VictorJuiz/thesis huggingface dataset:
Comparative Studies of C3 and C4 Atriplex Hybrids in the Genomics Era: Physiological Assessments
Keywords: C4 engineering
C4 photosynthesis
CO2 concentrating mechanism
photosynthetic hybrids
Rubisco

The C3 species Atriplex prostrata was crossed with the C4 A. rosea to produce F1 and F2 hybrids. All hybrids exhibited C3-like δ13C values, and had reduced rates of net CO2 assimilation compared to A. prostrata. The activities of three major C4 cycle enzymes were at most 36% of the C4 values. Photosynthetic CO2 compensation points (Г) were generally midway between the C3 and C4 values, and were generally accompanied by low, C3-like activities in one or more of the major C4 enzymes. Their anatomy resembled that of C3-C4 intermediate species using a glycine shuttle to concentrate CO2 in the bundle sheath. These results demonstrate the C4 cycle was disrupted in the hybrids, and that most hybrids use a photorespiratory glycine shuttle. Progeny of these hybrids should further segregate C3 and C4 traits and in doing so assist in the discovery of C4 genes using high-throughput methods of the genomics era.
Contending Intellectuals: State Formation and Cultural Transformations in Late 19th Century Egypt
Keywords: Abdallah Nadim
Ali Mubarak
British Colonialism
Egypt
Egyptian Press and Theatre
Nahda

The life and thought of the Egyptian intellectuals, Ali Mubarak and Abdallah al-Nadim, represented two intellectual trends that were emerging at the end of the century. They took shape at a critical time of history in which modernization projects gave rise to unprecedented social transformations and modern institution building. Although they both partook in the larger Arabic Nahda, and contributed in the formation of a public sphere that emerged at the intersection of state and culture, they had drastically different projects. Mubarak's intellectual project was pinned on the state institutions' intervention in educating the populace in order to achieve `national' progress modelled on European ways. Nadim's project on the other hand culminated in the need to build `national' consciousness in order to sever the economic dependency on Europe, and to create politically autonomous `Eastern' nations.
Application of Epigenetic Techniques to Study Lactase Expression
Keywords: Epigentics

DNA methylation is a highly studied epigenetic modification. Numerous techniques have been developed to investigate DNA methylation and its role in gene regulation. Lactose intolerance has been identified as a simple phenotype, regulated by a single gene. Due to its simple phenotype, lactose intolerance represents an ideal model to investigate the epigenetic mechanisms that govern gene expression. Here, we investigated lactase expression in aging mice, and used molecular inversion probe enrichment followed by DNA sequencing to study epigenetic modifications in segmental duplications and unique regions of the genome associated with the lactose intolerance in humans. Lactase was expressed in a mosaic pattern in the mouse small intestine, and expression significantly decreased in older mice. Molecular inversion probe enrichment of unique genomic regions proved challenging, and did not provide informative data. No associations between lactase expression levels and the DNA methylation profile of the lactase gene in segmental duplications was found.
Playing Spy Games: a Surveillant Platform Study of Microsoft's Xbox 360
Keywords: Game Studies
Microsoft
Platform Study
Privacy
Surveillance
Xbox

This thesis, a platform study of Microsoft's videogame console the Xbox 360, demonstrates how one of the defining traits of the videogame platform's design and architecture is pervasive surveillance of its users. By applying William Bogard's (1996) theory of surveillant "enclosures," this thesis will explain how the Xbox 360 uses a panopoly of methods and technologies to watch users and shape their use of the videogame system, forming them as easily governed subjects. In support of this argument, this thesis will examine not only the hardware and software layers of the Xbox 360, but also peripheral hardware and networks including the motion tracking sensor the Kinect and Xbox Live, the videogame console's online network. Of particular interest to this platform study will be an examination of how each of these layers performs surveillance, and how they collectively perform a project of governance over videogame players. References Bogard, William. (1996). The Simulation of Surveillance: Hypercontrol in Telematic Societies. Cambridge: Cambridge University Press.
Characterizing the Role of Protein Tyrosine Kinase 7 (PTK7) in Cancer Development and Cellular Fitness
Keywords: Cancer
Fitness
Immunotherapy
Protein Tyrosine Kinase 7
PTK7
Receptor Tyrosine Kinase

Protein Tyrosine Kinase 7 has been recently affiliated with the development and progression of various cancers. Contradictory results about its expression, localization and processing across various cancer types has left a major gap in understanding its molecular mechanism and function. In my thesis, I utilized large data sets from essentiality screens and RNAseq, as well as antibody-related tools, to investigate the role of PTK7 in cellular fitness. I observed a negative correlation between PTK7 processing and its degree of essentiality. Furthermore, I demonstrated that the PTK7 intracellular domain (ICD) is integral to its function. Treatment of mouse xenografts with PTK7 antibodies, capable of blocking PTK7 processing, inhibited tumour growth in an ICD-expression dependent manner. Lastly, mRNA profiling of PTK7-knockdown cells and ICD over-expression cells provided a list of putative downstream gene targets under PTK7 regulation. Collectively, these findings implicate PTK7 in cellular transformation and provide insight into its signaling mechanism. .
Hippocampal Neurogenesis-mediated Forgetting in Adult Mice
Keywords: adult neurogenesis
behavior
forgetting
memory
neural circuitry

New neurons are continuously generated in the dentate gyrus of the hippocampus throughout adulthood. These new neurons gradually integrate into hippocampal circuitry, which likely support the formation of new memories. Once sufficiently mature, however, as they integrate into existing circuits, they may also disrupt pre-existing memories stored in those circuits. Recently, we found artificially elevating levels of adult neurogenesis through voluntary running exercise or p53 ablation after memory formation promoted degradation in contextual fear memories and spatial memories. Besides, Mice with elevated neurogenesis levels immediately after training or after a 4 weeks delay had different freezing responses to a fearful context. Only increasing levels of neurogenesis immediately but not after a long delay after training induced forgetting, suggesting that as memories age, they become less vulnerable to neurogenesis-mediated forgetting possibly due to a reduced involvement of the hippocampus in the retrieval of memories over time.
Get Yours Today! On the Production and Consumption of the Televised Fatwā
Keywords: Commodification
Fatwa
Islam
Knowledge
Media
Public Sphere

This thesis explores Yastaftūnak, a program aired on Al-Resalah, an Arabic-language Islamic satellite television channel, as a prime example of the fatwā show genre. Scrutinizing Yastaftūnak from different theoretical angles, I enquire into how such fatwā programs operate, why they are made and watched, and what repercussions their increasing popularity has for Muslim worlds. Considering the utilization of fatwās as a tool of societal discipline, I examine simultaneously how such discipline is embodied and performed. These subjects feed into larger arguments concerning the role of television programs in the commodification of fatwās and concurrent establishment of an “intimate public sphere.” Throughout this, I probe into the ways a seemingly uniquely Islamic knowledge produced in the form of an unending stream of fatwās is given the impression of being objective, and contest this view, teasing the social, political, and economic out of what is presented as solely legal or religious.
Detailed Mineralogical and Petrological Analysis of Martian Shergottite NWA 6342
Keywords: EBSD
Mars
Meteorite
Petrology
Planetary Science
Raman Spectroscopy

NWA 6342 is an intermediate, ultramafic, poikilitic shergottite that was found in Algeria in 2010. As the poikilitic shergottite-group meteorites are thought to have originated from the same slow-cooling magma chamber, studying samples like NWA 6342 provides us with the unique opportunity to reconstruct and analyze an igneous body on Mars, diversifying our knowledge of volcanic and impact processes in our Solar System. The relatively homogeneous composition of the forsterite grains in NWA 6342 indicates that it was located at an intermediate level within the original magma chamber. The lack of maskelynite, and complete recrystallization of plagioclase observed in the sample also indicate that it was subjected to a higher degree of post-impact thermal metamorphism than the other poikilitic shergottites, and may have experienced two impact events. This could explain how these ultramafic rocks could have been relocated close enough to the surface to be ejected to Earth.
Trait Choice and Dimensionality Alter Estimates of Phenotypic Dissimilarity in Community Ecology
Keywords: intraspecific variation
methodology
Mimulus
niche overlap
plant functional traits
species similarity

The ecological niche is a multi-dimensional concept including aspects of resource use, environmental tolerance, and interspecific interactions, and the degree to which niches overlap is central to many ecological questions. Plant phenotypic traits are increasingly used as surrogates of species niches, but we lack an understanding of how key sampling decisions affect our ability to capture phenotypic differences among species. Using vegetative and floral trait data of ecologically distinct monkeyflower (Mimulus) congeners, I employed linear discriminant analysis, which uses proportional assignment of individuals to species, as an estimate of how well the traits we measure can capture phenotypic differences among species. Trait combinations that maximize species discrimination were not predictable a-priori based on the number of trait groups or inclusion of ‘key’ functional traits. Instead, high trait dimensionality consistently increased my ability to detect phenotypic differences among species. Population choice was similarly important and should be considered in trait-based studies.
ENDOGENOUS CELL-BASED THERAPY USING CYCLOSPORINE A PROMOTES COGNITIVE RECOVERY IN A MOUSE MODEL OF STROKE
Keywords: executive function
ischemia
medial prefrontal cortex
neural precursor cells
recovery
Stroke

Post-stroke executive function (EF) deficits can severely impact the quality of life. Current treatments provide limited motor or cognitive recovery. Recently, an endogenous repair strategy using Cyclosporine A (CsA) promoted neural stem and progenitor cells [collectively termed neural precursor cells (NPCs)] migration to the infarct site, tissue regeneration and functional recovery following sensorimotor stroke. Herein, we tested the efficacy of CsA in improving EF deficits in a cognitive stroke model in mice. The medial prefrontal cortical (mPFC) stroke produced long-term EF impairments in the Puzzle Box Task. CsA treatment increased the size of the NPC pool at day 7 and promoted NPC migration to the infarct site at day 60 post-stroke. Early CsA administration was not neuroprotective and did not affect neural degeneration or lesion volume. Long-term CsA treatment improved post-stroke cognitive performance at 3 and 5 weeks. We suggest CsA is a promising therapeutic candidate for post-stroke cognitive recovery.
Memory and Perception-based Facial Image Reconstruction
Keywords: face perception
face space
image reconstruction
memory

Face perception and face memory have been the focus of extensive research to investigate the mechanisms of face processing. However, the nature of the representations underlying face perception and face memory remains unclear, and the relationship between them is not well- known given that they are usually studied separately. The current work examines these issues by adopting an image reconstruction approach, to perform behavioural perception and memory- based reconstructions. Significant features underlying the representation of face perception were first derived, and then used to reconstruct face images that were visually seen and recalled from memory. Reconstructions of perception and memory data were above chance for both unfamiliar faces, faces learned throughout the experiment, and celebrity faces retrieved from long-term memory. This not only provides new insights into the content of face memory and its relationship to face perception, but also opens a new path for practical applications such as computer-based â sketch artistsâ .
Mechanical Properties of Graded Thermodynamic Nickel Titanium Archwires in Bending and Torsion
Keywords: nickel titanium
orthodontic wires
three-point bending
torsion

Background: Graded thermodynamic nickel titanium (GT-NiTi) wires purportedly deliver differential force levels in different archwire regions. No studies evaluating the force delivery characteristics of such wires currently exist. Objective: To evaluate the mechanical properties of GT-NiTi wires in bending and torsion. Methods: Six samples of 0.016 x 0.022â and 0.017 x 0.025â of GT-NiTi wires were divided into incisor, premolar, and molar sections and each segment was tested in bending and torsion. The characteristics of the unloading superelastic plateau were evaluated and compared with similar segments of non-graded, control NiTi wires. Results: Statistically significant differences in mean force and moment levels were found between the three sections of GT-NiTi wires, but not in control wires. Small but statistically significant differences in length and slope were also found. Conclusion: GT-NiTi wires deliver different forces and moments in different archwire sections. Clinicians can use this knowledge to optimize force delivery for treatment.
Small Nuclear RNA (snRNA) Transcription Elongation Regulator, ice1, is Required for Retinal Progenitor Cell Maintenance
Keywords: CMZ
ICE1
LEC
retina
snRNA
zebrafish

Maintaining a discrete population of retinal progenitors in the circumferential marginal zone (CMZ) is required for proper growth of a functional vertebrate retina after embryogenesis. In the zebrafish mutant kess546, the CMZ is reduced in size, and cells no longer express markers of cycling retinal progenitors. Mutant CMZ cells have an apparent loss of epithelial integrity and increased apoptosis. There is also progressive overgrowth of the retinal-pigmented epithelium at the CMZ in mutants. We mapped this mutation to kiaa0947l/ice1, which is orthologous to Drosophila and human ICE1. Pol II-dependent transcription of snRNAs requires the little elongation complex, or LEC, whose core protein is ICE1. RT-qPCR shows that ice1 mutants have decreased levels of Pol II snRNAs, and transcriptomic analyses reveal missplicing in a subset of genes. My analysis of ice1 provides critical insight into the role of LEC dependent snRNA expression in regulating progenitor cell maintenance in the postembryonic retina.
PrP and its Ancestral Relatives ZIP6 and ZIP10 Interact with NCAM1, Altering its Molecular Environment and Post-translational Modifications during Epithelial-to-mesenchymal Transition
Keywords: epithelial-to-mesenchymal transition
mass spectrometry
ncam
prion protein
ZIP6

The prion protein (PrP) was recently found to be evolutionarily linked to a subfamily of ZIP transporters which possess a PrP-like domain. A member of this subfamily, ZIP6, is of particular interest as separate studies have shown that morpholino knockdowns of ZIP6 or PrP in zebrafish leads to an impairment in gastrulation, a process dependent on epithelial-to-mesenchymal transition (EMT). Furthermore, the neural cell adhesion molecule (NCAM1), a known interactor of PrP, has itself been described as a mediator of EMT. Based on these findings, we hypothesized that both PrP and ZIP6 play crucial roles in the process of EMT by controlling the environment surrounding NCAM. We determined that ZIP6 forms a heteromeric complex with ZIP10 that affects NCAM1â s integration into adhesion complexes while also mediating its phosphorylation during EMT. Meanwhile, PrP was found to have a unique role in controlling the polysialylation of NCAM1 during EMT.
Low-Temperature Ozone Native Oxide – Silicon Nitride Bilayer Passivation of the Silicon Surface
Keywords: Characterization
Hydrogen
Nitride
Passivation
PECVD
Silicon

Passivation of crystalline silicon is critical for the development of high efficiency, low cost solar cells. The objective of this project is to advance low temperature passivation of silicon substrates for use in photovoltaics and in particular to investigate the recently reported native oxide – silicon nitride bilayer passivation scheme. Specifically, we report on the passivation of silicon using an ozone ambient native oxide – silicon nitride bilayer where the nanometer thin ozone native oxide layer is grown at low temperatures while the silicon nitride layer is deposited at 400oC. Further, we investigate the chemical composition across the crystalline silicon interface. Advanced ion spectroscopy techniques including medium energy ion spectroscopy (MEIS), elastic recoil detection (ERD), and Rutherford Backscattering (RBS) are used to determine the resulting compositional layers on the silicon surface as well as the hydrogen concentration in both the film and underlying crystalline silicon substrate.
The Role of Ventral Hippocampal Projections to the Amygdala on Anxiety Behavior
Keywords: Amygdala
Anxiety
Elevated Plus Maze
Optogenetics
Ventral Hippocampus

Anxiety is a natural and adaptive behavioral response that is evoked in anticipation of a threatening situation. In some cases, however, anxiety can be maladaptive, manifesting itself in the absence of a threatening cue. Previous studies showed that the ventral hippocampus and the amygdala have been implicated as being involved in anxiety. However, little is known about how they interact to modulate anxiety behavior. In light of this, experiments were performed to investigate how the ventral hippocampus inputs to the amygdala control anxiety. Specifically, ventral hippocampus axon terminals were modulated optogenetically in freely moving mice on an elevated plus maze test. Results revealed that activating ventral hippocampal inputs to the amygdala leads to an increase in anxiety behavior, whereas the inhibition of the same inputs results in a decrease in anxiety. Thus, our findings suggest that the ventral hippocampal inputs to the amygdala play a role in regulating anxiety.
Early Education and Care Program Quality and Children's Well-being: a Meta-Analysis and Systematic Review of the Early Childhood Environment Rating Scale
Keywords: Early Childhood Education
ECERS
ECERS-R
Meta-Analysis
Program Quality
Systematic Review

The Early Childhood Environment Rating Scale (-Revised) (ECERS/ECERS-R) is the most widely used assessment of global classroom quality in Early Childhood Education and Care programs. Despite prevalent use of the ECERS/ECERS-R in research and applied settings, its impact on child outcomes have not been systematically reviewed. The objective of this study was to evaluate the association between the ECERS/ECERS-R and children’s well-being. Searches of Medline, PsycINFO, ERIC, websites of large datasets and reference sections of all retrieved articles were conducted up to January 2013. Eligible studies provided a statistical link between the ECERS/ECERS-R and child outcomes. Sixty-three empirical studies met our inclusion criteria. All studies were included in the systematic review and 23 could be meta-analyzed. Associations between ECERS/ECERS-R total and factor scores and children’s cognitive, language, math, and social-emotional outcomes are evident but weak. Greater consistency in study methodology is critical in this area of research.
The Effect of RGS4 on Autophagic Flux in Min6 Pancreatic Beta Cells
Keywords: Atg12
autophagy
Beclin1
LC3
Min6 cells
mTOR

Defective autophagy can lead to dysregulation of metabolic homeostasis. Previous studies in our laboratory have shown that RGS4-overexpressing HEK cells show increased autophagic activity. Herein, we study the potential role of RGS4 as a regulator of autophagy in the Min6 mouse pancreatic beta cell line, via inhibition of Gαi3, an established attenuator of autophagy. Min6 cells exposed to nutrient-deprived conditions undergo autophagic initiation demonstrated by increased expression of autophagy markers. When RGS4-YFP is ectopically expressed in Min6 cells, confocal microscopy imaging revealed colocalization between RGS4-YFP (both wild type and loss-of-function mutants), Gαi3 (RC)-CFP, and autophagy markers including Beclin1-DsRed and Atg12-RFP on intracellular punctae. Despite its colocalization with known regulators of autophagy, RGS4 was apparently unable to modulate the activity of known mediators and markers of autophagic activity (phospho-p76S6K, LC3 II, phospho-Bcl-2). We conclude that Gαi3 and RGS4 are not major factors in the regulation of autophagic flux in Min6 cells.
Investigating the Role of the Small GTPase Rab25a during Zebrafish Epiboly
Keywords: Danio Rerio
Enveloping Layer
Epiboly
Rab25a
Small GTPase
Zebrafish

The earliest morphogenetic event during zebrafish development is epiboly, defined as the thinning and spreading of a multilayered cell sheet. In a coordinated manner, the epithelial enveloping layer (EVL), deep cells, and yolk syncytial layer all undergo epiboly to close the blastopore. Despite epiboly being essential for development, its molecular control is not well understood. rab25a encodes a small GTPase involved in cellular trafficking in epithelial cells. rab25a was identified as a gene that may be important for epiboly. Loss of rab25a resulted in delayed epiboly and defects suggestive of reduced cell adhesion and impaired trafficking. rab25a is expressed exclusively in the EVL during epiboly but surprisingly, deep cells were more delayed than EVL cells. Additional work showed that deep cell epiboly could be rescued by restoring Rab25a expression to the EVL. My analysis provides evidence for a novel role for EVL-deep cell signaling to mediate epiboly movements.
Novel Gluconeogenesis Regulators for Anti-diabetic Drug Repurposing using Transgenic Zebrafish pck1 Reporters
Keywords: drug repurposing
gluconeogenesis
zebrafish

Phosphoenolpyruvate carboxykinase is an enzyme that catalyzes the rate-limiting step of gluconeogenesis and is encoded by the pck1 gene. High levels of pck1 gene expression are associated with type 2 diabetes. The main goal of the present study is to identify compounds that can modulate pck1 expression. Furthermore, the knowledge gained from this study can streamline the process of identifying regulators by high-throughput screening in the future. A luminescent zebrafish reporter Tg(pck1:luc2) was used to screen the NIH Clinical Collections library containing 727 small molecules. Four leads were identified and validated using the fluorescence reporters Tg(pck1:Venus) and Tg(pck1:eGFP) as well as endogenous pck1 expression using quantitative PCR, where they down-regulated pck1 expression in larval zebrafish. One of the validated compounds (levofloxacin) altered glucose metabolism in adult zebrafish as determined by glucose tolerance tests. Methods were also established for efficient screening of future chemical libraries to identify novel anti-diabetic therapeutics.