VictorJuiz/thesis huggingface dataset:
Investigating the Relationship Between Cilia and Planar Cell Polarity Signalling During Zebrafish Development
Keywords: cilia
planar cell polarity

Cilia are microtubule-based organelles that project into the extracellular space and have various functions including transducing sensory information, regulating developmental signalling pathways, and generating directed fluid flow, making them important regulators of vertebrate development and homeostasis. Despite their importance, there are many aspects of cilia formation and function that remain poorly understood. The planar cell polarity (PCP) pathway is a branch of Wnt signalling that provides positional information to cells and is required for polarized morphogenic cell movements. Previous studies of PCP effector proteins suggested that PCP signalling was required for cilia formation. However, these proteins are not specific to the PCP pathway and are shared with other branches of Wnt signalling. To determine the role of a core and specific PCP regulator on ciliogenesis, I examined maternal-zygotic (MZ) vangl2 zebrafish mutants using an in vivo marker of cilia, Arl13b-GFP. Analysis of MZvangl2 mutants revealed that PCP is not required for cilia formation but is required for the posterior tilting and posterior positioning of motile cilia, essential for directed fluid flow. A parallel branch of studies suggested that cilia are actually required to regulate PCP signalling because defects in PCP-mediated morphogenic movements were observed with the knockdown of certain proteins that localize at or near cilia or basal bodies. To determine whether cilia were required to establish PCP, I generated MZ-intraflagellar transport-88 (IFT88) mutants, where ciliogenesis is completely abolished. Analysis of MZift88 mutants revealed that cilia are not directly required for PCP-mediated morphogenic movements. However, I observed that MZift88 mutants had defects in oriented cell divisions (OCD) occurring during gastrulation. Remarkably, these divisions occur prior to cilia formation, suggesting a cilia-independent role for IFT proteins in cell divisions, which may have important consequences on the interpretation of the role of cilia in disease.
Negotiating Responsibilization: Power at the Threshold of Capable Literate Conduct in Ontario
Keywords: neoliberal governmentality
adult literacy
regimes of calculation
learner-centred
welfare reform
activation

This thesis considers how statistics about adult literacy have produced a new transnational norm of what it means to “be literate” and asks what has been produced by demarcating a calculable threshold of capable literate conduct. Analyzing literacy as a form of conduct enables investigation of the political dimensions of governmental interest in literate conduct and consideration of what subjects, relationships and forms of power are produced by various problematizations. Genealogical analysis of the currently dominant governing rationality, what is termed the psychometrological regime, revealed that Level Three of the International Adult Literacy Survey (IALS) has been constructed as a threshold between people who can act as autonomous, entrepreneurial subjects and those who cannot. In the case of Ontario, this threshold becomes an indicator of “employability” and produces a singular and problematic population who are subjected to coercive educational interventions. Tactics and techniques in the province’s Literacy and Basic Skills (LBS) policy construct literacy programs as sites responsible for transforming subjects below the threshold into human capital assets; this represents a significant departure from the original mission of community-based agencies. Data from interviews with educators in these programs indicate that adult literacy workers occupy an uneasy position between the demands of policy, their pastoral relationships with learners, and the complex realities faced by adults who struggle with print. While these educators may choose to disobey some policy imperatives they nonetheless act, at times unwittingly, as agents of governance. By highlighting the impossibilities produced by the neoliberal problematization of literacy, and the negotiations that literacy workers perform in the face of such dilemmas, this research contributes to thinking through how to transform coercive and authoritarian tendencies currently governing literate conduct.
Ag Nanostructures:from Fabrication to Interaction
Keywords: Silver
Nanostructure
electrochemistry
Interaction

Electrochemical cycling of Ag surfaces under basic conditions has led to the discovery of a new, simple, rapid and cost effective method for the preparation of nano-structured Ag surfaces with features ranging from 30&ndash;150 nm in diameter. Our results indicated that during cyclic voltammetry, the surface was oxidized, resulting in the formation of soluble Ag complexes which were re-deposited as elemental Ag nanostructures (NSs) on the cathodic scan. The electrochemical properties of the Ag NSs were greatly affected by the presence of organophosphonates and other additives (vide infra), which also influenced the growth of nanostructures. The interaction of these Ag NSs with malathion and paraoxon were explored in more detail using Surface Enhanced Raman Spectroscopy. Results showed that generally smaller nanosized features resulted in high quality surface Raman enhancement. Next, Ag NSs&rsquo; properties in the presence of organophosphonates was investigated in tap water and apple juice in order to address issues related to matrix effects and potential interference from constituents in solution. Electrochemical and localized surface plasmon resonance results demonstrated the ability to detect organophosphonates in real samples, albeit at a lower limit of detections and without any selectivity to any particular organophosphonate. Next, the morphology and corrosion behaviour of Ag surfaces was explored in the absence and presence of surfactants and capping agents. Results demonstrated the protection of Ag surfaces against corrosion in the presence of Tween-20, while potassium citrate presence enhanceed corrosion of silver surfaces, resulting in the formation of a pitted surface with smaller Ag NSs. Lastly, the interactions of 2-cyano-3-(2&prime;-(5&prime;,10&prime;,15&prime;,20-tetraphenyl porphyrinato zinc-(II))yl) acrylic acid-modified Ag NSs with biomolecules were explored using spectro-electrochemical techniques. The photocurrent response of porphyrin-modified Ag NSs was quenched by the addition of adenosine-5&rsquo;-monophosphate (AMP), guanosine-5&rsquo;-monophosphate (GMP) and cytidine5&rsquo;-monophosphate (CMP), with a quenching efficiency of 80%, 68% and 48% for AMP, CMP and GMP, respectively.
Passive Air Samplers for Semivolatile Organic Compounds: Experiments, Modeling, and Field Application
Keywords: passive air sampler
semivolatile organic compound
kinetic resistance
sampling rate

Knowledge gaps related to mass transfer processes involved in passive air sampling of semivolatile organic compounds and factors potentially influencing passive sampling rates (PSRs) were addressed with controlled laboratory experiments, mass transfer modeling, and a field sampling campaign. The observed non-uniform SVOC distributions within porous passive sampling media (PSMs) contradict an assumption in an earlier passive air sampling theory and proved the existence of a kinetic resistance on the PSM side. This resistance can affect PSRs as revealed by a new PAS model which is based on fundamental laws of mass transfer in air and porous media. By considering mass transfer processes within the PSM, the model is able to explain the large variations of field calibrated PSRs with temperature and between SVOC species and the two-stage uptake process, which cannot be addressed by the earlier PAS theory. Because the PSM side kinetic resistance invalidates the assumption that depuration compounds added to the PSM prior to deployment are subject to the same kinetic resistance as the sampled SVOCs, PSRs derived from the loss rates of depuration compounds can differ from the actual PSRs of the sampled SVOCs. Using such PSRs could thus introduce additional uncertainty to PAS-derived air concentrations. Experiments using XAD-resin and silica-gel filled mesh cylinder as PSMs for the uptake of SVOCs and water vapor respectively revealed that sorbent in the inner portion of the PSM does not take part in chemical uptake; PSRs are thus proportional to the interfacial transfer area but not the amount of the sorbent. Accordingly, thinner PSM can be used to reduce the amount of sorbent while keeping or even increasing the PSRs. Optimized designs of PASs could be tested time efficiently using the gravimetrical approach based on water vapor uptake by silica gel.
The Influence of Growth and Development in the Expression of Human Morphological Variation
Keywords: non-metric traits
subadults
growth and development
ancestry

This analysis examined cranial epigenetic and morphological nonmetric traits in 756 subadults (fetal to <20 years), in European, African, and Asian samples. The goals of this research were to assess: the age and manner in which nonmetric traits develop and if variation between geographic groupings is present in subadults; the role of the adolescent growth spurt in trait expression; the feasibility of utilizing subadult crania in biological distance studies and ancestry assessment. A number of epigenetic and morphological traits show a primarily genetic versus developmental basis, suggested by the fact that there was no difference in trait frequencies between the fetal/0-3 and 15-20 year age categories. Eighty-five percent of epigenetic traits appear before 3 years; 54% were age stable by 3 years, and 75% were stable before age ten. Geographic cranial variation is present at an early age as demonstrated by the appearance of 58% of morphological traits before age 3, and 90% by age 10. Ten and a half percent of morphological traits are age stable before 3 years of age, 48% by age 10. Traits statistically significant between pre-pubertal and pubertal and/or pubertal and post pubertal individuals are hyperostotic, functional, and in some cases, sex dependent. Few epigenetic (1.3%) and morphological traits (7.9%) were found to be sex dependent, possibly because sexually dimorphism may not be fully expressed in individuals in the 15-20 year age category. Features that indicate ancestry develop before puberty, and do not require the onset of puberty and sexual dimorphism to be fully formed. Three-quarters of epigenetic traits were age stable and showed trait frequencies similar to adults before 10 years of age, suggesting subadults could be included in biodistance studies using these traits. Twenty-four morphological traits were statistically significant between geographic groups and show promise for future use in the forensic analysis of ancestry assessment in children.
Molecular Evolution and Functional Characterization of the Visual Pigment Proteins of the Great Bowerbird (Chlamydera nuchalis) and Other Vertebrates
Keywords: bowerbird
visual pigments
opsin
vertebrate phylogenetics
molecular marker
avian vision
visual behaviour
adaptation
mutagenesis
protein expression
short wavelength sensitive 1
SWS1
spectral tuning
evolution
ancestral sequence reconstruction
maximum likelihood
rhodopsin
rod opsin
RH1
retinal release
photoactivation cycle
dim light adaptation
molecular evolution
PAML

Visual pigments are light sensitive receptors in the eye that form the basis of sensory visual transduction. This thesis presents three studies that explore visual pigment proteins in vertebrates using a number of computational and experimental methods in an evolutionary framework. The objective is not only to identify, but also to experimentally investigate the functional consequences of genetic variation in vertebrate visual pigments. The focus is on great bowerbirds (Chlamydera nuchalis), which are a model system in visual ecology due to their spectacular behaviour of building and decorating courtship bowers. There are 4 chapters: Chapter 1 introduces background information on visual pigments and vision in birds. Among visual pigment types, the short-wavelength-sensitive (SWS1) pigments have garnered particular interest due to the broad spectral range among vertebrates and the importance of UV signals in communication. Chapter 2 investigates the evolutionary history of SWS1 in vertebrates with a view toward its utility as a phylogenetic marker. Chapter 3 investigates SWS1 evolution and short-wavelength vision in birds, with particular focus on C. nuchalis and its SWS1. The evolution of spectral tuning mechanisms mediating UV/violet vision in passerines and parrots is elucidated in this chapter using site-directed mutagenesis, protein expression, and phylogenetic recreation of ancestral opsins. While cone opsins mediate colour vision in bright light, the rhodopsin visual pigment contained in rod photoreceptors is critical for dim light vision. Detailed characterization of rhodopsin function has only been conducted on a few model systems. Chapter 4 examines C. nuchalis RH1 using a number of functional assays in addition to absorbance spectra, including hydroxylamine sensitivity and the rate of retinal release. This chapter includes an investigation into the role of amino acid mutations typical of dim-light adapted vertebrates, D83N and A292S, in regulating functional properties of bovine and avian RH1s using site-directed mutagenesis. Together these chapters describe naturally occurring mutations in visual pigments and explore the way they can influence visual perception. These represent one of the few investigations of visual pigments from a species that is not a model lab organism and form a significant contribution to the field of visual pigment biochemistry and evolution.
Trace Bases and Acids in the Troposphere: Importance in New Particle Formation and Atmospheric Oxidation Capacity
Keywords: Atmospheric Chemistry
Environmental Chemistry

Accurate measurements of the trace nitrogenous atmospheric species amines (NR3) and nitrous acid (HONO) are essential to understanding their chemistry and potential influence on new particle formation and oxidation capacity in the atmospheric boundary-layer, respectively. Ambient Ion Monitor – Ion Chromatography (AIM-IC) methods developed in this work have provided quantitative online observations of atmospheric amines in the gaseous and condensed phases with detection limits of pptv and ng m-3 at hourly time resolution. Size-resolved particle observations demonstrated maximum amine mass loadings in 320 – 560 nm particles, and an increase in importance relative to ammonium for the smallest particles measured (56 – 180 nm). In particular, the size-resolved samples analysed in this work indicate that bulk aerosol measurements may not be appropriate for modelling the atmospheric processes that govern the incorporation of amines and ammonia in to atmospheric particles. Measurements of HONO made during the two intensive field campaigns (NACHTT, CalNex) and a lab study provided a new perspective on the interactions of this trace compound with ground surfaces. Integrated atmospheric column measurements of HONO and NO2 during NACHTT provided clear evidence that the ground surface dominates HONO production and loss at night. Simultaneous measurements of the gas and particle phases made by the AIM-IC system during CalNex demonstrated the potential for reactive uptake of HONO on mineral dust/soil as a nocturnal sink. Similarly, the potential for nitrite salts to react with strong acids, displacing HONO during the day was suggested by this dataset. Lab study results showed that HONO is taken up irreversibly on carbonate salts and real soil extracts. Relative humidity-dependent reactive uptake coefficients were derived. Subsequent release of HONO by displacement reactions with HNO3 and HCl was also confirmed. Together, these field and lab studies have produced a new picture of HONO surface interactions by providing i) a more explicit description of a nocturnal sink of HONO that could act as a surface reservoir and ii) a new mechanism for daytime HONO formation that does not require NO2.
LIMK1 Regulation of Long-term Memory and Synaptic Plasticity
Keywords: synaptic plasticity
learning and memory
LTP
LIMK1
CREB

The LIM-Kinase family of proteins (LIMK) plays an important role in actin dynamics through its regulation of ADF/cofilin. A subtype of LIMK, LIMK1, is mostly expressed in neuronal tissues with high levels in the mature synapse. Previous studies from the Zhen Ping Jia laboratory have shown that LIMK1-/- mice exhibit abnormal spine morphology as well as altered hippocampal synaptic plasticity. LIMK1 has been shown to interact with CREB during neuronal development (Yang et al., 2004). We propose that LIMK1 is able to phosphorylate CREB in response to a synaptic activity. We hypothesize that if LIMK1 activates CREB in mature neurons, then LIMK1 knockout mice will have decreased L-LTP and deficits in long-term memory. My results show that LIMK1 and CREB exist in a complex and are bound to each other in mature neurons. LIMK1-/- mice exhibit deficits in the late phase of long-term potentiation and specific deficits in long-term memory while short-term memory remains unaltered. Pharmacological activation of CREB attenuates the observed deficits in synaptic plasticity and long-term memory. These results show a potentially novel mechanism of CREB activation in response to synaptic activity. Moreover, using peptides to manipulate actin dynamics in LIMK1 lacking animals only has effects on early LTP and is not able to rescue the late phase LTP deficits found in LIMK1 -/- mice. These results indicate a specific role of LIMK1 long-term memory and synaptic plasticity through regulation of CREB and not through regulation of the actin cytoskeleton.
Characterization of PilP from the Type IV Pilus System of Pseudomonas aeruginosa
Keywords: P. aeruginosa
virulence factors
protein-protein interactions
Type IV Pili

Pathogenic bacteria employ a number of mechanisms to induce infection and survive in host tissues, including toxin secretion and the formation of protective multicellular structures called biofilms. Type IV Pili (T4P) are highly conserved organelles essential for both the establishment of infection and biofilm maturation. The goal of this research is to gain a molecular level understanding of the function of the highly dynamic T4P of Pseudomonas aeruginosa. The pilMNOPQ operon encodes 5 members of a transmembrane complex that facilitates pilus function. While PilQ is the putative outer membrane secretin through which the pilus exits the cell, the roles of the PilM/N/O/P proteins are less well defined. Using both in vivo and in vitro techniques our characterization of PilP has provided significant insight into organization of the apparatus. PilP is an inner membrane lipoprotein essential for T4P function, but lipidation is dispensable, suggesting that its interactions with other T4P components are sufficient for PilP function. We showed that PilN/O/P form a stable heterotrimer when expressed in E. coli, and we suggest that they form a similar subcomplex in P. aeruginosa. Additionally we were able to show that PilP is also able to interact with a periplasmic fragment of the outer membrane pore protein PilQ. Structural and bioinformatics studies suggest that the organization of PilN/O/P/Q complex is similar to that of the transenvelope complex of another important Gram-negative virulence factor – the Type II Secretion System (T2SS). Our structural and functional characterization of PilP, the PilN/O/P complex and the striking similarities between the T4P and T2S systems, as well as important differences that make each molecular machine unique, will be presented.
Customizing the Composition of Web Services and Beyond
Keywords: Automated Composition
Preferences
Optimization
Hierarchical Task Network Planning
Planning
Planning Algorithms
Software Composition
Software Customization
Component-based Software
Web Services

Web services provide a standardized means of publishing diverse, distributed applications. Increasingly, corporations are providing services or programs within and between organizations either on corporate intranets or on the cloud. Many of these services can be composed together, ideally automatically, to provide value-added service. Automated Web service composition is an example of such automation where given a specification of an objective to be realized and some knowledge of the state of the world, the problem is to automatically select, integrate, and invoke multiple services to achieve the specified objective. A popular approach to the Web service composition problem is to conceive it as an Artificial Intelligence planning task. This enables us to bring to bear many of the theoretical and computational advances in reasoning about actions to the task of Web service composition. However, Web service composition goes far beyond the reaches of classical planning, presenting a number of interesting challenges relevant to a large body of problems related to the composition of actions, programs, and services. Among these, an important challenge is generating not only a composition, but a high-quality composition tailored to user preferences. In this thesis, we present an approach to the Web service composition problem with a particular focus on the customization of compositions. We claim that there is a correspondence between generating a customized composition of Web services and non-classical Artificial Intelligence planning where the objective of the planning problem is specified as a form of control knowledge, such as a workflow or template, together with a set of constraints to be optimized or enforced. We further claim that techniques in (preference-based) planning can provide a computational basis for the development of effective, state-of-the-art techniques for generating customized compositions of Web services. To evaluate our claim, we characterize the Web service composition problem with customization as a non-classical planning problem, exploit and advance preference specification languages and preference-based planning, develop algorithms tailored to the Web service composition problem, prove formal properties of these algorithms, implement proof-of-concept systems, and evaluate these systems experimentally. While our research has been motivated by Web services, the theory and techniques we have developed are amenable to analogous problems in such diverse sectors as multi-agent systems, business process modeling, component software composition, and social and computational behaviour modeling and verification.