VictorJuiz/thesis huggingface dataset:
Investigation of the Tail Fibres and Tail Fibre Assembly Proteins of Contractile-tailed Phages

The tail fibres of long-tailed phages are complex elongated protein assemblies capable of specific recognition of bacteria during the first step of viral infection. Correct assembly of these structures is crucial for successful phage propagation and often requires a phage-encoded tail fibre assembly (Tfa) protein. In Escherichia coli phage T4, the formation of the distal portion of tail fibres requires a Tfa (product of gene 38) which is absent from mature particles. Despite the essential role of Tfa proteins for many diverse phages, only a few studies have addressed their functional mechanisms. Here, I investigate the tail fibre and Tfa of E. coli phage Mu. I demonstrate that Tfa forms a stable complex with the tail fibre, and I present a 2.5 Å resolution X-ray crystal structure of this complex. The Tfa:tail fibre complex is shown to bind the phage baseplate wedge and lipopolysaccharide, the outer membrane receptor for this phage. My in vitro and bioinformatics studies reveal that Tfa proteins are comprised of two domains: a non-conserved N-terminal domain that binds to the fibre and a conserved C-terminal domain that likely mediates fibre oligomerization and assembly. I propose that the key role of Tfa proteins is to initiate multimerization and assembly at the C-terminus of fibres, ensuring that their intertwined and repetitive structural elements come together in the correct sequence. Surpringly, I also detected Mu Tfa in the mature particles of Mu. In addition, I discovered that the Tfa proteins of phages Mu and E. coli phage P2 bound to lipopolysaccharide. Despite sharing 93% sequence identity these Tfa proteins displayed different LPS-binding preferences, consistent with those of full phage particles. In summary, I conclude that Mu Tfa is required for tail fibre folding and oligomerization as was seen for phage T4. In contrast to T4, however, Mu Tfa binds stably to the tail fibre and stays bound even in the mature particle. This observation coupled to the demonstrated LPS-binding activity of Mu and P2 Tfa suggests that Tfa proteins may play a role in determining host specificity. Thus, the function of “chaperone” may not apply to many Tfa proteins.

Keywords: Bacteriophage
Phage
Phage receptor-binding proteins
Phage tail
Tail fibre assembly
Tail fibres
Advisor: Davidson, Alan R
The Role of the Transcription Factor FUSCA3 in Reproductive Development of Arabidopsis thaliana

Reproduction is a fundamental stage in the cycle of life. In flowering plants, this begins with flowering and ends with seed setting. Although extensive work has been done on these complex processes, there are many gaps in our understanding of the underlying mechanisms and genetic networks. The B3 transcription factor FUSCA3 (FUS3) plays a key role in controlling seed maturation processes and developmental phase transitions through the modulation of hormone levels. Many downstream targets have been identified through transcriptomic and chromatin immunoprecipitation studies, however, the regulation of FUS3 activity is poorly understood. Recently, it was shown that FUS3 interacts with and is phosphorylated by AKIN10, a kinase subunit of the Sucrose non fermenting 1 (Snf1)-RELATED KINASE 1 (SnRK1) complex. SnRK1 is a central regulator of carbon levels and stress response that is conserved among eukaryotes. This opens the possibility that stress signals working through SnRK1 may regulate seed development through FUS3 phosphorylation. In this study, I investigated the function of FUS3 phosphorylation in Arabidopsis thaliana. The SnRK1 phosphorylation site of FUS3 is embedded in the basic B2 domain, which is strongly conserved among eudicot species. Characterization of the loss-of-function fus3-3 mutant, as well as transgenic fus3-3 lines carrying phosphonull and phosphomimic FUS3 variants, showed that FUS3 phosphorylation does not affect seed maturation, but regulates reproductive and early seed development, uncovering novel roles for FUS3. FUS3 was found to regulate pollen viability and the developmental rate of the endosperm, integument and embryo. Fertility was reduced in fus3-3 as a result of both pollen defects and maternally-derived post-fertilization seed abortion. Intriguingly, pollen and seed abortion in fus3-3 were higher under heat stress compared to the wild type. Except for pollen defects, all these novel fus3-3 phenotypes were rescued by wild type and phosphomimic FUS3 variants, while the phosphonull FUS3 variant enhanced them. Together, these findings demonstrate that FUS3 phosphorylation plays an important role in reproductive and early seed development, and that FUS3 regulates adaptive reproductive responses by acting downstream of stress signals in Arabidopsis thaliana.

Keywords: FUSCA3
Reproduction
Seed Development
Advisor: Gazzarrini, Sonia
Shared Decision Making in Youth with Brachial Plexus Birth Injury and Their Families

Introduction: This dissertation used an overarching interpretivist qualitative framework in the development of a patient decision aid (PtDA) for youth with brachial plexus birth palsy (BPBI) and their parents when making preference-sensitive decisions regarding rehabilitation and surgical treatment options for an elbow flexion contracture. The objective was to develop a tool containing evidence-based information and a values clarification method to help these youth (ages 8 and 18 years) and their families discern what they value most related to their options. Methods: PtDA development was guided by a conceptual framework built on existing PtDA models and standards. A philosophical hermeneutic approach combined with arts-based methods was used to conduct a decisional needs assessment based on two qualitative sources: in-depth interviews with 5 young adults and 14 youth-parent dyads, and 15 participant observation sessions of families and clinicians in the clinic setting. These qualitative findings were integrated with evidence from knowledge synthesis methods on elbow flexion contractures and its treatment options to develop the PtDA prototype, which was in turn field-tested with 17 youth via cognitive-based interviewing. Results: Several substantive contributions to the fields of BPBI and pediatric shared decision making were achieved through the process of developing this PtDA. A PtDA for youth with BPBI was created and an arts-based qualitative approach provided a unique way to interpret and understand the family-team clinic experience. Overall, the shared decision making in youth with BPBI was influenced more by a family’s appearance-related concerns and the strength of their trust relationship with clinicians, and less by their activity and participation concerns. Although decisional conflict in these families seemed rare, once rehabilitation treatment was initiated, decision regret was sometimes expressed. Regret was associated with youth-parent decision discord that was influenced by parental emotions, youth’s response to external pressures, and experiences with treatment adherence. Conclusions: By revealing the complexities of shared decision making in youth with BPBI, this research reflects the real-world concerns of these families in the design of this PtDA. The insights gained offer guidance for future PtDA implementation that optimize its potential to promote positive health outcomes in youth with BPBI and their families.

Keywords: Adolescent
Brachial Plexus
Children
Decision Making
Decision Support Techniques
Elbow Contracture
Advisor: Wright, Virginia
Perceptions of Change Among Emergency Department Staff in a University Teaching Hospital in the United Kingdom

University teaching hospitals provide acute and emergency care in most healthcare systems. One of the priority areas in hospitals are emergency departments (ED) where practice changes are the norm due to the unpredictable and open “public good access” nature of service demands. At present changes to EDs are implemented to improve efficiency and reduce costs in the United Kingdom (UK) and other developed countries. Also, at present, there is limited evidence on how or why change is successful in some instances and not in others. The objective of this research was to study staff perceptions of change and the factors influencing the implementation of changes at a university teaching hospital in the UK. A modified grounded theory methodology was used to perform a secondary analysis of 41 interview transcripts to answer the research questions. Interview transcripts from participants consisted of 20 physicians, 13 nurses, two support workers and six managers involved in paediatric emergency care at the hospital. Data analysis provided answers to the first research question of how changes happen in the emergency department by identifying triggers and barriers to both planned and emergent changes. The second research question of what factors impact change identified three themes; communication, education and leadership. The concept that permeated all identified themes was that change provokes emotional responses at individual, team, and organizational levels. Good communication leading to staff involvement, education about new processes and credible trusted leadership, encouraged positive emotions and reduced negative emotions. In this study, negative emotions stemmed from a perceived inability of healthcare professionals to function effectively and efficiently to ensure safe patient care with changes. Professional values dictated the actions or inactions that transpired either as a result of these emotions or despite these emotions in health professionals. The study findings illustrate an emerging concept of emotions in change and the importance of acknowledging the reasons for negative emotions and fostering positive emotions in individuals and groups through communication, education and good leadership. I hope this concept will ultimately advance the theoretical understanding and practical strategies to help the process of change management in healthcare organizations.

Keywords: change management
continuing education of health professionals
hospitals
organizational change
organizational learning
staff attitudes
Advisor: Lang, Daniel W
Investigating the functional roles of NBEAL2 in megakaryocytes and platelets

Platelets are small anucleate blood cells that co-ordinate blood clotting in response to vascular injury. In additional to their hemostatic role, platelets are involved in a diverse range of physiological and pathological processes. Platelets contain abundant secretory vesicles associated with their functions, which are generally classed as α-granules, δ-granules and lysosomes. These vesicles originate in megakaryocytes (MK), hematopoietic cells that produce platelets in the bone marrow. The inherited bleeding disorder Gray Platelet Syndrome (GPS) is characterized by platelet α-granule deficiency arising from loss of function of neurobeachin-like 2 (NBEAL2). The goal of my study was to investigate the roles and functions of NBEAL2 in MKs and platelets. Using biochemical assays, it was found that NBEAL2 is a cytosolic protein capable of self-association and adopts two distinct oligomeric states in MKs. Immunoprecipitation-mass spectrometry was used to identify several potential NBEAL2-interacting proteins, providing insights into its cellular functions. Among these interactors, SEC22B was shown to be essential for the formation of α-granules, where loss of SEC22B expression resulted in an α-granule deficiency similar to that caused by the loss of NBEAL2. Forms of NBEAL2 expressing the GPS-associated mutations E1833K or R1839C failed to interact with SEC22B, indicating a functional significance for NBEAL2-SEC22B interactions in α-granule biogenesis. A Nbeal2-/- mouse strain was generated to model GPS. Studies of Nbeal2-/- mice revealed that NBEAL2 is required for normal platelet activation and aggregation, and for normal development and proplatelet-platelet production by MKs. Studies of the uptake and intracellular trafficking of the α-granule cargo protein fibrinogen (FGN) revealed that NBEAL2 is not essential for FGN endocytosis by MKs, nor its passage through endocytic compartments associated with RAB5, RAB7 and the α-granule membrane protein P-selectin. The latter compartment retains both endocytosed and MK-synthesized cargo proteins when NBEAL2 is present, but in cells lacking NBEAL2 cargo proteins are lost from this compartment and exit MKs via a RAB11-mediated secretory pathway. Intracellular protein colocalization and co-immunoprecipitation studies revealed a potential interaction between NBEAL2 and P-selectin in MKs and platelets. Thus we propose that NBEAL2 is required for the stabilization of α-granules during cargo loading, maturation and circulation within platelets.

Keywords: Granules
Gray Platelet Syndrome
Hematology
Megakaryocytes
NBEAL2
Platelets
Advisor: Kahr, Walter HA
Writing Rights, Writing Violence: The Bureaucracy of Palestinian Testimonies in Israeli Human Rights NGOs

This dissertation is an ethnography of Israeli non-governmental organizations (NGOs), that document the violations of Palestinians’ human rights (HR) perpetrated by Israel’s occupation of Palestinian territories. Israeli anti-occupation NGOs rely on a rigid bureaucratic logic in their processing of testimony – a written-down narration of a subjective experience of violence into a coherent narrative in document-form: violence is translated into a written text that can be used for legal-action purposes, research, media circulation, and is eventually archived. By anthropologically examining bureaucratic lugubriousness in NGOs, I theorize HR as a project of documentation and archiving that legitimates itself as a subversive bureaucracy. Simultaneously, this project’s own critical authority is undermined since it relies on colonial modes of knowledge production and representation. Based on 18 months of participant-observation in four NGOs, I trace the trajectory of Palestinians’ testimonies as NGOs’ main source of data and as HR’ dominant genre of representation. NGO practices are considered against the backdrop of growing disdain in Israel/Palestine towards HR, not only in the populist rhetoric and efforts of anti-liberal politicians, but also amongst activists, critical scholars, Palestinians living under the occupation, and within NGOs’ own staff. The main recurring critique is that HR fail to protect Palestinians or curb Israel’s settler-colonialism. Some detractors claim that NGOs are complicit with Israel’s violence. This study explores why Palestinians continue to testify for Israeli NGOs that, in turn, persist in documenting Palestinians’ testimonies. I suggest that HR are a genre of anti-colonial historiography that is itself based on colonial reason, mainly genealogies of surveying and bureaucratic writing: NGOs rely on what I term as “frames of in/validation” - phases of incessant verification and adaptation of Palestinian experiences of violence into simplified narrative structures, that conform to legal-moral discourses and definitions of HR. While the strictures of documentation and writing problematically limit the moral claims and political clout of NGOs, HR paradoxically remain relevant through the relational foundation affirmed by frames of in/validation, namely: between a violent past written as a bureaucratic document, and a distant future in which imagined publics make moral-political judgments based on NGOs’ archives.

Keywords: Bureaucracy
Human Rights
Israel/Palestine
NGOs
Violence
Witnessing
Advisor: Kalmar, Ivan
Paz, Alejandro
Exploring Latent Profiles of Writing in Linguistically Diverse Students in the Middle School Grades

This thesis consists of two studies that investigate longitudinally narrative writing development and factors that lead to low performance in writing in the middle school grades with native English speakers (EL1) and English Learners. The first study consists of two parts. Part A examined writing profiles in Grade 4 and 6 and the resulting relationships to reading outcome measures as well as the effect of language status and gender. Three distinct writing profiles were found in Grade 4 and 6 (low performing, average, and strong writers) which corresponded to similar ability levels on the word reading and reading comprehension outcome measures. There was no EL-EL1 effect on the writing profiles, however there was a gender effect showing that boys were more at risk for writing difficulties than girls. Part B investigated the transition patterns of these writing profiles between Grades 4 to 6. The writing profiles were fairly stable across the middle school grades with a high proportion of students remaining in the same latent profile across time (76.4%). Differences were noted in the transition profiles of boys and girls with more boys remaining in the low performing group over time.The second study investigated the contribution of oral language (vocabulary and syntactic skills) to low performing writing status, beyond that of a base set of predictors, that included rapid naming, working memory, and spelling. In Grade 4, both vocabulary and syntactic skills contributed independently to low performing writing status beyond the base measures. By Grade 6, only syntactic skills were found to be a unique predictor of low performing writing status beyond the base measures. Overall, this thesis provides support that distinct and stable writing profiles can be recognized by the middle school grades in EL and EL1 students and offers insight into the characteristics of low performing writers. The implications of these findings for assessment and intervention and directions for future research are discussed.

Keywords: English Learners
gender
literacy
narrative text writing
predictors of at-risk writing
Advisor: Geva, Esther
Shedding Light on Radiotherapy: Quantifying Radiiological Response of Irradiated Tissues with Functional Optical Coherence Tomography

Radiation therapy (RT), alone or in combination with other therapies, is one of the most commonly used treatment strategies for managing cancer. Recent advances in RT delivery and monitoring of radiobiological tumor effects have led to the development of stereotactic body radiotherapy (SBRT) with improved local control and lower damage to surrounding normal tissues. Despite the rapid dissemination of this tremendously advanced technology in the community to manage many disease sites, it remains somewhat ‘blind’ – its relative success and outcome are often not known for weeks or months following treatment. As well, there are indications that the radiobiology involved in the SBRT regime may be different from the conventional 2Gy/fraction RT, specifically with respect to its effect on microvascular response. This thesis investigates optical coherence tomography (OCT) as an imaging modality for the detection and quantification of early (days to weeks) and late (months) tissue changes induced by radiotherapy. Innovative methods are developed to apply non-invasive, depth-resolved and label-free OCT technology for in-vivo assessment of tumor microvascular and microstructural response to radiation and evaluation of late radiation toxicity to normal tissues at resolution approaching optical microscopy. Pre-clinical models of human tumor xenografts subjected to 10-30Gy single doses are investigated for vascular remodeling following RT. Texture analysis of volumetric OCT images of tissues is performed to delineate irradiated tumors and detect subtle changes within the first weeks after 15Gy single-dose irradiation with RT-response metrics. An OCT-based method for in-vivo assessment and quantification of radiation-induced fibrosis-associated microvascular changes in tissue is proposed and tested on murine models 6 months after a 40Gy single dose irradiation. Finally, a label-free lymphangiography / neurography method is developed and validated with histopathological studies, opening new exciting ways for assessment of tumor lymphatics and nerves development and response to RT. These innovative methods build a solid foundation for future studies that will aim to discover fundamental insights into SBRT radiobiology after specific dose-fractionation schedules (e.g., 8Gy per fraction at 5 fractions delivered within two weeks) and correlate the outcomes with clinical treatment and imaging protocols, in an effort to better understand and improve the SBRT treatment strategies.

Keywords: Biomedical Optics
Biophotonics
Imaging
Optical Coherence Tomography
Radiotherapy
Tumor Control
Advisor: Vitkin, I. Alex
Characterization and Modelling Studies of Turanite for the Catalytic Conversion of CO2 to Methanol

Capturing and converting greenhouse gas CO2 into carbon-based fuels and chemical feedstock offers a sustainable substitute to fossil resources in chemical manufacturing and a means to remove excess carbon emission from the atmosphere. This work offers a comprehensive study into the structural, chemical, and thermal properties of turanite, Cu5(VO4)2(OH)4, a naturally-occurring mineral, relevant to its catalytic activity towards methanol production from CO2. Activated Cu5(VO4)2(OH)4 is demonstrated to exhibit significant catalytic activity towards methanol formation at relatively low temperatures and ambient pressure conditions. The reduction of nanostructured Cu5(VO4)2(OH)4 by hydrogen is investigated using a combination of diffraction, microscopy, in situ spectroscopy, first-principles calculations, and kinetic analysis based on thermogravimetry. A two-step mechanism is proposed, in which Cu5(VO4)2(OH)4 is first reduced, following exponential growth kinetics, to form a stable intermediate consisting of a mix of Cu3VO4, Cu2O, and CuV2O5. The intermediate phase is then subsequently reduced in a diffusion-limited process to form two segregated phases consisting of Cu metal and V2O3 particles. Results obtained from in situ infrared spectroscopy and first-principles calculations suggest that the reaction pathway for methanol production involves a formate intermediate. This study demonstrates the importance of using combined in situ characterization techniques to study heterogeneous metal oxide catalysts and the potential for employing naturally-occurring minerals that contain earth-abundant metals for the conversion of CO2 to value-added products.

Advisor: Ozin, Geoffrey A.