Mechanisms of chloroperoxidase-catalyzed enantioselective reactions as probed by site-directed mutagenesis and isotopic labeling

Chloroperoxidase (CPO) is a heme-containing glycoprotein secreted by the marine fungus Caldariomyces fumago. Chloroperoxidase contains one ferriprotoporphyrin IX prosthetic group per molecule and catalyzes a variety of reactions, such as halogenation, peroxidation and epoxidation. The versatile catalytic activities of CPO coupled with the increasing demands for chiral synthesis have attracted an escalating interest in understanding the mechanistic and structural properties of this enzyme. In order to better understand the mechanisms of CPO-catalyzed enantioselective reactions and to fine-tune the catalytic properties of chloroperoxidase, asparagine 74 (N74) located in the narrow substrate access channel of CPO was replaced by a bulky, nonpolar valine and a polar glutamine using site-directed mutagenesis. The CPO N74 mutants displayed significantly enhanced activity toward nonpolar substrates compared to wild-type CPO as a result of changes in space and polarity of the heme distal environment. More interestingly, N74 mutants showed dramatically decreased chlorination and catalase activity but significantly enhanced epoxidation activity as a consequence of improved kinetic perfection introduced by the mutation as reflected by the favorable changes in k cat and kcat/KM of these reactions. It is also noted that the N74V mutant is capable of decomposing cyanide, the most notorious poison for many hemoproteins, as judged by the unique binding behavior of N74V with potassium cyanide. Histidine 105 (H105) was replaced by a nonpolar amino acid alanine using site-directed mutagenesis. The CPO H105 mutant (H105A) displayed dramatically decreased chlorination and catalase activity possibly because of the decreased polarity in the heme distal environment and loss of the hydrogen bonds between histidine 105 and glutamic acid 183. However, significantly increased enantioselectivity was observed for the epoxidation of bulky styrene derivatives. Furthermore, my study provides strong evidence for the proposed histidine/cysteine ligand switch in chloroperoxidase, providing experimental support for the structure of the 420-nm absorption maximum for a number of carbon monoxide complexes of heme-thiolate proteins. For the NMR study, [dCPO(heme)] was produced using 90% deuterated growth medium with excess heme precursors and [dCPO(Phe)] was grown in the same highly deuterated medium that had been supplemented with excess natural phenylalanine. To make complete heme proton assignments, NMR spectroscopy has been performed for high-resolution structural characterization of [dCPO(heme)] and [dCPO(Phe)] to achieve unambiguous and complete heme proton assignments, which also allows important amino acids close to the heme active center to be determined.

A study of the situations, features, and coping mechanisms experienced by Irish psychiatric nurses experiencing moral distress

Purpose: The purpose of this study was toinvestigate moral distress in Irish psychiatric nurses. Design: A qualitative descriptive methodology was used. Findings: The study confirmed the presence of moral distress and the situations that gave rise to moral distress within psychiatric nurses working in acute care settings. Practice Implications: The findings indicate that while multidisciplinary teams appear to function well on the surface, situations that give rise to moral distress are not always acknowledged or dealt with effectively. Furthermore, unresolved moral conflict impacts upon the quality of clinical decision-making by not allowing open and transparent discussions that allow clinicians the opportunity to address their concerns adequately.

Sleep Quality as a Mediator of the Relationship Between Attachment Anxiety and Health Outcomes During Romantic Conflict

Attachment anxiety, or a fear of abandonment by those close to you, is an important predictor of many individual and interpersonal outcomes. Individuals high in attachment anxiety are more likely to experience physical illness due to disrupted immune functioning and deregulated stress responses. I was interested in examining potential mechanisms accounting for why individuals high in attachment anxiety are more likely to become ill. One variable that has been demonstrated to mediate the relationship between stress and health is sleep quality. As attachment anxiety is characterized by the experience of stress and worry over abandonment by romantic partners, I predicted sleep quality would mediate the relationship between attachment anxiety and health. Further, I predicted attachment anxiety would interact with romantic threat, in that individuals high in attachment anxiety who perceive threat to their relationships would have poor sleep quality (compared with individuals low in attachment anxiety and individuals high in anxiety who do not perceive threat) which would mediate the most unhealthy outcomes. I tested these hypotheses using three online diary studies. In the first two studies, participants completed a seven-night diary describing their sleep quality, health, and interaction with their partner. In Study 3, I surveyed participants once a week for eight weeks to examine longer-term health outcomes. Sleep quality did indeed mediate the relationship between attachment anxiety and various health outcomes over one week (Study 2), and showed a trend towards mediating effects over two months (Study 3). Interestingly, however, attachment anxiety did not interact with perceived romantic threat to predict health in the mediation analyses. Implications for sleep as a mediating variable are discussed, as well as the lack of attachment anxiety by romantic threat interaction.

Lawyers & Truth Recovery Mechanisms: South Africa

Focusing on post-apartheid South Africa, the report explores the role of lawyers in truth recovery mechanisms.

The report was prepared by Dr Rachel Killean and draws on a series of interviews conducted in South Africa (with legal academics, ‘struggle’ lawyers, state lawyers, judges and human rights activists) as part of the wider Lawyers, Conflict and Transition project.

Dr Killean begins with an overview of the various roles the legal profession has played in South Africa, both during the apartheid era and post-transition.

The first half of the report then explores the role of lawyers as professional participants – firstly at the South African Truth and Reconciliation Commission and secondly in the Marikana Commission of Inquiry.

The report then considers the notion of lawyers as subjects of truth recovery, looking in particular at the Special Legal Hearing on the legal profession as part of the South African Truth and Reconciliation Commission.

In the concluding section Killean reflects on the extent to which lawyers influence the procedures and outcomes of truth recovery mechanisms and offers some concrete suggestions as to how the involvement of lawyers in such processes might be more effectively managed.

With regard to lawyers as subjects of truth recovery, she acknowledges the limitations of the South African model but posits that the endeavour must be applauded, not least because it demonstrated that it is possible to scrutinise the role of the legal profession in past conflict, and that it is worth wrestling with the associated challenges.

High resolution numerical simulation of triple point collision and origin of unburned gas pockets in turbulent detonations

A key issue in pulse detonation engine development is better understanding of the detonation structure and its propagation mechanism. Thus, in the present work the turbulent structure of an irregular detonation is studied through very high resolution numerical simulations of 600 points per half reaction length. The aim is to explore the nature of the transverse waves during the collision and reflection processes of the triple point with the channel walls. Consequently the formation and consumption mechanism of unreacted gas pockets is studied. Results show that the triple point and the transverse wave collide simultaneously with the wall. The strong transverse wave switches from a primary triple point before collision to a new one after reflection. Due to simultaneous interaction of the triple point and the transverse wave with the wall in the second half of the detonation cell, a larger high-pressurised region appears on the wall. During the reflection the reaction zone detaches from the shock front and produces a pocket of unburned gas. Three mechanisms found to be of significance in the re-initiation mechanism of detonation at the end of the detonation cell; i: energy resealed via consumption of unburned pockets by turbulent mixing ii: compression waves arise due to collision of the triple point on the wall which helps the shock to jump abruptly to an overdriven detonation iii: drastic growth of the Richtmyer–Meshkov instability causing a part of the front to accelerate with respect to the neighbouring portions.

Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08

Building peace by supporting post-conflict electoral processes

Les élections post-conflit ou élections de sortie de crise organisées sous l’égide de la communauté internationale en vue de rétablir la paix dans les pays sortant de violents conflits armés ont un bilan mixte caractérisé par le succès ou l’échec selon les cas. Ce bilan mitigé représente le problème principal auquel cette recherche tente de répondre à travers les questions suivantes : l’assistance électorale étrangère est-elle efficace comme outil de rétablissement de la paix dans les sociétés post-conflit? Qu’est ce qui détermine le succès ou l’échec des élections post-conflit à contribuer efficacement au rétablissement de la paix dans les sociétés déchirées par la guerre? Pour résoudre cette problématique, cette thèse développe une théorie de l’assistance électorale en période post-conflit centrée sur les parties prenantes à la fois du conflit armé et du processus électoral. Cette théorie affirme que l’élément clé pour le succès des élections post-conflit dans le rétablissement de la paix est le renforcement de la capacité de négociation des parties prenantes à la fois dans le processus de paix et dans le processus électoral post-conflit. Dans les situations post-conflit, une assistance électorale qui se voudrait complète et efficace devra combiner à la fois le processus électoral et le processus de paix. L’assistance électorale sera inefficace si elle se concentre uniquement sur les aspects techniques du processus électoral visant à garantir des élections libres, transparentes et équitables. Pour être efficace, l’accent devra également être mis sur les facteurs supplémentaires qui peuvent empêcher la récurrence de la guerre, tels que l’habilité des individus et des groupes à négocier et à faire des compromis sur les grandes questions qui peuvent menacer le processus de paix. De fait, même des élections transparentes comme celles de 1997 au Liberia saluées par la communauté internationale n’avaient pas réussi à établir des conditions suffisantes pour éviter la reprise des hostilités. C’est pourquoi, pour être efficace, l’assistance électorale dans les situations de post-conflit doit prendre une approche globale qui priorise l’éducation civique, la sensibilisation sur les droits et responsabilités des citoyens dans une société démocratique, le débat public sur les questions qui divisent, la participation politique, la formation au dialogue politique, et toute autre activité qui pourrait aider les différentes parties à renforcer leur capacité de négociation et de compromis. Une telle assistance électorale fera une contribution à la consolidation de la paix, même dans le contexte des élections imparfaites, comme celles qui se sont détenues en Sierra Leone en 2002 ou au Libéria en 2005. Bien que la littérature sur l’assistance électorale n’ignore guère l’importance des parties prenantes aux processus électoraux post-conflit (K. Kumar, 1998, 2005), elle a fortement mis l’accent sur les mécanismes institutionnels. En effet, la recherche académique et professionnelle est abondante sur la réforme des lois électorales, la reforme constitutionnelle, et le développement des administrations électorales tels que les commissions électorales, ainsi que l’observation électorale et autres mécanismes de prévention de la fraude électorale, etc. (Carothers & Gloppen, 2007). En d’autres termes, les décideurs et les chercheurs ont attribué jusqu’à présent plus d’importance à la conception et au fonctionnement du cadre institutionnel et des procédures électorales. Cette thèse affirme qu’il est désormais temps de prendre en compte les participants eux-mêmes au processus électoral à travers des types d’assistance électorale qui favoriseraient leur capacité à participer à un débat pacifique et à trouver des compromis aux questions litigieuses. Cette approche plus globale de l’assistance électorale qui replace l’élection post-conflit dans le contexte plus englobant du processus de paix a l’avantage de transformer le processus électoral non pas seulement en une expérience d’élection de dirigeants légitimes, mais aussi, et surtout, en un processus au cours duquel les participants apprennent à régler leurs points de vue contradictoires à travers le débat politique dans un cadre institutionnel avec des moyens légaux et légitimes. Car, si le cadre institutionnel électoral est important, il reste que le résultat du processus électoral dépendra essentiellement de la volonté des participants à se conformer au cadre institutionnel et aux règles électorales.

Conflict and Stability in the Neoliberal Era: Explaining Urban Unrest in Latin America

Thesis (Ph.D.)--University of Washington, 2016-08

TWO-PHASE HEAT TRANSFER MECHANISMS WITHIN PLATE HEAT EXCHANGERS: EXPERIMENTS AND MODELING

Two-phase flow heat exchangers have been shown to have very high efficiencies, but the lack of a dependable model and data precludes them from use in many cases. Herein a new method for the measurement of local convective heat transfer coefficients from the outside of a heat transferring wall has been developed, which results in accurate local measurements of heat flux during two-phase flow. This novel technique uses a chevron-pattern corrugated plate heat exchanger consisting of a specially machined Calcium Fluoride plate and the refrigerant HFE7100, with heat flux values up to 1 W cm-2 and flow rates up to 300 kg m-2s-1. As Calcium Fluoride is largely transparent to infra-red radiation, the measurement of the surface temperature of PHE that is in direct contact with the liquid is accomplished through use of a mid-range (3.0-5.1 µm) infra-red camera. The objective of this study is to develop, validate, and use a unique infrared thermometry method to quantify the heat transfer characteristics of flow boiling within different Plate Heat Exchanger geometries. This new method allows high spatial and temporal resolution measurements. Furthermore quasi-local pressure measurements enable us to characterize the performance of each geometry. Validation of this technique will be demonstrated by comparison to accepted single and two-phase data. The results can be used to come up with new heat transfer correlations and optimization tools for heat exchanger designers. The scientific contribution of this thesis is, to give PHE developers further tools to allow them to identify the heat transfer and pressure drop performance of any corrugated plate pattern directly without the need to account for typical error sources due to inlet and outlet distribution systems. Furthermore, the designers will now gain information on the local heat transfer distribution within one plate heat exchanger cell which will help to choose the correct corrugation geometry for a given task.

Tectonic expression of an active slab tear from high-resolution seismic and bathymetric data offshore Sicily (Ionian Sea)

Subduction of a narrow slab of oceanic lithosphere beneath a tightly curved orogenic arc requires the presence of at least one lithospheric scale tear fault. While the Calabrian subduction beneath southern Italy is considered to be the type example of this geodynamic setting, the geometry, kinematics and surface expression of the associated lateral, slab tear fault offshore eastern Sicily remain controversial. Results from a new marine geophysical survey conducted in the Ionian Sea, using high-resolution bathymetry and seismic profiling reveal active faulting at the seafloor within a 140 km long, two-branched fault system near Alfeo Seamount. The previously unidentified 60 km long NW trending North Alfeo Fault system shows primarily strike-slip kinematics as indicated by the morphology and steep-dipping transpressional and transtensional faults. Available earthquake focal mechanisms indicate dextral strike-slip motion along this fault segment. The 80 km long SSE trending South Alfeo fault system is expressed by one or two steeply dipping normal faults, bounding the western side of a 500+ m thick, 5 km wide, elongate, syntectonic Plio-Quaternary sedimentary basin. Both branches of the fault system are mechanically capable of generating magnitude 6-7 earthquakes like those that struck eastern Sicily in 1169, 1542, and 1693.

Paths to peace: conflict management trajectories in militarized interstate disputes

When multiple third-parties (states, coalitions, and international organizations) intervene in the same conflict, do their efforts inform one another? Anecdotal evidence suggests such a possibility, but research to date has not attempted to model this interdependence directly. The current project breaks with that tradition. In particular, it proposes three competing explanations of how previous intervention efforts affect current intervention decisions: a cost model (and a variant on it, a limited commitments model), a learning model, and a random model. After using a series of Markov transition (regime-switching) models to evaluate conflict management behavior within militarized interstate disputes in the 1946-2001 period, this study concludes that third-party intervention efforts inform one another. More specifically, third-parties examine previous efforts and balance their desire to manage conflict with their need to minimize intervention costs (the cost and limited commitments models). As a result, third-parties intervene regularly using verbal pleas and mediation, but rely significantly less frequently on legal, administrative, or peace operations strategies. This empirical threshold to the intervention costs that third-parties are willing to bear has strong theoretical foundations and holds across different time periods and third-party actors. Furthermore, the analysis indicates that the first third-party to intervene in a conflict is most likely to use a strategy designed to help the disputants work toward a resolution of their dispute. After this initial intervention, the level of third-party involvement declines and often devolves into a series of verbal pleas for peace. Such findings cumulatively suggest that disputants hold the key to effective conflict management. If the disputants adopt and maintain an extreme bargaining position or fail to encourage third-parties to accept greater intervention costs, their dispute will receive little more than verbal pleas for negotiations and peace.

Effects of efficient fronto-temporal circuitry on lexical ambiguity resolution: converging evidence from cross-age comparisons in eye-tracking and ERP data

Eye-tracking was used to examine how younger and older adults use syntactic and semantic information to disambiguate noun/verb (NV) homographs (e.g., park). We find that young adults exhibit inflated first fixations to NV-homographs when only syntactic cues are available for disambiguation (i.e., in syntactic prose). This effect is eliminated with the addition of disambiguating semantic information. Older adults (60+) as a group fail to show the first fixation effect in syntactic prose; they instead reread NV homographs longer. This pattern mirrors that in prior event-related potential work (Lee & Federmeier, 2009, 2011), which reported a sustained frontal negativity to NV-homographs in syntactic prose for young adults, which was eliminated by semantic constraints. The frontal negativity was not observed in older adults as a group, although older adults with high verbal fluency showed the young-like pattern. Analyses of individual differences in eye-tracking patterns revealed a similar effect of verbal fluency in both young and older adults: high verbal fluency groups of both ages show larger first fixation effects, while low verbal fluency groups show larger downstream costs (rereading and/or refixating NV homographs). Jointly, the eye-tracking and ERP data suggest that effortful meaning selection recruits frontal brain areas important for suppressing contextually inappropriate meanings, which also slows eye movements. Efficacy of fronto-temporal circuitry, as captured by verbal fluency, predicts the success of engaging these mechanisms in both young and older adults. Failure to recruit these processes requires compensatory rereading or leads to comprehension failures (Lee & Federmeier, in press).

Mechanisms of Chloroperoxidase-catalyzed Enantioselective Reactions as Probed by Site-directed Mutagenesis and Isotopic Labeling

Chloroperoxidase (CPO) is a heme-containing glycoprotein secreted by the marine fungus Caldariomyces fumago. Chloroperoxidase contains one ferriprotoporphyrin IX prosthetic group per molecule and catalyzes a variety of reactions, such as halogenation, peroxidation and epoxidation. The versatile catalytic activities of CPO coupled with the increasing demands for chiral synthesis have attracted an escalating interest in understanding the mechanistic and structural properties of this enzyme. In order to better understand the mechanisms of CPO-catalyzed enantioselective reactions and to fine-tune the catalytic properties of chloroperoxidase, asparagine 74 (N74) located in the narrow substrate access channel of CPO was replaced by a bulky, nonpolar valine and a polar glutamine using site-directed mutagenesis. The CPO N74 mutants displayed significantly enhanced activity toward nonpolar substrates compared to wild-type CPO as a result of changes in space and polarity of the heme distal environment. More interestingly, N74 mutants showed dramatically decreased chlorination and catalase activity but significantly enhanced epoxidation activity as a consequence of improved kinetic perfection introduced by the mutation as reflected by the favorable changes in kcat and kcat/KM of these reactions. It is also noted that the N74V mutant is capable of decomposing cyanide, the most notorious poison for many hemoproteins, as judged by the unique binding behavior of N74V with potassium cyanide. Histidine 105 (H105) was replaced by a nonpolar amino acid alanine using site-directed mutagenesis. The CPO H105 mutant (H105A) displayed dramatically decreased chlorination and catalase activity possibly because of the decreased polarity in the heme distal environment and loss of the hydrogen bonds between histidine 105 and glutamic acid 183. However, significantly increased enantioselectivity was observed for the epoxidation of bulky styrene derivatives. Furthermore, my study provides strong evidence for the proposed histidine/cysteine ligand switch in chloroperoxidase, providing experimental support for the structure of the 420-nm absorption maximum for a number of carbon monoxide complexes of heme-thiolate proteins. For the NMR study, [dCPO(heme)] was produced using 90% deuterated growth medium with excess heme precursors and [dCPO(Phe)] was grown in the same highly deuterated medium that had been supplemented with excess natural phenylalanine. To make complete heme proton assignments, NMR spectroscopy has been performed for high-resolution structural characterization of [dCPO(heme)] and [dCPO(Phe)] to achieve unambiguous and complete heme proton assignments, which also allows important amino acids close to the heme active center to be determined.