VictorJuiz/thesis huggingface dataset:
Shaman as Saviour? The Trope of the Amazonian Shaman in Recent Latin American Literature and Film
Keywords: Amazon
anthropology
cinema
environment
literature
shamanism

This dissertation analyzes the trope of the Amazonian shaman in recent Latin American literature and film. References to shamanism have become increasingly popular in recent years. Shamans have gained importance in environmentalism and struggles for Indigenous rights, as well as academic writing interested in radical social change. Meanwhile, shamanic tourism attracts thousands to the Amazon region each year. The books and films of this dissertation participate in this trend by mobilizing the shaman as a figure that holds privileged solutions to contemporary problems like ecological decline, climate change, and persistent coloniality. I argue that these shamanic solutions are often superficial and aimed at satisfying Western desires for progress and limitless growth. Furthermore, they reproduce problematic colonialist tropes, including Western fascination with the ‘wild man.’ Nevertheless, my readings also show how these works may suggest possibilities for change. I draw on critical environmental scholarship, including the work of Elizabeth Povinelli, Stacy Alaimo, Déborah Danowski and Eduardo Viveiros de Castro to show how the shaman characters’ risk-laden and grounded negotiations with materiality may sometimes challenge anthropocentrism and narratives of progress. Moreover, through their frequent references to the Amazonian archive of colonial texts, anthropology, literature and film, the works themselves model a similar process of negotiation that transforms the notion of shamanism. My own contribution via this dissertation is also an inevitable part of this ongoing engagement. Chapter 1 analyzes the influence of shamanic ayahuasca tourism and desires for reconciliation with Indigenous peoples over the abuses of colonialism in the film El abrazo de la serpiente (2015). Chapter 2 addresses how the film Ícaros: A Vision (2016) undermines the drama of shamanic miracle healing and tourism through a focus on the characters’ imbrication with materiality. Chapter 3 compares the ambivalence of shamanic pharmakon remedies in the novels Todas as coisas são pequenas (2008) and El último guerrero de’Aruwa (2006), and the film Chamán: El último guerrero (2016). Chapter 4 analyzes shaman Davi Kopenawa’s techniques for maneuvering restrictions on Indigenous discourse in The Falling Sky: Words of a Yanomami Shaman (2010).
Global Post-Transcriptional Regulation during Human Neuronal Development and Disease
Keywords: Neurodevelopment
Post-transcriptional
Rett
RNA

Globally coordinated post-transcriptional mechanisms that regulate the transcriptome through mRNA stability and translation are relatively understudied during human neurodevelopment and disease. Our lab uses human induced pluripotent stem cells (iPSC) to model neurodevelopment in vitro by directed differentiation into neural progenitor cells (NPC) and cortical neurons. The iPSC model illuminates the mRNA regulatory programs that act during neurodevelopment and disease. Deficiency in the global transcription and chromatin regulator methyl-CpG-binding protein 2 (MECP2) leads to a neurodevelopmental disorder, Rett Syndrome (RTT). Recent molecular studies in RTT focused on transcriptionally altered genes. However, changes in the overall protein synthesis and microRNA biogenesis in RTT neurons point to the contribution of post-transcriptional mechanisms. I dissect the post-transcriptional regulatory layer by measuring mRNA synthesis, degradation, translation rates, and microRNA abundance in neurodevelopment and RTT. First, I described global changes in translation during neurodevelopment and identified genes bound by RNA-binding protein TIA1 that substantially influence MECP2 translation during differentiation to neurons. Second, I studied whether MECP2-deficient neurons have altered mRNA translation. I detected widespread and global changes in ribosomal engagement, agreeing with decreased protein synthesis in RTT neurons. I also captured translational misregulation of NEDD4-family E3-ubiquitin ligases. It highlights altered ubiquitination as a novel molecular signature in RTT. Third, I explored the contribution of mRNA stability to shaping the transcriptome during normal development and RTT. I observed significant shifts in median RNA stability during neuronal differentiation. This global change in RNA stability differentially affects gene isoforms, shaping the transcriptome. A concurrent shift in microRNA copy number per cell suggests a common genome-wide mechanism that drives the process. Next, I probed the degree of coupling between transcription and mRNA stability. I observed a widespread boosting and buffering of transcription rate shifts during neurodevelopment. This crosstalk between nuclear and cytoplasmic machinery is striking upon loss of MECP2. Reanalysis of mouse Mecp2-deficient neurons supported the existence of global buffering, suggesting that mRNA stability response is a conserved feature of RTT models. In summary, I identified a unique role of mRNA stability and translation in the regulation of transcriptome and in mounting a genome-wide balancing response to altered transcription.
Improving Allele Calling in Highly Polymorphic and Repetitive Genomic Regions
Keywords: genotyping
k-mers
pangenome
PRDM9
repetitive

Many regions of the human genome are highly polymorphic, containing numerous variants not found in the current reference genome and making it difficult for variant calling software to accurately identify variants. The effects are particularly pronounced when analyzing structural variants and repetitive regions with short-read sequencing owing to unmapped reads. Long-read sequencing greatly improves structural variant identification, but there is an abundance of data already available generated from short-read technology. Adapting current variant calling approaches for problematic regions of the genome can provide novel insights about variation from existing datasets. This thesis focuses on developing and assessing methods to improve variant calling for polymorphic repetitive genomic regions using the highly variable minisatellite-like zinc finger repeat array of the gene PRDM9 as a proof-of-concept region. I developed short-read models that utilize k-mer information to distinguish between the numerous PRDM9 alleles that differ by single nucleotide polymorphisms and copy number variants of zinc finger repeats. These models were able to call haploid and diploid PRDM9 genotypes with average F1 scores of up to 0.99 and 0.73, respectively, using simulated sequencing reads under typical conditions. Using real Illumina data, the models were able to genotype 43% of 101 samples correctly and ranked the correct genotype in the top 10 for 69% of the samples. I also developed long-read models that use realignment or consensus sequences to validate the short-read models and identify novel alleles. The models correctly genotyped 98% of 101 samples using PacBio reads and found five novel alleles. Finally, I assessed the use of graph-based reference genomes, which are flexible data structures that incorporate known variants to improve polymorphic representation. I constructed different PRDM9 reference graphs and observed modest improvements in read alignment over mapping to GRCh38, with larger improvements for samples with more divergent PRDM9 genotypes or with novel alleles. Overall, my thesis provides insight into how genotyping PRDM9 can be improved by avoiding reliance on mapping reads to the GRCh38 reference. These approaches—utilizing k-mers, long-read sequencing, and graph-based reference genomes—can be further refined and adapted to improve variant identification for additional polymorphic and repetitive genomic regions.
Genes and Neural Cell Types Influencing Reading and the Overlap with Neurodevelopmental Disorders
Keywords: Attention Deficit Hyperactivity Disorder
Autism Spectrum Disorder
Dyslexia
Genome Wide Association Study
Reading Disabilities
RNA sequencing

Although a breadth of research has been conducted on Reading Disabilities (RD), the genes, molecular mechanisms, and cell types involved in its etiology remain to be elucidated. Understanding these processes is complicated by the frequent overlap between RD and other neurodevelopmental disorders. The purpose of this dissertation was to identify genes and neural cell types involved in the development of RD, while considering the genotypic/phenotypic overlap with comorbid disorders. To that end, genome-wide association studies (GWAS) and polygenic risk scores (PRS) were used to identify genes associated with word reading and examine shared genetic etiology with neurodevelopment/psychiatric disorders. We identified two novel loci for word reading, with top SNPs in or near ARHGAP23 (n=624) and the CCNT1/LINC00935 region (n=4430) (p~10-7) (significant by gene-based analysis (p~10-6)). We also identified significant genetic overlap for word reading and intelligence, word reading and educational attainment, and word reading and attention deficit hyperactivity disorder (ADHD) (threshold for significance=7.14x10−3) and observed shared genes between word reading and Autism Spectrum Disorder (ASD) and language. We observed genes involved in neuronal migration among top results. To increase power to identify genes for word reading, we performed Hypothesis-Driven GWAS in a larger sample. SNPs in DOCK7, CDH4 (n~26,000), and intergenic between BTG3-C21orf91 (n=4152) showed significant association. Top SNPs were eQTLs/sQTLs, providing hints to the molecular mechanism of risk for these genes. We also found that genes previously implicated in ASD cumulatively and significantly contributed to word reading (n=624). We hypothesized the link between RD-ASD was through deficits in language systems. To determine neural cell types, we used Linkage Disequilibrium Score Regression to look for cell enrichment in our GWAS results and correlated traits -- as determined by PRS. We demonstrated enrichment of adult excitatory neurons in word reading; adult excitatory neurons in ADHD; and adult and fetal excitatory neurons, inhibitory neurons, astrocytes, and oligodendrocytes in educational attainment and cognitive ability. This thesis contributed novel genes and neural cell types to RD, as well as an understanding of the shared overlap between its comorbid disorders. It can inform future functional studies examining the molecular mechanisms of reading.
Inventing Texture: Food Science and Culinary Culture in Postwar America
Keywords: cuisine
culture
food
industry
science
texture

In the second half of the twentieth century, food scientists in North America and eventually across the globe focused their attention on the human sense of texture. Largely ignored by scientists before them, and seemingly without cultural precedent, corporate and public research scientists set out to define texture as a measurable phenomenon, to ascertain what was generally desirable to chew, and to operate this knowledge in service of the ongoing global industrialization of food production and retailing. Above all, texture was staked as the solution to overlapping crises in the global food system, promising the Global South abundant meat prepared cheaply from plants and offering a palatable alternative to excessive dietary fat in the Global North. Through an examination of their research methods, published ideas, and the new products that resulted, this dissertation explores the messy entanglement between food science and culinary culture. As scientists drew upon cultural intermediaries like home economists, marketers, and vegetarians to direct their research, so too did increasing scientific control over the physical features of processed foods shape broader cultural understandings about normative taste. While the desired outcomes for texture research have thus far resulted in spectacular market failure, this dissertation suggests how the core concepts of modern food science have succeeded nevertheless in becoming part of culinary discourse, offering a terminology and indeed a terrain for navigating contemporary global cultural exchanges.
Systematic Investigations of the Regulation and Nuclear Organization of Alternative Splicing
Keywords: Alternative splicing
CRISPR screens
Exon definition
Nuclear organization
Nuclear speckles
Post-transcriptional gene regulation

Alternative splicing is a key process by which precursor (pre)-mRNAs generate multiple mRNA isoforms and greatly expands transcriptomic and proteomic diversity. It is often precisely regulated by intricate RNA-protein interaction network, and tightly coordinated on a global level to modulate gene activities and interactions in diverse cellular, developmental, and pathological processes. Therefore, comprehensively dissecting the regulatory landscape of alternative splicing and its organization in the cell nucleus is of significant interest. During the course of my PhD thesis research, I co-led the development of a CRISPR-based strategy for the genome-wide elucidation of pathways that control alternative splicing, and applied this to alternative microexons with critical functions in nervous system development and that are commonly misregulated in autism. Approximately 200 genes associated with functionally diverse regulatory layers and enriched in genetic links to autism control neuronal microexons. Remarkably, the widely expressed RNA binding proteins Srsf11 and Rnps1 directly, preferentially, and frequently co-activate these microexons. These factors form critical interactions with the master neuronal splicing activator Srrm4 and bi-partite intronic splicing enhancer elements to promote the recognition and splicing of most neuronal microexons. Multiple steps of gene expression are highly compartmentalized in the cell nucleus. In particular, membraneless nuclear domains play an important role in the organization of gene expression and RNA processing. However, the composition and function of many of these structures are not well understood. I utilized APEX2-mediated proximity labeling and RNA sequencing to survey human transcripts associated with nuclear speckles, several additional domains, and the lamina. Remarkably, speckles and lamina are associated with distinct classes of retained introns enriched in genes that function in RNA processing, translation, and the cell cycle, among other processes. In contrast to the lamina-proximal introns, retained introns associated with speckles are relatively short, GC-rich, highly differentially regulated across diverse cellular contexts, and enriched for functional sites of RNA-binding proteins that are concentrated in these domains. Together, this thesis dissertation presents a versatile system for the comprehensive identification of splicing regulatory pathways impacting exons of interest, and further reveals speckles and lamina as hubs engaged in the splicing of distinct classes of retained introns.
Exploring the Body Language of Children with Autism Spectrum Disorder (ASD) during Physical Activity
Keywords: Autism
Body language
Engagement
Physical activity

Introduction: Children with autism spectrum disorder (ASD) participate in less physical activity (PA) than their peers. Research has shown that one reason is that some instructors lack awareness about ASD and how best to support these children. Differences with body language expression are a feature of ASD that limit social interactions and may compromise participation. This dissertation used mixed methods to explore how body language of children with ASD is demonstrated and perceived in PA settings and reports the first-stage validation and associated refinement of the Body Language Coding Scale (BLCS) to help instructors with body language identification and interpretation.Methods: Twelve parents of children with ASD (7-12 years) were interviewed to explore thoughts about their child’s body language and their impressions of its interpretation by PA instructors. Next, the BLCS was used to quantify body language during a motor assessment performed by 31 children with ASD (6-12 years). BLCS reliability and its association with motor proficiency and skill enjoyment were evaluated. A content validity evaluation was undertaken with three parents of children with ASD (8-12 years) to review cue valence. The BLCS scoring was revised and reliability was re-evaluated. Results: Misinterpretation of non-basic emotions expressed through body language was identified by parents as a knowledge gap. The BLCS showed excellent intra-rater and moderate inter-rater reliability. No significant associations were shown between body language, motor performance and enjoyment. Parents’ evaluation of cue meaning demonstrated concurrence with BLCS cue valence. Further refinement of the BLCS (including renaming of positive/negative categories to engaged/not engaged) resulted in the BLCS-v2-revised, which demonstrated excellent intra-rater and good inter-rater total score reliability, and excellent intra- and inter-rater category reliability. Discussion: The BLCS-v2-revised is a reliable and valid measure of body language of children with ASD. Further research is needed on the feasibility of using the BLCS-v2-revised in the community context. Conclusion: The BLCS is ready for introduction to PA instructors as a tool to help them communicate better with children with ASD. Bringing awareness of body language differences in children with ASD may help instructors create a more inclusive environment to support participation and enjoyment.
Supporting Kindergarten Student’s Development of Knowledge, Skills and Understanding about Truth and Reconciliation
Keywords: Kindergarten
Truth and Reconciliation

In Kindergarten, educators and students are called to action to engage in learning related to truth and reconciliation. The purpose of this study is to explore how educators can engage Kindergarten students in learning about truth and reconciliation within three Kindergarten classrooms. Using a qualitative case study approach, this study investigates the question: What practices support Kindergarten student’s development of knowledge, skills and understanding about truth and reconciliation? This study will extend our understanding of how to respond to the Calls to Action in the early years theoretically and pedagogically and contribute to the literature.The results from this study indicate that there are practices that educators can engage in as they move through a continual process of teaching and learning about truth and reconciliation and adopt a ‘reconciliatory stance’ to support Kindergarten students’ knowledge, skills and understanding of truth and reconciliation. Challenges related to teaching and learning about truth and reconciliation in Kindergarten include encountering resistance or pushback from others regarding the appropriateness of this work and the lack of capacity building for educators. The seven major findings from this study include: 1) there is a continual process that educators must engage in throughout the school year to develop knowledge, skills and understanding about truth and reconciliation; 2) there are practices that educators can use to support the development of knowledge, skills and understanding about truth and reconciliation; 3) educators need to have a strong understanding of how to connect teaching and learning about truth and reconciliation to the Ontario Kindergarten Program document and other guiding documents; 4) educators must continue to engage in professional learning to have the knowledge and understanding of how to bring this work into their practice; 5) more Kindergarten-specific resources need to be developed; 6) adopting a ‘reconciliatory stance’ allows educators to respond to teachable moments within the classroom related to teaching and learning about truth and reconciliation; and 7) this work needs to be done in relation and in community. Implications of this study suggest that there are powerful possibilities for developing a strong foundation for truth and reconciliation with students in Kindergarten.
Validating the WD Repeat Protein CDC40 as a Potential Therapeutic Target for Lung Cancer
Keywords: CDC40
Drug discovery
Protein-protein interaction
shRNA knockdown
Splicing
WD Repeat protein

Lung cancer is the second most diagnosed and most lethal cancer globally. Presently, there is a need for novel targets for the development of improved therapeutics. Data mining of whole genome genetic dependency screens suggested that the pre-mRNA splicing factor Cell Division Cycle 40 (CDC40) is essential for lung cancer cell survival. In this study, I characterized the effects of CDC40 knockdown in a panel of lung cancer cells. I show that CDC40 knockdown induced cell cycle defects resulting in strong growth inhibition and activation of late-stage apoptotic markers in all lung cancer cells tested. To further understand the cellular consequences of CDC40 suppression, I investigated global transcriptional and splicing changes and found that CDC40 knockdown resulted in a perturbation of splicing and translation-related genes in addition to a higher number of transcripts with intron retention. I explored one specific intron retention event in the mRNA transcript of the cell cycle regulatory protein CDCA5, a potential prognostic marker for cancer, and showed that CDC40 knockdown induced retention of its first intron leading to an increase in the unspliced CDCA5 transcript, and subsequent decrease in CDCA5 protein expression. Finally, I explored the direct protein interactions of CDC40 in lung cancer lines and found spliceosome components as the predominant binding partners for CDC40, further highlighting the major role of CDC40 in splicing. CDC40-CDC5 interaction, identified in the current thesis, was investigated using peptide displacement assay for drug development purpose. So far, no hits have been confirmed from screens. In addition, no disruption was observed even with quadruple mutations within the putative binding pocket on CDC40. This implies that it may be difficult to disrupt key protein-protein interactions using small molecules within this very large complex. In summary, I was able to demonstrate that CDC40 is important for lung cancer cell survival and has potential as a novel therapeutic target for lung cancer treatment. I confirmed that CDC40 is involved in the human pre-mRNA splicing process as it is an important component of the spliceosome like its yeast counterpart. Furthermore, I characterized several CDC40 interactors to look for pockets for future therapeutic intervention.