VictorJuiz/thesis huggingface dataset:
The Development of Functionalized Metal Complexes as Selective Phosphopeptide Molecular Recognition Agents

The development of dimetallic metal complexes into functional and selective recognition agents for monophosphorylated peptides is described. The development of dimetallic metal complexes into functional and selective phosphopeptide recognition agents is described. Scaffold functionalization was conducted to assess whether binding affinity for phosphate monoesters could be modulated. A protocol for the facile synthesis of symmetric and asymmetric pyridine-functionalized bis-dipicolylamine (BDPA) scaffolds was thus first optimized. Zn(II) complexes were screened for the ability to bind to various phosphate monoesters of biological relevance using isothermal titration calorimetry (ITC). An expanded family of compounds was then screened using a variety of biophysicial and biological techniques for the ability to bind to disrupt Stat3 dimer both in biophysical assays and in whole cells. Several compounds displayed the ability to potently disrupt Stat3 dimer formation at low micromolar doses. Moreover, one compound emerged as having potent anti-cancer activity against MDA468, a solid breast cancer tumor line. Efforts were subsequently redirected towards the development of Zn(II)-BDPA receptors which mimicked the pY, pY+X recognition motif displayed by human SH2 domains. A family of ditopic biphenyl-based receptors, computationally predicted to adopt this binding mode, were synthesized and screened against a family of high-profile pY-containing phosphopeptides. The reported family of mimetics displayed a wide variance in cytotoxicity against common cancer cell lines, supporting our structure-activity hypothesis. Selectivity observed in our fluorescence intensity assay did not hold in a cellular context. We next pursued the development of selective receptors for phosphopeptides containing pS instead of pY. A diverse family of Zn(II)-BDPA receptors featuring a 2’ substituted benzothiazole core were synthesized, and their binding affinities toward model phosphopeptides assessed. A central conclusion of this project is that development of potent, selective receptors for anionic and hydrophobic peptides will likely be possible only by using receptors with cationic or hydrophobic pendants, and by maximizing phosphopeptide-specific interactions. Lastly, investigations into the use of bowl-type receptors as phosphopeptide recognition agents are presented. Synthesis of a prototype bowl receptor and early efforts to characterize the receptor’s binding preferences using ITC are reported. Progress-to-date in the development of a FRET system, which will be used to measure the receptor’s affinity for different dephosphorylation motifs, is also reported.

Keywords: molecular recognition
metal complex
Advisor: Gunning, Patrick T.
A Characterization of the Role of Post-translational Modification in Transcriptional Regulation by the Histone Variant H2A.Z

H2A.Z is an essential histone variant that has multiple chromosomal functions. One such role is transcriptional regulation. However, its role in this process is complex since it has been reported to function both as a repressor and activator. Earlier work in our lab showed that H2A.Z can be post-translationally modified with monoubiquitin (H2A.Zub1) and this form of H2A.Z is linked to transcriptional silencing. We further predicted that changes in the H2A.Z ubiquitylation status directly modulated its function in transcription. Furthermore, H2A.Z-containing nucleosomes possess a unique set of post-translational modifications (PTMs), compared to H2A nucleosomes, many of which are linked to transcriptional activation. The central aim of this thesis was to characterize the role of PTMs on H2A.Z nucleosomes in transcriptional regulation. To this end, I have provided the first evidence linking H2A.Z deubiquitylation to transcriptional activation. I demonstrated that ubiquitin specific protease 10 (USP10) is a deubiquitylase that targets H2A.Z in vitro and in vivo. Moreover, I found that both H2A.Z and USP10 are required for activation of androgen-receptor (AR)-regulated genes, and that USP10 regulates the levels of H2A.Zub1 at these genes. To understand how H2A.Z engages downstream effector proteins, in the nucleosome context, we used a mass spectrometry approach to identify H2A.Z-nucleosome-interacting proteins. Many of the identified proteins contained conserved structural motifs that bind post-translationally modified histones. For example, we found that Brd2 contains tandem bromodomains that engage H2A.Z nucleosomes through acetylated H4 residues. To investigate the biological relevance of this interaction, I present evidence that Brd2 is recruited to AR-regulated genes in a manner dependent on H2A.Z and the bromodomains of Brd2. Consistent with this observation, chemical inhibition of Brd2 recruitment greatly inhibited AR-regulated gene expression. Collectively, these studies have defined how H2A.Z mediates transcriptional regulation through multiple mechanisms and pathways.

Keywords: chromatin
histone variants
H2A.Z
transcription
androgen receptor
post-translational modifications
Advisor: Cheung, Peter
The Debt-contracting Value of Accounting Numbers, Renegotiation, and Investment Efficiency

This study investigates the impact of the debt-contracting value (DCV) of borrowers' accounting information on the likelihood of private debt renegotiation and the implication of renegotiation for borrowing firms' investment efficiency. Accounting numbers, as contractible signals, are broadly used in formal debt contracting. DCV captures the inherent ability of firms' accounting numbers to predict future credit quality. Building on incomplete contract theory, I hypothesize that a lower DCV of a borrower's accounting numbers creates ex post incentives for both parties to renegotiate the terms of the initial contract, leading to a higher probability of renegotiation. During the renegotiation, the lenders can extract partial gains from the borrowers' investment according to their relative bargaining power. Anticipating the high-probability of renegotiation reduces the ex ante investment incentives of borrowers, inducing underinvestment. Using a sample of 3,720 private debt contracts, I find that 76% of the contracts are renegotiated before maturity, and 75% of renegotiation cases are related to the changes of accounting-based contractual terms. I further find that firms with a higher DCV have a lower probability of renegotiation and less underinvestment. Moreover, the impact of DCV on investment increases with lenders' relative bargaining power.

Advisor: Callen, Jeffrey
Wong, Franco
Polymorphism and Genome Assembly

When Darwin introduced natural selection in 1859 as a key mechanism of evolution, little was known about the underlying cause of variation within a species. Today we know that this variation is caused by the acquired genomic differences between individuals. Polymorphism, defined as the existence of multiple alleles or forms at a genomic locus, is the technical term used for such genetic variations. Polymorphism, along with reproduction and inheritance of genetic traits, is a necessary condition for natural selection and is crucial in understanding how species evolve and adapt. Many questions regarding polymorphism, such as why certain species are more polymorphic than others or how different organisms tend to favor some types of polymorphism among others, when solved, have the potential to shed light on important problems in human medicine and disease research. Some of these studies require more diverse species and/or individuals to be sequenced. Of particular interest are species with the highest rates of polymorphisms. For instance, the sequencing of the sea squirt genome lead to exciting studies that would not be possible to conduct on species that possess lower levels of polymorphism. Such studies form the motivation of this thesis. Sequencing of genomes is, nonetheless, subject to its own research. Recent advances in DNA sequencing technology enabled researchers to lead an unprecedented amount of sequencing projects. These improvements in cost and abundance of sequencing revived a greater interest in advancing the algorithms and tools used for genome assembly. A majority of these tools, however, have no or little support for highly polymorphic genomes; which, we believe, require specialized methods. In this thesis, we look at challenges imposed by polymorphism on genome assembly and develop methods for polymorphic genome assembly via an overview of current and past methods. Though we borrow fundamental ideas from the literature, we introduce several novel concepts that can be useful not only for assembly of highly polymorphic genomes but also genome assembly and analysis in general.

Keywords: Genome assembly
Polymorphism
Advisor: Brudno, Michael
A High-speed Fiber-optic Receiver for Plastic Optical Fiber Applications in 65 nm CMOS process

This dissertation explores a few techniques to realize a low-cost monolithic fiber-optic receiver with large-area photo detectors in advanced CMOS processes that could potentially support multi-gigabit digital data across 10 to 20 meters plastic optical fibers (POF). The first techniques investigated in this dissertation are the use of an external pseudo-differential photo detector chip to reduce the impact of the inductive parasitics, and the use of a cross-coupled regulated-cascode (CC-RGC) buffer to relieve the DC voltage headroom issues found in conventional regulated-cascode (RGC) buffers in technologies with low power supply voltages. The second technique investigated in this thesis is the super-Gm transimpedance amplifier (SGM-TIA) that can be used to produce a very small input impedance in order to drive a very large parasitic capacitance exhibited by an integrated photo detector in advanced CMOS processes. The third technique investigated is a linear equalizer with multiple shunt-shunt feedbacks that can be utilized to produce a slowly-rising peaking response in order to compensate for the frequency-dependent losses exhibited by the integrated NW/P-sub photo detector. Two prototype POF receiver test chips have been implemented in TSMC’s 65 nm CMOS processes and non-return-to-zero optical data transmissions have been demonstrated at data rates up to 3.125 Gbps and 4.25 Gbps, respectively, with a 2.5 Gbps grade 670 nm vertical-cavity surface-emitting laser based electro-optical transmitter.

Keywords: Optical Receiver
POF
Advisor: Martin, Kenneth
Spacing Freud: Space and Place in Psychoanalytic Theory

This project is interested in developing a spatial reading of Sigmund Freud’s work to understand how psychoanalysis employs a variety of different spatial categories. Proceeding by way of a close and analytical reading of Freud’s texts, I begin by surveying theories of space coming from both philosophy and geography before applying these understandings to consider Freud’s use of topographical metaphors, the formation of the subject as presented through descriptions of the fort-da game and the oceanic feeling, and Freud’s description of the limits of phantasy and reality. Freud’s writings on religion figure prominently here. I conclude by examining the deployment of individual relations through social space in Freud’s writings and the link between place and character laid out in Moses and Monotheism. The result demonstrates the importance of space in a number of aspects of Freudian psychoanalysis and frames Freud as a thinker with important contributions to make to the spatial turn in the humanities and social sciences.

Keywords: Freud
space
psychoanalysis
religion
Advisor: DiCenso, James
Hewitt, Marsha
Vittoria Pica e Carlo Dossi: Teoria e pratica dell'estetica decadente nella letteratura fin de sie'cle

This dissertation examines the general traits of Decadentismo and Scapigliatura and the position of the art and literary critic Vittorio Pica and the writer Carlo Dossi in representing and promoting themes directly linked to these two literary trends. Pica’s essays on the leading European writers of the day are published in All’avanguardia (1890) and Letteratura d’eccezione (1898). These two books are responsible for the introduction of French Decadentism in Italy. Pica is also known for categorizing decadent authors under the literary phenomenon of “arte aristocratica.” This is the term that Pica resorts to when classifying the ‘ultra aristocratic’ tendencies of authors worthy of this prestigious stature. Carlo Dossi is one of the most appealing figures within the Scapigliatura. His position within the movement is examined in light of the narrative and linguistic divertissement displayed in his works, the interplay of the subjective narratorial voice of the “I” and the writer’s revolutionary role within the Italian literary canon. Special emphasis is given to Dossi’s dismantling of the traditional literary text, the literature of the fantastic, humor and the role of the reader. These themes are exemplified in his personal journal Note azzurre and in the novels, L’altrieri, Vita di Alberto Pisani and La desinenza in A. Although Dossi the writer and Pica the critic produced works that are entirely different in nature, the dissertation attempts to draw attention to a series of convergences and divergences between the two of them.

Keywords: Carlo Dossi
Vittorio Pica
Scapigliatura
Decadence
Advisor: Somigli, Luca
Exploring Professional Knowledge in Music Education: A Narrative Study of Choral Music Educators in St. John's, NL

This thesis explores the professional knowledge of three choral music educators from St. John’s, Newfoundland and Labrador. My primary research purpose was to explain what constitutes the professional knowledge of each of the research participants as revealed through their life stories; to illustrate how such professional knowledge has been shaped by experiences throughout each of the participants’ lives; and to understand how the participants’ experiences of developing as educators within the specific social, cultural, and political contexts of Newfoundland and Labrador have shaped their professional knowledge. Through this inquiry, three choral music educators engaged in a process of teacher development, as they discovered for themselves, through a narrative process of self-exploration, the meaning that could be made of the relationships between their life experiences and their knowledge of music teaching and learning. Data-gathering included a series of four in-depth interviews, which consisted of open-ended questions that engaged the participants in reconstructing their life experiences and articulating their professional knowledge within the context of developing as choral music educators. Choral rehearsal observations provided another source of data. These observations enhanced my understanding of the participants’ teaching practice, and assisted in my understanding of the relationships between the personal and the professional that they expressed in initial interviews. Analysis of the data is represented through narratives of the participants’ life stories and a thematic discussion of their professional knowledge as revealed through those stories. Each participant’s narrative and professional knowledge are presented in individual chapters, followed by a chapter that explores the resonances (Conle, 1996) amongst the participants’ narratives and my own personal-professional narrative. I propose that we begin to reconceptualize professional development in order to acknowledge the complexity and personal nature of professional knowledge, and I assert that the exploration of life stories is a meaningful form of professional development for music educators.

Keywords: music education
narrative inquiry
professional knowledge
music teachers
choral music education
life story
Advisor: Bartel, Lee
Limitations and Improvements in Methods for Precise U-Pb Isotopic Dating of Precambrian Zircon

This thesis addresses various issues in U-Pb zircon geochronology, proposing new experimental protocols in conventional chemical abrasion-isotope dilution thermal ionization mass spectrometry or CA-(ID)-TIMS and developing a new method for Pb evaporation-condensation from zircon that allows high precision Pb-Pb age determination on Precambrian samples. Various experiments are also done on zircon to extract U-Pb information by in situ flux aided fusion methods and to optimize a better silica gel Pb-ionization activator. Radiation damage caused by U decay in zircon disrupts its ‘closed system’ behavior leading to the loss of daughter radiogenic Pb and resulting in inaccurate ages. A high temperature thermal annealing procedure has been proposed to prevent such Pb loss. Studies presented here have been carried out using Laser Raman Spectroscopy and Scanning Electron Microscopy to characterize radiation damage and effects of laboratory induced thermal annealing on such damage. Backscattered electron images reveal a variety of textures for ZrO2 overgrowths on zircon annealed at 1450oC. Highly damaged zircon produces finer polycrystalline aggregates (<5µm) than zircon with less damage. Raman spectroscopy indicates that crystals with different levels of radiation damage are only partially restored by annealing at 1000oC for 2–3 or 20 days. Annealing at 1450oC for 1 h results in partial breakdown of zircon but restores Raman peak widths and wave numbers. Raman spectra are much less sensitive to polarization angle for annealed highly damaged grains than for weakly damaged zircon showing that when highly damaged zircon is recrystallized, it becomes a polycrystalline aggregate that pseudomorphs the original single crystal. The whole grain Pb evaporation-condensation method is based on 206Pb-207Pb age analyses where zircon grains are pre-treated at 1450oC to drive out all disturbed Pb and then they are kept at 1600oC for an hour or two during which Pb atoms are evaporated out of the grain and deposited directly into a clean Savillex teflon vial or a wide Re filament. This technique allows the use of a 202Pb-205Pb double spike for precise isotopic fractionation correction. Examples are shown in which application of this technique to zircon from Precambrian samples has successfully yielded sub-million year age precisions.

Keywords: Uranium-Lead zircon geochronology
Alpha radiation damage
zircon
Raman spectroscopy
Advisor: Davis, Donald W.
Molecular Mechanisms Involved in Insulin- and Leptin-mediated Regulation of Hypothalamic Proglucagon Gene Expression and Action of Glucagon-like Peptides on Hypothalamic Neuropeptides

The hypothalamus is a central regulator of energy homeostasis. Recently, proglucagon-derived peptides have emerged as potential appetite regulators. The proglucagon gene is expressed in the periphery and also in selective hypothalamic neurons. The regulation of hypothalamic proglucagon by two key regulators of energy balance, insulin and leptin, remains unstudied. Central glucagon-like peptide (GLP)-1 receptor (GLP-1R) activation by exendin-4, a long-acting GLP-1R agonist, induces anorexia; however, the specific hypothalamic neuronal populations activated by exendin-4 remain largely unknown. The role of GLP-2 as a central appetite regulator is poorly understood. In this thesis, using murine hypothalamic cell lines and mice as experimental models, mechanisms involved in the direct regulation of proglucagon gene by insulin and leptin were studied, and the actions of exendin-4 and GLP-2 on hypothalamic neuropeptides were determined. It was found that insulin and leptin regulate hypothalamic proglucagon mRNA by activating Akt and signal transducer and activator of transcription 3, respectively. Insulin and leptin did not regulate human proglucagon promoter regions, but affected proglucagon mRNA stability. In mice, intracerebroventricular exendin-4 and GLP-2 induced anorexia, activated proopiomelanocortin- and neuropeptide Y-expressing neurons in the arcuate nucleus and neurotensin- and ghrelin-expressing neurons in major hypothalamic appetite-regulating regions. In the hypothalamic neuronal models, exendin-4 and GLP-2 activated cAMP-response element-binding protein/activating transcription factor-1, and regulated neurotensin and ghrelin mRNA levels via a protein kinase A-dependent mechanism. Overall, the in vivo and in vitro findings suggest that these neuropeptides may serve as potential downstream mediators of exendin-4 and GLP-2 action. This research demonstrates direct regulation of hypothalamic proglucagon by insulin and leptin in vitro, and reports a previously unrecognized link between central GLP-1R and GLP-2R activation and regulation of hypothalamic neuropeptides. A better understanding of the regulation of hypothalamic proglucagon and central GLP-1R and GLP-2R activation is important to further expand our knowledge of feeding circuits.

Keywords: Endocrinology
Hypothalamic regulation of feeding neuropeptides
Advisor: Belsham, Denise
The Role of Mitochondrial Alternative Oxidase in Plant-pathogen Interactions

Alternative oxidase (AOX) is a non-energy conserving branch of the mitochondrial electron transport chain (ETC) which has been hypothesized to modulate the level of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in plant mitochondria. The aim of the research presented herein is to provide direct evidence in support of this hypothesis and to explore the implications of this during plant-pathogen interactions in Nicotiana tabacum. We observed leaf levels of ROS and RNS in wild-type (Wt) tobacco and transgenic tobacco with altered AOX levels and we found that plants lacking AOX have increased levels of both NO and mitochondrial O2 - compared Wt plants. Based on the results we suggest that AOX respiration acts to reduce the generation of ROS and RNS in plant mitochondria by dampening the leak of electrons from the ETC to O2 or nitrite. We characterized multiple responses of tobacco to different pathovars of the bacterial pathogen Pseudomonas syringae. These included a compatible response associated with necrosis (pv tabaci), an incompatible response that included the hypersensitive response (HR) (pv maculicola) and an incompatible response that induced defenses (pv phaseolicola). We show that the HR is accompanied by an early mitochondrial O2 - burst prior to cell death. Also, we found iii that the appearance of HR and the appearance of the mitochondrial O2 - burst are delayed in transgenic plants lacking AOX. A similar delay is seen in transgenic plants treated with the complex III inhibitor antimycin A. In Wt plants, expression of Aox1a is suppressed during the HR response to pv maculicola despite the accumulation of signaling molecules known to induce Aox1a transcription. Also, MnSOD activity declined during the HR. We suggest that the mitochondrial ROS burst controlled by AOX and MnSOD is an important component for the induction and coordination of the HR during plant-pathogen interactions.

Keywords: Mitochondria
Respiration
Plant pathogens
Disease resistance
Advisor: Vanlerberghe, Greg