has shown the involvement of NADPH oxidase (NOX)-derived ROS downstream of oncogenic protein-tyrosine kinases in both processes, and the related pathways have been partially identified. FLT3-ITD, an important oncoprotein in a subset of AML, causes activation of AKT and subsequently stabilization of p22phox, a regulatory subunit for NOX1-4. This process is linked to ROS formation and DNA damage. Moreover, FLT3-ITD signaling through STAT5 enhances expression of NOX4, ROS formation and inactivation of the protein-tyrosine phosphatase DEP-1/PTPRJ, a negative regulator of FLT3 signaling, by reversible oxidation of its catalytic cysteine residue. Genetic inactivation of NOX4 restored DEP-1 activity and attenuated cell transformation by FLT3-ITD in vitro and in vivo. Future work is required to further explore these mechanisms and their causal involvement in leukemic cell transformation, which may result in the identification of novel candidate targets for therapy.

Mechanisms Governing the Eyewall Replacement Cycle in Numerical Simulations of Tropical Cyclones

Eyewall replacement cycle (ERC) is frequently observed during the evolution of intensifying Tropical Cyclones (TCs). Although intensely studied in recent years, the underlying mechanisms of ERC are still poorly understood, and the forecast of ERC remains a great challenge. To advance our understanding of ERC and provide insights in improvement of numerical forecast of ERC, a series of numerical simulations is performed to investigate ERCs in TC-like vortices on a f-plane. The simulated ERCs possess key features similar to those observed in real TCs including the formation of a secondary tangential wind maximum associated with the outer eyewall. The Sawyer-Eliassen equation and tangential momentum budget analyses are performed to diagnose the mechanisms underlying the secondary eyewall formation (SEF) and ERC. Our diagnoses reveal crucial roles of outer rainband heating in governing the formation and development of the secondary tangential wind maximum and demonstrate that the outer rainband convection must reach a critical strength relative to the eyewall before SEF and the subsequent ERC can occur. A positive feedback among low-level convection, acceleration of tangential winds in the boundary layer, and surface evaporation that leads to the development of ERC and a mechanism for the demise of inner eyewall that involves interaction between the transverse circulations induced by eyewall and outer rainband convection are proposed. The tangential momentum budget indicates that the net tendency of tangential wind is a small residual resultant from a large cancellation between tendencies induced by the resolved and sub-grid scale (SGS) processes. The large SGS contribution to the tangential wind budget explains different characteristics of ERC shown in previous numerical studies and poses a great challenge for a timely correct forecast of ERC. The sensitivity experiments show that ERCs are strongly subjected to model physics, vortex radial structure and background wind. The impact of model physics on ERC can be well understood with the interaction among eyewall/outer rainband heating, radilal inflow in the boundary layer, surface layer turbulent processes, and shallow convection in the moat. However, further investigations are needed to fully understand the exhibited sensitivities of ERC to vortex radial structure and background wind.

Barriers of sentiment : Identity -formation, -regulation and subjectification in preschools

This thesis studies preschool socialization in terms of identity -formation, -regulation, and subjectification. Both the methodology and theoretical backdrop draws on Critical Management Studies, and the contribution to research comes from studying a subject otherwise non-prioritized. I have performed a qualitative study entailing interviews of pedagogues and preschool chiefs working within the same company in the Stockholm region. The study indicate that preschool discourse emphasize the importance of social competences and rituals, and moreover that the institution also accentuates its role in setting the proper ‘preconditions’. Furthermore, the study demonstrates how pedagogues – using mechanisms such as individual discourses, the children’s agency, and the milieu – try to form individuals who are: social, independent, self-reliant, have a strong ‘self’, joyful towards learning, and ‘can do it themselves’. I make a liaison between the aforementioned ideals and certain trends discussed by managerial literature, like for instance currents towards: self-management, neo-normative control, self-entrepreneurial attitudes, ambidextrousness, and the ‘principle of potential’ (Costea et al., 2012; Fleming & Study, 2009; Holmqvist & Spicer, 2013; Maravelias, 2011; Pongratz & Voß, 2003). Finally the thesis concludes by firstly underscoring that the Discourse of for example ‘joyful learning’ and ‘independency’ in preschools tend to demolish physical modes of control in place of psychological ones; and secondly, by discussing historical practices, the thesis brings attention to a shift from safekeeping children to preparing them for industrial, urbanistic, and capitalistic social existence. 

Capital 2.0 capital formation and legal risk in a new global economic order from fiat to exit: including case studies of the proposed transatlantic trade and investment partnership between the United States and the European Union and the financing relation between the United States and the People’s Republic of China

Following the intrinsically linked balance sheets in his Capital Formation Life Cycle, Lukas M. Stahl explains with his Triple A Model of Accounting, Allocation and Accountability the stages of the Capital Formation process from FIAT to EXIT. Based on the theoretical foundations of legal risk laid by the International Bar Association with the help of Roger McCormick and legal scholars such as Joanna Benjamin, Matthew Whalley and Tobias Mahler, and founded on the basis of Wesley Hohfeld’s category theory of jural relations, Stahl develops his mutually exclusive Four Determinants of Legal Risk of Law, Lack of Right, Liability and Limitation. Those Four Determinants of Legal Risk allow us to apply, assess, and precisely describe the respective legal risk at all stages of the Capital Formation Life Cycle as demonstrated in case studies of nine industry verticals of the proposed and currently negotiated Transatlantic Trade and Investment Partnership between the United States of America and the European Union, TTIP, as well as in the case of the often cited financing relation between the United States and the People’s Republic of China. Having established the Four Determinants of Legal Risk and its application to the Capital Formation Life Cycle, Stahl then explores the theoretical foundations of capital formation, their historical basis in classical and neo-classical economics and its forefathers such as The Austrians around Eugen von Boehm-Bawerk, Ludwig von Mises and Friedrich von Hayek and most notably and controversial, Karl Marx, and their impact on today’s exponential expansion of capital formation. Starting off with the first pillar of his Triple A Model, Accounting, Stahl then moves on to explain the Three Factors of Capital Formation, Man, Machines and Money and shows how “value-added” is created with respect to the non-monetary capital factors of human resources and industrial production. Followed by a detailed analysis discussing the roles of the Three Actors of Monetary Capital Formation, Central Banks, Commercial Banks and Citizens Stahl readily dismisses a number of myths regarding the creation of money providing in-depth insight into the workings of monetary policy makers, their institutions and ultimate beneficiaries, the corporate and consumer citizens. In his second pillar, Allocation, Stahl continues his analysis of the balance sheets of the Capital Formation Life Cycle by discussing the role of The Five Key Accounts of Monetary Capital Formation, the Sovereign, Financial, Corporate, Private and International account of Monetary Capital Formation and the associated legal risks in the allocation of capital pursuant to his Four Determinants of Legal Risk. In his third pillar, Accountability, Stahl discusses the ever recurring Crisis-Reaction-Acceleration-Sequence-History, in short: CRASH, since the beginning of the millennium starting with the dot-com crash at the turn of the millennium, followed seven years later by the financial crisis of 2008 and the dislocations in the global economy we are facing another seven years later today in 2015 with several sordid debt restructurings under way and hundred thousands of refugees on the way caused by war and increasing inequality. Together with the regulatory reactions they have caused in the form of so-called landmark legislation such as the Sarbanes-Oxley Act of 2002, the Dodd-Frank Act of 2010, the JOBS Act of 2012 or the introduction of the Basel Accords, Basel II in 2004 and III in 2010, the European Financial Stability Facility of 2010, the European Stability Mechanism of 2012 and the European Banking Union of 2013, Stahl analyses the acceleration in size and scope of crises that appears to find often seemingly helpless bureaucratic responses, the inherent legal risks and the complete lack of accountability on part of those responsible. Stahl argues that the order of the day requires to address the root cause of the problems in the form of two fundamental design defects of our Global Economic Order, namely our monetary and judicial order. Inspired by a 1933 plan of nine University of Chicago economists abolishing the fractional reserve system, he proposes the introduction of Sovereign Money as a prerequisite to void misallocations by way of judicial order in the course of domestic and transnational insolvency proceedings including the restructuring of sovereign debt throughout the entire monetary system back to its origin without causing domino effects of banking collapses and failed financial institutions. In recognizing Austrian-American economist Schumpeter’s Concept of Creative Destruction, as a process of industrial mutation that incessantly revolutionizes the economic structure from within, incessantly destroying the old one, incessantly creating a new one, Stahl responds to Schumpeter’s economic chemotherapy with his Concept of Equitable Default mimicking an immunotherapy that strengthens the corpus economicus own immune system by providing for the judicial authority to terminate precisely those misallocations that have proven malignant causing default perusing the century old common law concept of equity that allows for the equitable reformation, rescission or restitution of contract by way of judicial order. Following a review of the proposed mechanisms of transnational dispute resolution and current court systems with transnational jurisdiction, Stahl advocates as a first step in order to complete the Capital Formation Life Cycle from FIAT, the creation of money by way of credit, to EXIT, the termination of money by way of judicial order, the institution of a Transatlantic Trade and Investment Court constituted by a panel of judges from the U.S. Court of International Trade and the European Court of Justice by following the model of the EFTA Court of the European Free Trade Association. Since the first time his proposal has been made public in June of 2014 after being discussed in academic circles since 2011, his or similar proposals have found numerous public supporters. Most notably, the former Vice President of the European Parliament, David Martin, has tabled an amendment in June 2015 in the course of the negotiations on TTIP calling for an independent judicial body and the Member of the European Commission, Cecilia Malmström, has presented her proposal of an International Investment Court on September 16, 2015. Stahl concludes, that for the first time in the history of our generation it appears that there is a real opportunity for reform of our Global Economic Order by curing the two fundamental design defects of our monetary order and judicial order with the abolition of the fractional reserve system and the introduction of Sovereign Money and the institution of a democratically elected Transatlantic Trade and Investment Court that commensurate with its jurisdiction extending to cases concerning the Transatlantic Trade and Investment Partnership may complete the Capital Formation Life Cycle resolving cases of default with the transnational judicial authority for terminal resolution of misallocations in a New Global Economic Order without the ensuing dangers of systemic collapse from FIAT to EXIT.

Kinetics and coverage dependent reaction mechanisms of the copper atomic layer deposition from copper dimethylamino-2-propoxide and diethylzinc

Atomic layer deposition (ALD) has been recognized as a promising method to deposit conformal and uniform thin film of copper for future electronic devices. However, many aspects of the reaction mechanism and the surface chemistry of copper ALD remain unclear. In this paper, we employ plane wave density functional theory (DFT) to study the transmetalation ALD reaction of copper dimethylamino-2-propoxide [Cu(dmap)2] and diethylzinc [Et2Zn] that was realized experimentally by Lee et al. [ Angew. Chem., Int. Ed. 2009, 48, 4536−4539]. We find that the Cu(dmap)2 molecule adsorbs and dissociates through the scission of one or two Cu–O bonds into surface-bound dmap and Cu(dmap) fragments during the copper pulse. As Et2Zn adsorbs on the surface covered with Cu(dmap) and dmap fragments, butane formation and desorption was found to be facilitated by the surrounding ligands, which leads to one reaction mechanism, while the migration of ethyl groups to the surface leads to another reaction mechanism. During both reaction mechanisms, ligand diffusion and reordering are generally endothermic processes, which may result in residual ligands blocking the surface sites at the end of the Et2Zn pulse, and in residual Zn being reduced and incorporated as an impurity. We also find that the nearby ligands play a cooperative role in lowering the activation energy for formation and desorption of byproducts, which explains the advantage of using organometallic precursors and reducing agents in Cu ALD. The ALD growth rate estimated for the mechanism is consistent with the experimental value of 0.2 Å/cycle. The proposed reaction mechanisms provide insight into ALD processes for copper and other transition metals.

Geochemistry of crustal formation and evolution

Terrestrial planets produce crusts as they differentiate. The Earth’s bi-modal crust, with a high-standing granitic continental crust and a low-standing basaltic oceanic crust, is unique in our solar system and links the evolution of the interior and exterior of this planet. Here I present geochemical observations to constrain processes accompanying crustal formation and evolution. My approach includes geochemical analyses, quantitative modeling, and experimental studies. The Archean crustal evolution project represents my perspective on when Earth’s continental crust began forming. In this project, I utilized critical element ratios in sedimentary records to track the evolution of the MgO content in the upper continental crust as a function time. The early Archean subaerial crust had >11 wt. % MgO, whereas by the end of Archean its composition had evolved to about 4 wt. % MgO, suggesting a transition of the upper crust from a basalt-like to a more granite-like bulk composition. Driving this fundamental change of the upper crustal composition is the widespread operation of subduction processes, suggesting the onset of global plate tectonics at ~ 3 Ga (Abstract figure). Three of the chapters in this dissertation leverage the use of Eu anomalies to track the recycling of crustal materials back into the mantle, where Eu anomaly is a sensitive measure of the element’s behavior relative to neighboring lanthanoids (Sm and Gd) during crustal differentiation. My compilation of Sm-Eu-Gd data for the continental crust shows that the average crust has a net negative Eu anomaly. This result requires recycling of Eu-enriched lower continental crust to the mantle. Mass balance calculations require that about three times the mass of the modern continental crust was returned into the mantle over Earth history, possibly via density-driven recycling. High precision measurements of Eu/Eu* in selected primitive glasses of mid-ocean ridge basalt (MORB) from global MORs, combined with numerical modeling, suggests that the recycled lower crustal materials are not found within the MORB source and may have at least partially sank into the lower mantle where they can be sampled by hot spot volcanoes. The Lesser Antilles Li isotope project provides insights into the Li systematics of this young island arc, a representative section of proto-continental crust. Martinique Island lavas, to my knowledge, represent the only clear case in which crustal Li is recycled back into their mantle source, as documented by the isotopically light Li isotopes in Lesser Antilles sediments that feed into the fore arc subduction trench. By corollary, the mantle-like Li signal in global arc lavas is likely the result of broadly similar Li isotopic compositions between the upper mantle and bulk subducting sediments in most arcs. My PhD project on Li diffusion mechanism in zircon is being carried out in extensive collaboration with multiple institutes and employs analytical, experimental and modeling studies. This ongoing project, finds that REE and Y play an important role in controlling Li diffusion in natural zircons, with Li partially coupling to REE and Y to maintain charge balance. Access to state-of-art instrumentation presented critical opportunities to identify the mechanisms that cause elemental fractionation during laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analysis. My work here elucidates the elemental fractionation associated with plasma plume condensation during laser ablation and particle-ion conversion in the ICP.

THE PHYSICS OF IDEAS: INFERRING THE MECHANICS OF OPINION FORMATION FROM MACROSCOPIC STATISTICAL PATTERNS

In a microscopic setting, humans behave in rich and unexpected ways. In a macroscopic setting, however, distinctive patterns of group behavior emerge, leading statistical physicists to search for an underlying mechanism. The aim of this dissertation is to analyze the macroscopic patterns of competing ideas in order to discern the mechanics of how group opinions form at the microscopic level. First, we explore the competition of answers in online Q&A (question and answer) boards. We find that a simple individual-level model can capture important features of user behavior, especially as the number of answers to a question grows. Our model further suggests that the wisdom of crowds may be constrained by information overload, in which users are unable to thoroughly evaluate each answer and therefore tend to use heuristics to pick what they believe is the best answer. Next, we explore models of opinion spread among voters to explain observed universal statistical patterns such as rescaled vote distributions and logarithmic vote correlations. We introduce a simple model that can explain both properties, as well as why it takes so long for large groups to reach consensus. An important feature of the model that facilitates agreement with data is that individuals become more stubborn (unwilling to change their opinion) over time. Finally, we explore potential underlying mechanisms for opinion formation in juries, by comparing data to various types of models. We find that different null hypotheses in which jurors do not interact when reaching a decision are in strong disagreement with data compared to a simple interaction model. These findings provide conceptual and mechanistic support for previous work that has found mutual influence can play a large role in group decisions. In addition, by matching our models to data, we are able to infer the time scales over which individuals change their opinions for different jury contexts. We find that these values increase as a function of the trial time, suggesting that jurors and judicial panels exhibit a kind of stubbornness similar to what we include in our model of voting behavior.

Glycosylation and Glycodiversification in Polyketide Antibiotics: Unraveling Biosynthetic Steps in Nogalamycin Formation

Soil-dwelling Streptomyces bacteria are known for their ability to produce biologically active compounds such as antimicrobial, immunosuppressant, antifungal and anticancer drugs. S. nogalater is the producer of nogalamycin, a potential anticancer drug exhibiting high cytotoxicity and activity against human topoisomerases I and II. Nogalamycin is an anthracycline polyketide comprising a four-ring aromatic backbone,a neutral deoxy sugar at C7, and an amino sugar attached via an O–C bond at C1 and a C–C bond between C2 and C5´´. This kind of attachment of the amino sugar is unusual thus making the structure of the compound highly interesting. The sugar is also associated with the biological activity of nogalamycin, as it facilitates binding to DNA. Furthermore, the sugar moieties of anthracyclines are often crucial for their biological activity. Together the interesting attachment of the amino sugar and the general reliance of polyketides on the sugar moieties for bioactivity have made the study of the biosynthesis of nogalamycin attractive. The sugar moieties are typically attached by glycosyltransferases, which use two substrates: the donor and the acceptor. The literature review of the thesis is focused on the glycosylation of polyketides and the possibilities to alter their glycosylation patterns. My own thesis work revolves around the biosynthesis of nogalamycin. We have elucidated the individual steps that lead to its rather unique structure. We reconstructed the whole biosynthetic pathway in the heterologous host S. albus using a cosmid and a plasmid. In the process, we were able to isolate new compounds when the cosmid, which contains the majority of the nogalamycin gene cluster, was expressed alone in the heterologous host. The new compounds included true intermediates of the pathway as well as metabolites, which were most likely altered by the endogenous enzymes of the host. The biological activity of the most interesting new products was tested against human topoisomerases I and II, and they were found to exhibit such activities. The heterologous expression system facilitated the generation of mutants with inactivated biosynthetic genes. In that process, we were able to identify the functions of the glycosyltransferases SnogE and SnogD, solve the structure of SnogD, discover a novel C1-hydroxylase system comprising SnoaW and SnoaL2, and establish that the two homologous non-heme α-ketoglutarate and Fe2+ dependent enzymes SnoK and SnoN catalyze atypical reactions on the pathway. We demonstrated that SnoK was responsible for the formation of the additional C–C bond, whereas SnoN is an epimerase. A combination of in vivo and in vitro techniques was utilized to unravel the details of these enzymes. Protein crystallography gave us an important means to understand the mechanisms. Furthermore, the solved structures serve as platforms for future rational design of the enzymes.

L'évaluation de l'autonomie fonctionnelle des personnes âgées : contribution de la didactique professionnelle à la formation des travailleuses et travailleurs sociaux au Québec

Résumé : Le vieillissement démographique est statistiquement indiscutable au Québec. Ce singulier trompeur masque les différentes manières de vieillir. Pour ceux qui ne parviennent pas à vieillir en santé, les solidarités familiales, comme les solidarités institutionnelles, c’est à dire publiques viennent en principe compenser ce qu’il est convenu de désigner de perte d’autonomie. Les politiques de santé publique au Québec organisent les services de soutien à domicile sous condition d’avoir estimé la situation de la personne avec l’outil d’évaluation multiclientèle (OEMC). Il est en usage dans l’ensemble du réseau de la santé et des services sociaux, et utilisé par les professionnels dont les travailleuses et les travailleurs sociaux (TS). Or, la gérontologie est peu soutenue dans la formation initiale des TS. Nous nous sommes interrogée sur les savoirs mobilisés par les TS quand ils évaluent. S’agissant des savoirs inscrits dans la pratique, nous avons orienté la recherche dans les théories de l’activité, la didactique professionnelle et le cadre conceptuel de la médiation. Nous avons étudié l’activité de professionnels en travail social expérimentés afin d’identifier certains des savoirs mobilisés pour les rendre disponibles à la formation des étudiant (e)s en travail social au Québec. Cent-cinquante heures d’observations et vingt-deux entretiens individuels et collectifs ont été réalisés avec des intervenants volontaires du service de soutien à domicile. Les résultats préliminaires de la recherche ont été présentés lors de groupes de discussion avec les TS ayant participé à la recherche, puis avec des enseignants en travail social. Nos résultats permettent de décrire les procédures de l’évaluation dans l’organisation du service d’aide à domicile et d’en différencier le processus de l’activité par laquelle le TS évalue l’autonomie fonctionnelle de la personne. Nous constatons que les savoirs mobilisés par les TS reposent premièrement sur une connaissance fine du territoire, de l’outil d’évaluation et des institutions. Un deuxième registre de savoir concerne la conceptualisation de l’autonomie fonctionnelle par l’outil OEMC comme objet et domaine d’intervention des TS. Enfin, un troisième registre se réfère aux savoirs mobilisés pour entrer en relation avec les personnes âgées, avec leur entourage. Or, ces trois registres de savoir n’apparaissent pas dans le discours des TS et résultent de notre propre analyse sur leur pratique. L’évaluation de l’autonomie fonctionnelle analysée par le concept de médiation est révélatrice du rapport aux savoirs du TS. S’agissant de savoirs de la pratique, nous constatons que leur classification entre les catégories usuelles de savoirs théoriques ou pratiques était inopérante. Nous empruntons le vocabulaire de la didactique professionnelle : celui des invariants opératoires reliés à l’autonomie fonctionnelle et celui des schèmes d’activité reliés à l’activité d’évaluation. C’est ainsi que nous avons identifié deux moments dans l’évaluation. Le premier assemble la collecte des informations et l’analyse des données. L’autonomie fonctionnelle se décline dans des conditions d’existence de la personne sur l’axe allant de la mobilité à la cognition avec comme balises d’intervention la sécurité et l’intégrité de la personne. Dans ce processus itératif, le TS identifie avec la personne ce qui nuit à son quotidien. L’évaluation formule comment résoudre cette incidence, comment la perte d’autonomie pourrait être compensée. La collecte d’information et le raisonnement du TS est alors un mouvement itératif, les deux éléments du processus sont liés et en continu. Le second moment de l’évaluation apparait si, dans le processus itératif, le TS perçoit une dissonance. Il est essentiel d’en identifier la nature pour la prendre en compte et maintenir la finalité de l’activité qui consiste à évaluer l’autonomie fonctionnelle à des fins compensatrices. Le TS doit identifier l’objet de la dissonance pour pouvoir cerner avec la personne le besoin inhérent à la perte d’autonomie et envisager d’y remédier. La prise en compte de cette dissonance vient ralentir le déroulement de l’activité. Le raisonnement qui, jusque-là, était relié à la collecte d’informations s’en dissocie pour analyser ce qui vient faire obstacle à l’activité d’évaluation à partir de la situation. Les composantes qui génèrent la dissonance paraissent reliées à la quotidienneté, aux conditions de vie à domicile de la personne (cohérence/incohérence, refus de services, autonégligence, maltraitance, agressivité). La dissonance génère une activité plus complexe pour évaluer la situation. L’autonomie fonctionnelle se décline toujours sur l’axe mobilité/cognition avec comme balises d’intervention la sécurité et l’intégrité de la personne. Or, pour ce faire, les TS raisonnent selon trois schèmes. Dans les situations où, pour décider de la suite du dossier, il faut en référer à une norme (de service, de profession, etc.) le raisonnement est déontologique. Il est aussi des situations où le TS agit au regard de valeurs et de représentations qui relèvent de sa sphère personnelle. Nous désignons ce raisonnement d’instinctuel. Enfin, le TS peut naviguer entre ces deux orientations et choisir la voie du raisonnement clinique que nous qualifions d’éthique et se rapproche alors des pratiques prudentielles qui sont marquées par l’incertitude.