VictorJuiz/thesis huggingface dataset:
Preclinical Potentiators of Statin-induced Anticancer Effects

Statins have been used for decades in the treatment of hypercholesterolemic patients to decrease the incidence of adverse cardiovascular events. Statins target the rate-limiting enzyme of the mevalonate (MVA) pathway, 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR). Statin-mediated HMGCR inhibition in hepatocytes leads to depletion of MVA derived sterols, including cholesterol, and a subsequent uptake of low-density lipoprotein (LDL) cholesterol from the plasma. Aside from the intended cholesterol-lowering properties, statins exert many pleiotropic effects including anti-tumour activity. The well characterized pharmacokinetic profiles, safety and the fact that many statins are off patent has ensured their prompt entry into clinic for evaluation of anti-cancer efficacy. We hypothesize that the therapeutic window of statins can be increased through (i) the use of a pharmacological screen to identify compound/s that synergize with statins to induce tumour-specific apoptosis and (ii) the use of a genome-wide small hairpin ribonucleic acid (shRNA) screen to identify novel pathways/targets whose knockdown enhances the vulnerability of tumour cells to statin-inhibition. Firstly we carried out a screen in a multiple myeloma (MM) cell line where we combined atorvastatin with other off-patent FDA approved drugs. We identified dipyridamole, a commonly used anti-platelet agent as synergizing with and potentiating statin-induced apoptosis in a variety of MM and acute meylogenous leukemia (AML) cell lines and primary patient samples. The efficacy of the combination was demonstrated in vivo. Secondly, through genome-wide shRNA screen, we identified several putative targets whose knockdown potentiated statin induced anti-cancer effects in the A549 lung cancer cell line. Amongst the most promising hits, sterol regulatory element binding transcription factor 2 (SREBF2) was validated in lung and breast cancer cell lines. The knockdown of SREBF2 was found to dramatically potentiate statin-induced apoptosis and block the upregulation sterol-responsive gene targets. Taken together, this research has uncovered a novel combination of clinically translatable drugs with strong preclinical efficacy in hematological malignancies. Furthermore we have identified several novel validated targets that sensitize the MVA pathway to statin-induced apoptosis.

Keywords: Statins
anti-cancer agents
shRNA screen
pharmacological screen
Advisor: Penn, Linda
Biochemical Determinants of Methanol Developmental Toxicity in Rabbits

The teratogenic potential of methanol (MeOH) in New Zealand white (NZW) rabbits was examined, with emphasis on the biochemical basis for species differences in susceptibility. A comparison of MeOH and formic acid (FA) elimination profiles was first carried out in NZW rabbits, CD-1 mice and cynomolgus monkeys to evaluate the relationship between MeOH metabolism and its teratogenic potential, and to provide a more accurate assessment of human developmental risk than is currently available. Rabbits and the C3H mouse strain were resistant to MeOH-associated external birth defects, whereas CD-1 and C57BL/6 mice were susceptible. Rabbits were similarly resistant to the entire sprectrum of MeOH-initiated skeletal anomalies found in rodents, but exhibited a novel skeletal defect, notably a decrease in post-lumbar vertebrae, which is not found in rodents. MeOH and FA pharmacokinetics were comparable between susceptible and resistant mouse strains, yet different between resistant rabbits and mice, indicating that adult pharmacokinetics cannot explain strain and species differences in susceptibility to MeOH teratogenicity. Catalase and alcohol dehydrogenase (ADH1) activity were compared in adult and embryonic samples from MeOH-resistant NZW rabbits and susceptible CD-1 mice. Antioxidative and peroxidative catalase activities were substantially lower in rabbits than mice, whereas ADH1-catalyzed EtOH metabolism was faster in rabbits than mice. This suggests that: (1) rabbit MeOH metabolism is catalzyed by ADH1 as opposed to catalase, and (2) MeOH-initiated reactive oxygen species (ROS) formation may contribute to the mechanism of MeOH teratogenicity in susceptible mouse strains. Catalase exhibits antioxidative acivity in all species, but peroxidatively metabolizes MeOH to formaldehyde only in rodents. Humans, and possibly rabbits, however, oxidize MeOH using ADH1. The higher peroxidative catalase activity in mice than rabbits, suggests reduced catalase-mediated MeOH metabolism in the latter species, which would increase catalase capacity for ROS scavenging, and protection, in rabbits.

Keywords: Methanol
Teratology
Rabbit
Advisor: Wells, Peter G.
Developmental and Neurobehavioural Effects of Prenatal Exposure to a Ketogenic Diet

Inappropriate gestational nutrition can have detrimental effects on the developing fetus. With the in- creasing popularity and therapeutic applications of the ketogenic diet (KD), it is important to investigate whether it can be consumed during gestation. Previous studies on gestational ketosis have primarily investigated ketosis resulting from starvation or diabetes. However, these ketotic conditions do not pro- vide adequate energy and nutrients to the mother or the fetus, and cannot properly imitate the stable ketosis resulting from KD consumption. This thesis aims to elucidate some of the developmental, neurological, and behavioural effects of gestational consumption of a KD on the offspring. To identify such effects, young adult CD-1 mice were fed the KD prior to and during gestation. Their offspring were compared with those from a control group fed a Standard Diet (SD). Comparison was conducted at fetal, neonatal, and early adulthood periods. Regardless of prenatal diet, all mice were adopted by lactating SD foster dams at postnatal-day (P) 2.5 and were weaned to the SD at P21.5. Optical projection tomography was used to image the embryos at embryonic-day (E) 13.5, Magnetic Resonance Imaging was used to image the E17.5 embryos, the neonatal brains at P11.5 and P21.5, and the young-adult brains at P90. Physical activity and susceptibility to anxiety and depression were assessed in adult offspring via standardized neurobehavioural tests. Several morphological differences were noted between the KD and SD offspring at each time-period. Compared with the SD counterpart, the KD embryo was significantly larger at E13.5, but significantly smaller at E17.5. The relative volumes of its brain and heart were also altered. The average KD pup gained weight slower and its brain morphology at P21.5 was significantly altered. For example, the hippocampus and corpus callosum were relatively smaller, while the hypothalamus and cerebellum were relatively enlarged. Neuroanatomical changes also existed in adulthood, and were accompanied by altered susceptibility to anxiety, depression, and hyperactivity. Taken together, prenatal exposure to a KD during programs the offspring anatomy and behaviour, despite exposure to the same diet in postnatal life.

Keywords: Ketogenic diet
maternal nutrition
prenatal nutrition
Atkins diet
Low carbohydrate
high fat diet
Optical Projection Tomography
MRI
development
epigenetics
epigenetic programming
maternal protein undernutrition
low protein
ketone
ketosis
anatomy
behaviour
neurobehavior
mouse
brain
neonatal development
ketoacidosis
lactation
brain structure
neuroanatomy
morphology
clinical imaging
3D imaging
metabolism
growth
gestation
pregnancy
gestational nutrition
Diffusion Tensor Imaging
mouse embryo
Advisor: Henkelman, R. Mark
Association between Oral Health Literacy and Patient-Centred and Clinical Outcomes

During the last decade, oral health literacy (OHL) has received significant attention as an important factor that might affect oral health outcomes. Few published instruments are available to measure OHL. Most of these instruments focus on measuring the functional OHL (word recognition, comprehension and numeracy skills) with no attempt in the literature to measure other levels of oral health literacy (communicative and critical OHL). The aim of this PhD thesis was to cover some of the deficiencies in OHL research. A conceptual framework for the factors or outcomes affecting or affected by OHL was developed. Several factors and outcomes were included in the model, including: socio-demographics, dental usage and oral health behaviour variables, self-perceived oral health status, dental knowledge, oral health impact, quality of patient-dentist communication, caries experience and periodontal condition. In the first part of the project, a new communicative and critical OHL instrument (CCOHLI) was developed. CCOHLI displayed high internal consistency and good test-retest reliability. Construct validity of the CCOHLI was established against other health literacy and OHL instruments. Predictive validity was established by significant associations with oral hygiene behaviours, self-perceived oral health status, and caries experience at a multivariate level. The aim of the second part was to confirm the predictive and construct validity of the previously developed and validated OHL instrument (OHLI). The construct validity of the OHLI was confirmed against medical and dental word recognition tests. The predictive validity of the OHLI was confirmed with significant associations with some of the socio-demographics, oral health knowledge, prevalence of oral health impact, and caries experience at multivariate level. In the third part, the validity of a set of questions as a quick tool to identify patients with limited OHL was established. These screening questions can provide a rapid and inexpensive way to identify patients with limited oral health literacy in a busy clinical setting or to conduct large-scale studies. The fourth part shed light on patient-dentist communication as one of the factors that might be influenced by the level of OHL. This area requires special attention in order to improve the quality of the communication process.

Keywords: adults
instrument validation
oral health literacy
patient-dentist communication
screening
critical
communicative
barrier
Advisor: Lawrence, Herenia
Identification of Key Organisms, Genes and Pathways in Benzene-degrading Methanogenic Cultures

Benzene is a carcinogenic hydrocarbon and a widespread groundwater contaminant. Microbial mineralization of benzene is possible, but the process is slow and not well understood under the anaerobic conditions that are often prevalent at contaminated sites. The goals of this study were to gain a better understanding of key organisms, genes and metabolic pathways associated with benzene degradation in methanogenic enrichment cultures. Conditions required for the successful growth of the cultures were also explored. Potential key organisms were identified via 16S rRNA gene cloning studies, performed using several cultures that had been enriched in parallel from the same hydrocarbon-contaminated site. In all cultures, closely related members of the Syntrophobacterales were found to have survived and thrived over nearly a decade of enrichment. These organisms, referred to as ORM2-like organisms, were phylogenetically most similar to those present in cultures enriched from other benzene-contaminated sites. To link organisms with their potential roles in anaerobic benzene biodegradation, we sequenced, assembled and analyzed the metagenome of one of the benzene-degrading methanogenic cultures. Several assemblies were created from Illumina sequencing data and a combination of these proved to be optimal. An unsupervised binning method was developed to achieve near-complete genomes of the three most abundant phylotypes, including a group of three closely-related ORM2-like species, a hydrogen-utilizing Methanoregula sp., and a previously unidentified organism in the culture, classified as a member of the Candidate Division OD1. The ORM2-like organisms were found to harbor a suite of genes linked to the degradation of the central metabolite benzoyl-CoA. Proteomic data confirmed that these genes were expressed under benzene-degrading conditions, providing strong evidence for the role of ORM2-like organisms as benzene fermenters. Activity of hydrogenotrophic and acetoclastic methanogens was confirmed; other organisms may play peripheral roles that increase the culture robustness. The absence of an easily identified putative anaerobic benzene carboxylase in the ORM2-like genomes suggests a novel mechanism for benzene activation by these organisms. The work presented here provides a valuable blueprint that could be used in identifying biomarkers of anaerobic benzene biodegradation, or in exploring the genomes of organisms from novel genera, orders and even phyla.

Keywords: anaerobic benzene biodegradation
bioremediation
Advisor: Edwards, Elizabeth A.
Effect of Blending and Degradation on the Morphology of Polyferrocenylsilane Block Copolymer Micelles

This thesis describes the study of the self-assembly of polyferrocenylsilane (PFS) block copolymers in solution, with a focus on how the length and nature of the corona forming block affected the nature and properties of micelles formed. Most experiments were carried out with four samples: PFS50-PI1000, PFS48-PI264, PFS53-PDMS285, and PFS80-PDMS960, where PI = polyisoprene, PDMS = polydimethylsiloxane, and the subscripts refer to the degree of polymerization. When each polymer was added to a suspension of short pre-formed seed micelles, long uniform fiber-like micelles formed. Polymers with long corona and core forming blocks had the lowest linear aggregation numbers (micelles per nm). When binary blends of these polymers were added to the seed micelles, the micelle length varied with polymer composition in the blend. Complex structures were formed from the self-assembly of blends of PFS homopolymer and PFS48-PI264. These structures had a central lamella with fibers attached to both short ends of the lamella. The physical dimensions of the structures did not change with increasing homopolymer loadings for blends containing PFS20. However the area of the lamellar structures increased, and the fiber length decreased, with increased loading of PFS50. I infer that PFS homopolymer cocrystallized with PFS48-PI264 to decrease the grafting density of the PI corona chains in the blend structure. I used intense sonication to produce a new type of seed micelle that formed multiarm-star (multipod) micelles when additional block copolymer was added. These stars have fiber-like micelles attached to a small central point. Stars with more than 4 arms become more prevalent iii for regrowth after longer sonication times. These stars have multiple fiber-like arms growing from a large dark central structure. In order to understand the origin of this phenomenon, I undertook a detailed study of polymer degradation during sonication. I found cleavage of the corona chains from the micelles, some crosslinking, but less degradation of PFS in the semicrystalline micelle core. I learned that polymer degradation is the main driving force for star formation in star-shaped structures with fewer than 4 arms, and that aggregates of small micelle fragments nucleate stars with more than 4 arms.

Keywords: Polymer
Self-assembly
Block Copolymer
Advisor: Winnik, Mitchell A.
Vision-Based Estimation and Tracking Using Multiple Unmanned Aerial Vehicles

Small unmanned aerial vehicles (UAVs) have very limited payload capacity and power supply, while they are envisioned to be deployed in complicated environments to perform challenging tasks; therefore, it is imperative to improve their overall autonomy and energy efficiency. This thesis presents a vision-based target surveillance system for small fixed-wing UAVs, which provides them with the capability of autonomously localizing and tracking an uncooperative ground moving target (GMT) using passive vision sensors such as monocular cameras. This system could greatly improve the autonomy of UAVs since target estimation and tracking are critical functions involved in many UAV missions. In this thesis, the UAV-GMT tracking problem is studied from various perspectives, and three different tracking algorithms are developed. The first tracking algorithm is based on sliding mode control, and it enables a fixed-wing UAV to maintain a constant distance relative to a GMT with a speed up to the UAV's cruising speed. The second tracking algorithm is designed to deal with an evasive GMT. It is derived in the framework of the pursuit-evasion game theory and guarantees persistent observation of the GMT. The third one, based on visual servoing control, directly uses visual measurements as feedback signals to close the control loop, so it does not require the GMT's states to assist tracking. The second part of this thesis presents a formation flight algorithm which enables multi-UAV cooperation in target tracking and target motion analysis. The motion of the formation is solely determined by its virtual leader; therefore, tracking algorithms developed for a single UAV can be directly extended to a multi-UAV formation through implementations on the virtual leader. The third part of this thesis develops a cooperative nonlinear filter in order to recover the states of a GMT using multiple vision-enabled UAVs. Through fusing visual measurements from multiple sources, the observability of this bearing-only estimation problem is ensured. Special attention is taken in the filter design in order to accommodate the GMT's unknown dynamics. The tracking, estimation, and formation algorithms developed in this thesis are verified in extensive numerical simulations.

Keywords: Unmanned Aerial Vehicle
Target Tracking
Advisor: Liu, Hugh
Genetic and Functional Genomic Approaches to Characterize Regulatory Proteins in Saccharomyces cerevisiae

BAR domain proteins participate in a variety of membrane trafficking processes that require membrane deformation, particularly in endocytosis. In yeast, endocytosis is achieved by four distinct protein modules: the coat, WASP/MYO, actin and scission modules. The scission step requires the combined action of the BAR domain proteins, Rvs161 and Rvs167, the phosphoinositide phosphatase, Inp52, and the pulling force of actin polymerization to generate sufficient interfacial force to culminate in scission. I took a structure-motivated mutational approach to dissect the function of the BAR domains in Rvs161 and Rvs167 in vivo and validate the significance of Rvs-membrane interaction during the endocytosis process. I find that residues important for lipid binding and bending are required for the initial recruitment of Rvs to endocytic sites and for their function in vesicle scission. Kinases and transcription factors (TFs) are key modulators of important signaling pathways. A systematic assessment of genetic interactions involving the combined perturbation of kinases and TFs may elucidate new aspects of the complex kinase-TF regulatory network. I constructed a collection of yeast strains, each of which contains a chromosomally-integrated kinase or TF gene that can be inducibly overexpressed, and used a variety of assays to characterize the phenotypic consequences of their overexpression. To identify novel genetic interactions, I used Synthetic Genetic Array (SGA) analysis to systematically overexpress 239 different TFs in 13 kinase mutant backgrounds. I assessed dosage-dependent interactions between a loss-of-function or a gain-of-function allele of kinase and TF overexpression allele, and obtained a genetic network iii consisting of 111 confirmed interactions between 72 TF overexpression alleles and 9 kinase mutants. Several of these genetic interactions were further characterized to delineate regulatory relationships between the kinase and TF, suggesting that genetic interactions between kinase and TF overexpression alleles will be a rich source of new functional information.

Keywords: molecular biology
genetics
genomics
systems biology
regulatory pathway
signaling
overexpression
kinase
transcription factor
BAR domain
Rvs167
Rvs161
amphiphysin
endocytosis
vesicle scission
membrane invagination
cell biology
Advisor: ANDREWS, BRENDA
Molecular Pathogenesis of T Lymphoblastic Lymphomas in an Atm-deficient Mouse Model

T lymphoblastic lymphoma/leukemia (T-LL) represent malignant disease of T-cell progenitors. Dysregulation of Notch1 and IL-7R pathways promotes T-LL, however the timing of these events remains unclear. Furthermore, the spectrum of Notch1 mutations has not been fully characterized in T-LL models. Chapter 2 demonstrated 3 T-LLs classified based on activated Notch1 (ICN1) expression that arose spontaneously in mice lacking ataxia telangiectasia mutated (ATM) protein. One group expressed truncated forms of ICN1 (T-ICN1) resulting from frame-shifting PEST mutations. T-LL cells but not normal thymocytes expressed a proteoglycan, syndecan 1 (SDC1). SDC1+ blasts were detected in thymi with normal cellularity from clinically healthy mice, thus representing the earliest discernible stage of T-LL progression. T-ICN1 and IL-7Rα were both aberrantly expressed at this early T-LL stage. Therefore, these data suggest that Notch1 mutations, aberrant expression of IL-7Rα and SDC1 arise early during T-LL progression. Chapter 3 demonstrated a paucity of HD mutations, yet T-LL cells proliferated in a Notch ligand-independent fashion. Analysis of ICN1+ T-LLs revealed truncated Notch1 mRNAs lacking ligand-binding domain and part of negative regulatory region. All truncated transcripts contained the intramembranous methionine that has previously been shown to serve as the translational start site. Collectively, our data identify truncated Notch1 mRNAs in T-LLs that likely encode for polypeptides undergoing ligand-independent activation. The third group lacked ICN1 expression (UD-ICN1). Chapter 4 revealed that UD-ICN1 T-LLs expressed low levels of Notch targets and proliferated independently of Notch signal. Gene set enrichment analyses of genes differentially expressed between UD-ICN1 and T-ICN1 T-LLs revealed higher levels of transcription factor krüppel-like factor 9 (Klf9) and other transcriptional regulators associated with the highly proliferative pre-DP stage of normal T-cell development. siRNA knockdown experiments demonstrated that Klf9 promoted proliferation of UD-ICN1 T-LL cells. Although further studies are warranted, the findings in this thesis reveal oncogenic activation of Notch1 as an early event in Atm-/- T-LL progression, and truncated Notch1 transcripts likely represent a novel mode of ligand-independent Notch1 activation. On the other hand, Klf9 promotes proliferation of Notch-independent T-LLs and may represent a potential therapeutic target for this T-LL group.

Keywords: T lymphoblastic lymphoma and leukemia
Notch1 mutations
Klf9
Microarray
Gene expression profiles
Notch1 deletions
Advisor: Danska, Jayne
Guidos, Cynthia