VictorJuiz/thesis huggingface dataset:
Intraspecific Variation in Chlorophyll Fluorescence and Pigment Composition in White Spruce (Picea glauca): New Physiological Traits for Identifying Trees Better Adapted to New Climates

Analysis of intraspecific variation in photosynthetic productivity and phenology can help us to better understand local adaptation and inform breeding decisions for optimally performing genotypes in extreme and changing environments. We used chlorophyll fluorescence, pigment composition, ground and drone-based spectral reflectance measurements to quantify the variation in photosynthesis of ten 5-year-old white spruce genotypes across a latitudinal gradient in summer, and within one site over a year to determine differences between the ten genotypes in seasonal changes of photosynthesis. The results reveal no genotype-environment interactions or differences between genotypes for pigment composition or fluorescence parameters likely due to a lack of stressful events. However one genotype performed consistently across environments, potentially having stable higher photoprotective capacity than other genotypes. The strong relationship found between vegetation indices measured from the drone and ground based physiological data will enable the high-throughput monitoring of the phenology of photosynthesis in conifer forests.

Keywords: chlorophyll fluorescence
climate change
intraspecific variation
phenotyping
photosynthesis
white spruce
Advisor: Ensminger, Ingo
Using Non-adhesive Microfluidic Wound Dressing to Enhance Wound Healing in Burn Patients

Effective wound closure is crucial for the survival of burn patients but is limited by skin graft thickness and availability. We report a novel non-adhesive wound dressing which participates actively and dynamically in wound repair by allowing cell delivery through built-in channels. We hypothesize that the skin cells will be delivered in clusters and show enhanced proliferation compared to randomly distributed cells. An array of channels is built within the wound dressing with one inlet diverging into several outlets. Fibroblasts and keratinocytes were shown to segregate into clusters upon delivery, illustrating cellular distribution through the microfluidic device. The delivery of fibroblasts through the device in clusters resulted in enhanced proliferation of fibroblasts compared to randomly dispersed cells in 3D and 2D. Animal studies showed successful incorporation and function retainment of delivered cells upon delivery. This design offers a potential therapeutic method to optimize the rate of tissue and wound repair.

Keywords: Dynamic Cell delivery
Efficient Cell delivery
Microfluidics
Smart Dressing
Stem Cells
Wound dressing
Advisor: Amini-Nik, Saied
Using In Vitro Approaches to Study Relationships between Key Members of the Murine Gut Microbiota

The gut microbiota comprises a diverse community of organisms that have co-evolved intricate relationships with each other, leading to its involvement in a number of key roles in the host. Investigating the interactions between microbes in this community is integral to understanding these complex microbial ecosystems and their effects on the host. Mice are one of the most commonly used animal models yet their gut microbiota remains relatively uncharacterized, complicating the interpretation of data. My research has leveraged in vitro techniques to explore the mouse gut microbiota. I have shown that, unlike human gut bacteria, diverse communities of mouse gut bacteria cannot be cultured despite testing a range of growth conditions. I have also identified and characterized both antagonistic and synergistic relationships between prevalent members of the mouse gut microbiota. These findings provide valuable insight into the mouse gut microbiota and the bacterial interactions that influence this microbial ecosystem.

Advisor: Navarre, William
Methionine-Mediated Protection of Fetal Programming Induced by Synthetic Glucocorticoid Treatment

S-adenosylmethionine (SAM) is a modified amino acid that is produced by the methionine cycle and used during DNA methylation. We investigated the methionine cycle as a mechanism through which prenatal synthetic glucocorticoid (sGC) treatment affects DNA methylation and gene expression in the fetus, and whether maternal supplementation with methionine (SAM precursor) could protect against sGC effects. Results indicate that sGC treatment was associated with increased methionine cycle metabolite levels (male plasma SAM and trend for hippocampal SAM-SAH ratio in females) and increased placental gene expression of methyl-donor transporters (Lat2, Rfc). Maternal methionine supplementation led to upregulation of key methylation-related enzymes (Mat2a, Dnmt3a, Dnmt3b) in the female and male hippocampus, though DNA methylation was unaffected. These findings suggest a potential rebound phenomenon in sGC-treated fetuses, and that maternal methionine supplementation can promote DNA methylation in offspring. Future research will further investigate the effects of sGCs and methionine on region-specific DNA methylation.

Keywords: Antenatal Glucocorticoid
Developmental Programming
Gene Expression
Hippocampus
Methionine Cycle
Advisor: Matthews, Stephen G
Imprinting and recalling amygdala ensembles

In the lateral amygdala (LA), memory allocation is a competitive process governed by changes in neuronal excitability. Enhanced levels of excitability can be sustained as a result of previous experience, making those neurons more likely to be allocated to subsequent events. However, the temporal window in which excitability can influence neuronal competition has not been defined, and it is not known whether transient increases in excitability can drive the events required for allocation to occur. Here, we bidirectionally manipulated the activity of a random, sparse subset of LA neurons in mice at various time intervals prior to auditory fear conditioning. Transient optogenetic excitation was sufficient to induce allocation 1-6 hours (but not 12-24 hours) prior to conditioning, evidenced by impaired freezing when photostimulated cells were inhibited during memory retrieval. These findings suggest that in the LA, a limited time window exists in which excitability can bias the outcome of allocation.

Keywords: Amygdala
Behavioural neuroscience
Learning and memory
Memory allocation
Optogenetics
Viral vectors
Advisor: Josselyn, Sheena A
Augmenting ORKAMBI® Rescue of F508del-CFTR Primary Respiratory Tissue with L-Arginine-Nitric Oxide Pathway Agonists

Cystic Fibrosis (CF) is a common autosomal recessive disease in the Caucasian population caused by a mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene, which codes for a major Cl- and HCO3- channel protein. Mutations in CFTR, F508del-CFTR, being the most common mutant, results in airway surface liquid depletion and defects in mucociliary clearance defects, leading to pulmonary dysfunction. ORKAMBI®, the firstan FDA approved therapy to address the basic defects of mutated CFTR in F508del-CFTR patients, only results in modest and variable lung function improvements in lung function. Genome wide association studies may help explain this variability by identifying modifier genes of the CF lung disease phenotypes, such as SLC6A14, a major apical arginine transporter in the airways. L-arginine has beenis regarded as a substrate for activating CFTR channel function through the L-Arginine-Nitric Oxide Pathway and could be used in conjunction with ORKAMBI® to improve lung function. We tested primary human respiratory cell cultures (both bronchial and nasal cells derived from delF508-CFTR patients) with Our an array of assays to determined an individual’s cells’ CFTR function, ciliary beat frequency, and mucociliary clearance velocity using primary F508del patient respiratory cell cultures. Although ORKAMBI® treatment alone improved CFTR function and mucociliary functions, combining ORKAMBI® treatment with NO- pathway agonists further augmented in vitro outcome measurements. This work suggests that stimulation of the arginine-NO pathway in combination with CFTR modulation may result in improved restoration of CFTR function and mucociliary clearance in both in vitro and in vivo models.

Keywords: CFTR Modulators
Cystic Fibrosis
L-Arginine Nitric Oxide Pathway
Mucociliary Clearance
Personalized Medicine
Primary human respiratory epithelial cells
Advisor: Bear, Christine E
Moraes, Theo
Elevational Differentiation Increases Rates of Trait Evolution but not Diversification in Neotropical Passerine Birds

The importance of ecologically-mediated divergent selection in elevating rates of trait evolution has been poorly studied in the most species-rich biome of the planet, the continental tropics. I performed a macroevolutionary analysis of trait divergence and diversification rates across closely-related pairs of passerine birds, belonging to the Amazon basin and adjacent Andean slopes, to assess whether the difference in elevational range separating species pairs influences the speed of trait evolution and diversification rates. Difference in elevation was used as a proxy for the degree of ecological divergence. I found that the amount of elevational separation is associated with faster differentiation of song frequency, a trait important for premating isolation, and several morphological traits, which may contribute to extrinsic postmating isolation. However, ecological differentiation does not primarily drive bird diversification and, thus, may have limited influence on patterns of species richness along the eastern slope of the tropical Andes.

Keywords: Birds
Ecological divergence
Elevation
Neotropics
Speciation
Trait evolution
Advisor: Weir, Jason T.
To believe or not to believe: Stereotypes about agnostics

The present study investigated which stereotypes agnostics share with atheists, and which stereotypes are unique to each group. In Study 1, participants reported stereotypes that they believed society held about agnostics, atheists, Christians, and Muslims. Common stereotypes for agnostics were indecisive and questioning, but for atheists were immoral and intolerant. In Study 2, participants rated how representative 10 key traits from Study 1 were of agnostics, atheists, and four religious groups. Results revealed that agnostics were stereotyped less negatively than atheists. In Study 3, participants had to judge whether a target’s actions, such as being immoral, morally indecisive, or indecisive in general were representative of an agnostic/atheist/Christian/Muslim. Inconsistent with Studies 1 and 2, no significant differences were found for perceptions of agnostics versus atheists. Findings from Studies 1-2 suggest that nonreligious individuals are sometimes viewed as a heterogeneous group, but future research must determine when stereotypes converge and diverge.

Keywords: agnostics
atheists
psychology
religion
stereotypes
Advisor: Chasteen, Alison L
Mechanisms of anoxia tolerance in non-excitable cells: investigating the role of the mitochondria in Western Painted Turtle hepatocytes

Organisms like the Western Painted Turtle (Chrysemys picta), which overwinter in ice-covered ponds, can survive long periods of limited oxygen availability by dramatically reducing their metabolic rate. Cellular mechanisms underlying this adaptation have predominantly been studied in brain tissue - excitable cells. This study aims to investigate the role of mitochondria in the anoxia tolerance of C. picta hepatocytes, non-excitable cells. Using the membrane potential sensitive compound Rhodamine-123, mitochondrial membrane potential depolarized in anoxic hepatocytes, just as in brain. Furthermore, pharmacological activation of mitochondrial ATP-sensitive potassium channels (mKATPs) simulated the anoxic response, while inhibition of mKATPs under anoxic conditions abolished the anoxic response, suggesting that mKATPs are important in the maintenance of mitochondrial membrane potential and subsequent changes during anoxia in both cell types. Hepatocytes differ in their calcium response, as calcium imaging using Oregon Green found no change in intracellular calcium levels under anoxia.

Advisor: Buck, Leslie T
Zeta Adsorption Isotherm: From Specific Surface Area Determination to Equilibrium and Kinetics of Water Vapour Adsorption on Silica Nanopowders

We use the zeta adsorption isotherm (ZAI) and propose a method for the long standing problem of determining the specific surface area (SSA) of powders using the N2 adsorption measurements at 77 K, which reduces the error of the conventional BET method, up to an order of magnitude. The consistency of the results obtained is demonstrated using two alpha-alumina samples that have different total surface areas. When the proposed method is applied to convert the amount adsorbed per unit mass to the amount adsorbed per unit area, we show that there is no measurable difference between their adsorption isotherms. In addition, using the ZAI, a new possible criteria for studying the reversibility of water vapour adsorption on silica nanopowders is introduced. Finally, the kinetic experiments of this solid--vapour system are conducted and a proper theoretical model is developed by combining the statistical rate theory (SRT) and the ZAI.

Keywords: Adsorption
Equilibrium
Kinetic
Nanopowder
Surface Science
Thermodynamics
Advisor: Ward, Charles A
Development of Indium Arsenide Nanowire Field-Effect Transistors as Chemical Sensors

Chemical sensors based on field-effect transistors were fabricated from hundreds of aligned indium arsenide nanowires which show promise for high performance based on their high electron mobility and charge sensitivity. Sensing responses to analytes in vapour and solution phases were collected from these multi-wire devices via real-time current measurements and parameters extracted from electrical transport characterization. In the vapour phase, a linear response to acetic acid was observed in surface charge densities determined from a model for the sub-threshold behaviour. These responses distinguished between strongly chemisorptive bonding of acetic acid versus weaker bonding of methanol and 2-butanone. In the solution phase, near-Nernstian sensitivity to sodium ions of a crown ether functionalized, fluorosilicone membrane was determined from the threshold voltage and hysteresis in transport characteristics. A Nernst-Planck-Poisson model was investigated to interpret the electro-diffusive processes but did not accurately capture the electric field dependence. Suggestions to address the shortcomings are given.

Keywords: chemical sensor
field-effect transistor
indium arsenide
ion-sensitive
nanowire
Advisor: Ruda, Harry E
Testing for Convergent Evolution in Semi-aquatic Anolis Lizards

Twelve species from six different clades of Anolis lizard exhibit a semi-aquatic lifestyle. These unusual species are found only along neotropical streams, and are known to swim, capture aquatic prey, and dive to escape predators. Based on ecomorphology theory, and anoles’ famed predisposition for convergence, we would predict that these anole lineages should have undergone convergent evolution. However, previous morphometric research suggested that semi-aquatic anoles are not convergent. This thesis reinvestigates whether semi-aquatic anoles have convergently evolved using novel morphometric and experimental approaches. I assessed the morphology, swimming speed, and diving performance of semi-aquatic and non-aquatic anole species from throughout the neotropics. My results suggest that semi-aquatic anoles have converged upon similar morphologies, superior swimming performance, and a previously undiscovered potential adaptation for diving: underwater rebreathing. Semi-aquatic anoles show evidence of repeated multidimensional convergence, and, somewhat uniquely for Anolis, provide strong evidence for convergence between mainland and island forms.

Keywords: Anolis lizards
Convergent evolution
Macroevolution
Morphology
Swimming performance
Advisor: Mahler, D. Luke
Microfluidics for Measuring Mutual Properties of the CO2–Crude Oil System

Successful implementation of CO2 enhanced oil recovery critically relies on detailed measurements of CO2–oil properties at relevant reservoir conditions. In this work, a microfluidic platform was developed to quantify the comprehensive suite of mutual properties of a CO2 and crude oil mixture. The time-lapse oil swelling/extraction in response to CO2 exposure under step-wise increasing pressure was quantified via fluorescence microscopy, leveraging the inherent fluorescence property of the oil. The solubility and diffusion coefficient of CO2 in the crude oil as well as CO2–oil MMP were determined from the oil swelling/extraction data with measurements in strong agreement with previous results. In addition, the oil–CO2–silicon contact angle was measured, with contact angle increasing with pressure. In contrast with conventional methods which require days and ~500 mL fluid sample, this approach provides a comprehensive suite of measurements, 100-fold faster with less than 1 μL of sample.

Keywords: CO2-oil
Contact angle
Diffusivity
Microfluidics
solubility
swelling
Advisor: Sinton, David
FuNTAP: A Fusarium graminearum Protein-Protein Interaction Network to Study Deoxynivalenol Biosynthesis Pathways

Protein interaction networks provide invaluable information on the complexity of biological pathways within organisms. These networks help identify proteins of interest along with groups of closely associated proteins with common functions. The fungus Fusarium graminearum is a pathogen of agriculturally significant crops such as wheat. The infection process includes production of harmful mycotoxins such as deoxynivalenol (DON). To study the signalling pathways leading to biosynthesis of DON in F. graminearum, we constructed the Fusarium Network of Trichothecene Associated Proteins (FuNTAP) based on yeast two-hybrid interactions of proteins differentially expressed under DON inducing conditions. The FuNTAP network categorizes the metabolic pathway which produces this important mycotoxin without the drawbacks of previous predicted-based model interactomes. As such, we present the FuNTAP network as a tool to identify proteins regulating the biosynthesis of DON. This network may also integrate other sources of data including gene expression profiles and biological function through sequence similarity.

Keywords: Deoxynivalenol
Fusarium graminearum
Protein-protein interaction network
Tricothecene
Yeast-Two-Hybrid
Advisor: Subramaniam, Rajagopal
Desveaux, Darrell
High-Speed Baud-Rate Clock and Data Recovery

This thesis presents an adaptive baud-rate CDR with CTLE and 1-tap DFE. The novelty in this design is the adaptation engine tailored for baud-rate clock and data recovery where the comparators for the DFE and the PD are shared to save power. A testchip was fabricated in TSMC 28nm CMOS. The adaptation engine is demonstrated for 34-36Gb/s operation with a Tyco 5" channel resulting in 15.05-18.25dB channel losses. At 35Gb/s, the total power consumption is measured to be 106.3mW or a FOM of 3.04pJ/bit. This thesis also presents a 2x half-baud-rate clock and data recovery technique with 2x oversampling at half-baud-rate (every other UI). A testchip was also fabricated in TSMC 28nm CMOS. A 30Gb/s 2x half-baud-rate CDR was tested with a Tyco 5" channel with 13.06dB of loss. The total power consumption is measured to be 79.2mW or a FOM of 2.64pJ/bit.

Keywords: Baud-rate
Circuits
Clock and Data Recovery
High-speed Signalling
Receiver
Wireline
Advisor: Sheikholeslami, Ali
Widening the Gap Between Egoists and Altruists: A Computational Study of Altruistic Choice under Time Pressure.

Popular models of altruistic choice typically assume some universal disposition that is curbed by the employment of control. The “self-control model” assumes humans are fundamentally self-interested and require self-control to overcome their egoistic impulses. Meanwhile, the “social-intuitionist model” posits that humans are intuitively prosocial and self-interests require controlled deliberation. Many studies investigating these theories measure changes in altruistic choice under time pressure, assuming that time pressure reveals our most automatic preferences. However, these studies yield mixed support for both theories and report overwhelming interindividual variability in the effects of time pressure: selfish individuals may become more selfish while generous individuals become more generous. Using novel computational modelling and eye-tracking, we propose a resolution to these conflicting findings. We show that individuals vary widely in their social preferences and that time pressure multiply disrupts choice processes, simultaneously increasing choice errors and interacting with existing preferences and biases to extremify choice behavior.

Keywords: Altruism
Computational Modelling
Eye-Tracking
Social-Decision Making
Time Pressure
Advisor: Hutcherson, Cendri A
Cunningham, William A
The Role Of Oxidative Stress Following Antenatal Synthetic Glucocorticoid Therapy

We investigated the role of oxidative stress following sGC treatment in a guinea pig model of gestation through measures including: expression of antioxidant enzyme genes, protein carbonylation, and the glutathione ratio in the hippocampus, placenta, and liver of female and male fetuses treated with two courses of betamethasone in utero. Results indicated no significant differences in hippocampal or placental gene expression. Peroxiredoxin-6 expression was significantly downregulated in the male liver following sGC, but there were no differences in the female liver. There were no differences in protein carbonylation or glutathione ratio in the fetal placenta or liver. To investigate long-term outcomes of sGC exposure in utero, we used gene set enrichment analysis of post-natal day 40 female hippocampi, and found significant downregulation of a gene set for oxidative phosphorylation. These finding suggest that while the fetus is acutely protected from oxidative stress following sGC, there might be long-term programming of mitochondrial functions.

Keywords: Antenatal
Glucocorticoid
Oxidative stress
Advisor: Matthews, Stephen G
Direct Sensing of Hydrocarbon Pollutants via Soluble Polymeric Sensors

Hydrocarbon leakages are a prominent environmental and economic issue in today’s oil and gas transportation infrastructure. In the US alone, over 100 hydrocarbon spills occur yearly, resulting in billions of dollars of civil and environmental damage. To mitigate the impacts of this issue, development and implementation of leak detection systems are prominently applied in industry. However, current state-of-the-art sensor systems utilize indirect methods of sensing that feature poor hydrocarbon selectivity and low detection accuracies of 16-17%. Herein we employ hydrocarbon-soluble polymers in fabrication of sensor designs for direct and selective crude oil sensing. Composite EVA/carbon fiber sensors are fabricated and show 421% sensor responses after 6 hours of oil exposure, while reflectometry sensing via EVA and silicone coaxial cables show sensor responses of 9.71% to 115% after 24 hours of oil exposure. Overall, high efficacy in hydrocarbon leak detection is achieved, validating the sensing effectiveness of hydrocarbon-soluble polymers.

Keywords: Composites
Environment
Hydrocarbons
Pollutants
Polymers
Sensors
Advisor: Naguib, Hani E