VictorJuiz/thesis huggingface dataset:
The Effects of the Novel Reproductive Peptide Phoenixin-20 Amide on GnRH and Kisspeptin Hypothalamic Cell Models
Keywords: gonadotropin-releasing hormone
kisspeptin
phoenixin

Reproductive function is coordinated by the actions of specific neuropeptides and hormones, which converge on GnRH neurons in the hypothalamus. Phoenixin-20 amide (PNX-20) is a recently described peptide that increases GnRH-stimulated LH secretion and upregulates GnRH receptor mRNA in the anterior pituitary. However, to date no studies have looked at the role of PNX-20 in the hypothalamus, where it is most highly expressed. Using cell lines representative of GnRH and kisspeptin neurons, the effects of PNX-20 in the hypothalamic cells were explored. PNX-20 increases GnRH mRNA expression, protein levels and secretion in a GnRH cell model and Kiss-1 mRNA in anteroventral periventricular and arcuate nuclei kisspeptin cell models. PNX-20 also activates the adenylyl cyclase and MAPK pathways. Furthermore, we report that kisspeptin increases gene expression of the PNX precursor protein, SMIM20. These results indicate that PNX-20 may be involved in the regulation of reproduction at the level of the hypothalamus.
Contact Imager for Integrated Functional Assessment of Organs-on-a-chip
Keywords: Contact imaging
Lab on a chip
Lenless imaging
Microfluidic
organ on a chip
Reversible seal

We describe a microfluidic platform for the assessment of small blood vessel function. The new, compact modular platform allows to reversibly host mouse mesenteric arteries on a microfluidic chip, without the need for any manual on-chip manipulation. The luminal and abluminal sides of chip-hosted vessels are exposed to well-defined chemical microenvironments, and physiological levels of transmural pressure and temperature are established. Vasoconstriction was induced by abluminal presentation of phenylephyrene and dose-response experiments were conducted. Vessel constriction was directly determined by direct projection of the chip-hosted artery via a fiber-optic faceplate onto a CMOS sensor, therefore removing the need for a microscope and an external camera. We believe the demonstrated approach will be broadly applicable for the routine functional assessment of different microtissues and organs-on-a-chip. In the context of intact arteries, the approach may ultimately enable the clinical assessment of patient microvascular status.
Cholesterol Plays a Crucial Role in High-fat-diet Induced ER stress and Non-alcoholic Fatty Liver Disease
Keywords: Cholesterol
ER-stress
High fat diet
Murine
NAFLD/NASH
Obesity

By comparing C57 mice with two dyslipidemic models, LDL-receptor null (LDLR-/-) and LCAT/LDL-receptor null mice (LCAT-/-xLDLR-/-), our lab showed an observation of ER-membrane cholesterol being necessary to modulate ER-stress in a high-cholesterol-diet feeding paradigm. Here, we hypothesized that hepatic cholesterol biosynthesis plays an important role in mediating high-fat-diet-induced hepatic ER stress and NAFLD. In vivo, we fed C57, LDLR-/-, LCAT-/-xLDLR-/- mice a high-fat-diet for 16 weeks. Markers for hepatic ER-stress, cholesterol biosynthesis, ER-cholesterol, NAFLD and inflammasome were measured. High-fat-diet feeding induced ER-stress, NAFLD, cholesterol biosynthesis, NLRP3 activation and ER-membrane cholesterol accumulation in both C57 and LDLR-/- mice, while LCAT-/-xLDLR-/- mice were protected. In vitro, HepG2 cells were treated with palmitate overnight with/without zaragozic acid (ZA), to inhibit cholesterol biosynthesis. Treatment with palmitate induced ER-stress, cholesterol biosynthesis and NLRP3 activation, which were abrogated by ZA treatment. These findings implicate the role of cholesterol in nutritional excess-induced hepatic metabolic complications.
Optical Detection of Interaction between Alzheimer's Disease Biomarkers and Carbon Nanotubes
Keywords: acetylcholinesterase
Alzheimer's
amyloid-beta
butyrylcholinesterase
Carbon nanotubes
Ellman's method

Alzheimer's disease (AD) is a debilitating neurodegenerative disorder characterized by cognitive impairment. During AD, Amyloid Beta (A) is deposited extracellularly and forms plaques, disrupting neuronal communication. Acetylcholinesterase (AChE) and carbon nanotubes (CNTs) modulate amyloid fibrillation pathways. We explored effect of multi-walled CNTs (MWCNTs) and A
The Role of Chirality in Self-assembly of Ferrocene Peptide Conjugates
Keywords: Ferrocene-peptides
nanofibril
sellf-assembly

In this report, the self-assembling behavior of four diastereomeric peptides has been investigated. A series of four Ferrocene tripeptides namely Fc-(L)Phe(L)Phe(L)Leu-OMe, Fc-(D)Phe(L)Phe(L)Leu-OMe, Fc-(L)Phe(D)Phe(L)Leu-OMe and Fc-(L)Phe(L)Phe(D)Leu-OMe have been synthesized and characterized. Next, the gelation performance has been thoroughly investigated and compared in different organic solvents. Interestingly, it has been found that only two peptides namely Fc-(L)Phe(L)Phe(L)Leu-OMe and Fc-(D)Phe(L)Phe(L)Leu-OMe form gel in toluene suggesting the potential effect of chirality in self-assembling process. The conformation and self-assembly have been investigated by variable concentration and variable temperature dependent NMR studies which suggest the involvement of multiple intermolecular hydrogen bonds for gelation. Gels have also been characterized by minimum gelation concentration, Fourier transform infrared spectroscopy and circular dichroism spectroscopy. The morphologies of their self-assembled states have been characterized by transmission electron microscopy. Interestingly, two of the Fc-peptides showed the presence of nanofibrillar network structure.
Proteomic Analyses of Human Fetal Atria and Ventricles
Keywords: Bioinformatics
Chamber specificity
Fetal tissue
Mass spectrometry
Q-Exactive
Ventricle

In this study we carried out a mass spectrometry-based proteome analysis of human fetal atria and ventricles. Heart protein lysates were analyzed on the Q-Exactive mass spectrometer in biological triplicates. Protein identification using MaxQuant yielded a total of 2,754 atrial (91%) and 2,825 ventricular protein groups (83%) in at least 2 of the 3 runs with 2 unique peptides. Statistical analyses using fold-enrichment (>2) and p-values (0.05) selected high confidence chamber enriched atrial (134) and ventricular (81) protein groups. Several previously characterised cardiac chamber-enriched proteins were identified in this study including atrial isoform of myosin light chain 2 (MYL7), atrial natriuretic peptide (NPPA), and connexin 40 (GJA5) for atria, and ventricular isoforms of myosin light chains (MYL2 and MYL3), myosin heavy chain 7 (MYH7), and connexin 43 (GJA1) for ventricle. Our data was compared to in-house generated and publicly available human microarrays, several human cardiac proteomes, and phenotype ontology databases.
Investigating the Role of MicroRNAs in the Pathogenesis of Kidney Cancer Subtypes and their Clinical Utility as Cancer Biomarkers
Keywords: Cancer biomarker
Focal adhesion pathway
MET
microRNA
miR-199a-3p
Renal cell carcinoma

Renal cell carcinoma (RCC) is the most common adult kidney neoplasm and constitutes a number of distinct subtypes. Papillary RCC (pRCC), a poorly characterized RCC subtype, can be subdivided into type 1 or 2. The objective of this study was to understand the pathogenesis of pRCC type 1. We identified genes and microRNAs (miRNAs) that are dysregulated in pRCC type 1. Pathway analysis showed enrichment of the focal adhesion pathway. We showed that miR-199a-3p, which is downregulated in pRCC type 1, regulates members of this pathway. Moreover, RCC subtypes may be difficult to differentiate by microscopy due to overlapping features. We demonstrated that miR-221 and -222 can discern chromophobe (chRCC) and renal oncocytoma, a benign neoplasm, from clear cell RCC (ccRCC) and pRCC. miR-126 can distinguish ccRCC from pRCC, whereas miR-15b and miR-22 had overlapping expression levels in chRCC and oncocytoma.
New Kinematic and Geochronologic Evidence for the Quaternary Evolution of the Central Anatolian Fault Zone
Keywords: Central Anatolia
Intracontinental Deformation
Neotectonics
Slip Rates

In this study new structural, geomorphic and geochronologic data are provided for several key faults within the southern and central parts of the Central Anatolian Fault Zone, which suggest Quaternary left-lateral motion has been previously overstated. Our neotectonic mapping along the southern part of the CAFZ, coupled with 36Cl exposure dating, documents a left lateral slip rate of 0.77 ± 0.22 mm a-1 during the Late- Pleistocene, lower than rates of 3 mm a-1 originally proposed. To the north, the Erciyes fault is characterized by a linear array of monogenetic vents which suggest maximum horizontal extension in a WNW-ESE direction during the Late-Quaternary. Further north, mapping and structural analysis shows that the Erkilet and Gesi faults within the northern Erciyes basin are predominantly extensional. We re-characterize the CAFZ as one of an array of weakly active, highly segmented, transtensional fault systems in Central and Eastern Anatolia which have re-activated paleotectonic structures.
Testing the Similarity Fit/Misfit Hypothesis in Adolescents and Parents with ADHD
Keywords: Adolescent-parent conflict
Adolescents
Attention-Deficit/Hyperactivity Disorder
Parental ADHD
Similarity Fit hypothesis
Similarity Misfit hypothesis

Parents and adolescents with ADHD may engage in excessive conflict due to the nature of adolescent ADHD behaviours (impulsivity, inattention) and the difficulties associated with parenting them. This may be magnified when parents struggle with ADHD and when comorbid adolescent externalizing problems exist. Despite the logic of an exacerbative effect when adolescents and parents have ADHD, research suggests that parents with ADHD show more tolerance, empathy and less conflict with their children who share similar cognitive traits (i.e., similarity-fit hypothesis). This study tested the similarity-fit/misfit hypotheses in a sample of 156 adolescents (mean age = 15.25) and their parents. Results supported the similarity-fit process in fathers whereby fathers and adolescents with higher inattention levels engaged in fewer conflicts. In mothers, the similarity-misfit hypothesis was supported: frequency of conflict was highest when mothers and adolescents had highest levels of inattention. Results were interpreted in the context of gender and parental roles.
The Impact of Microbiome Alterations in the NOD Mouse Model of Type 1 Diabetes
Keywords: Microbiota
NOD mouse
Type 1 Diabetes

Epidemiological and experimental data suggest Type 1 Diabetes (T1D) and gut inflammatory disorders share genetic and environmental risk factors. Genetics and microbiome composition differentiate T1D-prone NOD mice and T1D-resistant NOR mice. In the first part of this study, we examined the possible protective effects of NOR-derived microbiome transplant in NOD mice. We report, despite quantifiable, durable changes in the gut microbiome of NOD recipients of NOR-derived microbiome transplant compared to NOD and NOR controls, these mice were not protected from T1D. Studies have also suggested that probiotic bacteria can have protective effects in T1D and gut inflammatory disorders. In the second part of this study, we examined the possible protective effects of treatment with probiotic microbes in the NOD mice. We report Protecflor probiotic-treated NOD mice showed quantifiable, durable changes in gut microbiome composition, and were protected from autoimmune infiltration of the islets compared to vehicle-treated controls.
The Roles of Phosphodiesterase (PDE) 3A and 3B as Regulators of Cardiac Function in Disease
Keywords: cAMP/cGMP signaling
Cardiac hypertrophy
Heart failure
Phosphodiesterases

Cyclic nucleotide phosphodiesterases (PDEs) are enzymes that hydrolyze the 3'-5'-phosphodiester bonds of cAMP and/or cGMP. PDE3 family variants (PDE3A, PDE3B) are highly expressed in the heart. The roles of PDE3A, and PDE3B as regulators of cardiac function in disease have not been definitively established. We investigated the roles of PDE3A and PDE3B as regulators of cardiac function in the setting of heart failure (HF) of non-ischemic etiology. PDE3A and not PDE3B protein expression was elevated in failing hearts subjected to sustained biomechanical stress (pressure-overload). Chronic ablation of PDE3A and not PDE3B activity attenuated cardiac contractile dysfunction and pathological remodelling induced by pressure-overload. We propose ablation of PDE3A activity to prevent functional deterioration and compensatory remodelling induced by chronic biomechanical stress by stimulating ANP release from cardiac myocytes, and consequently enhancing paracrine and endocrine activities of ANP. Accordingly, we propose PDE3A to negatively regulate ANP release from cardiac myocytes.
Membrane Leakage and Antimicrobial Activity of Nylon-3 Polymers and Surfactants
Keywords: antimicrobial peptide
efflux
fungicide
lipid clustering
liposome
synthetic antimicrobial peptide mimic

This study was part of an effort to gain insight into biological modes of action of membrane-active antimicrobial agents with vesicle leakage experiments. Specific systems tackled here were three nylon-3 type polymers, introduced by Prof. S.H.Gellman's group (U of Wisconsin at Madison), which have shown great potential to serve as antibacterials and fungicides. A comprehensive set of vesicle leakage experiments, performed on different lipid models, included (i) the fluorescence lifetime-based leakage assay, which yields not only the active concentration but also the mechanism of leakage (ii) kinetics of leakage, and (iii) concerted action tests with detergents. Results suggest that there are different, characteristic vesicle leakage patterns that can be assigned to specific modes of action. Vesicle data often, but not always, correlates with biological activity. We speculate that the correlation may depend on the type of leakage - some mechanisms of vesicle disruption may be more directly relevant in vivo than others.
Design, Development, and Calibration of a 3D Sensory System for Surface Profiling of 3D Micro-scale Parts
Keywords: 3D Sensing
Analytical Calibration
Micro-scale
Microscope
Phase shifting
Structured Light Technique

This thesis first presents the development of the SL sensory system and the extensive experiments to verify the use of the SL sensory system for measuring macro-scale 3D parts. This thesis further presents the development of a SL sensor system for Micro-scale applications. A novel calibration method for micro-scale applications is presented to determine the overall SL system calibration parameters. The method includes a novel calibration model which explicitly considers the microscope lenses parameters for the hardware components (camera and projector) as well as addresses the limitation of narrow DOF behaviour of these lenses. The latter is achieved by incorporating an image focus fusion technique. The proposed approach is implemented and tested on a designed SL system. The measurement ability of the SL sensory system was provided by measuring micro-scale features. The measurements results demonstrate great potential for using this sensory system in obtaining 3D information of micro-scale complex parts.
The Effect of Adsorption on Energy Transport at a Solid-Vapour Interface
Keywords: Adsorption
Ethanol
Heat Transfer
Interfacial
Isotherm
Vapour

An apparatus was configured to measure steady-state energy transport between ethanol vapour and a polished copper surface. The magnitude of energy transport increased with pressure until the ratio of the vapour pressure to its saturation pressure reached 0.2. The adsorption of ethanol on copper was measured and the energy transport was found to strongly increase with adsorption until approximately 4 mol/m
Mechanical Insult Uncouples the Protective Function of PEA15 on Extracellular Matrix Remodeling and Apoptosis
Keywords: Apoptosis
Astrocytes
Extracellular Matrix Remodeling
Matrix Metalloproteinase 2
Mechanical Insult
PEA15

Glaucoma is an optic neuropathy in which the eye's intraocular pressure can become elevated and exert mechanical insult on the optic nerve head (ONH). This leads to dramatic ONH remodeling, astrocyte activation, and retinal ganglion cell death, causing vision loss. Proteomic analysis of human ONH astrocytes exposed to pathologically relevant mechanical insult revealed increased phospho-protein enriched in astrocytes (PEA15). PEA15 plays roles in extracellular matrix (ECM) remodeling and apoptosis, however this has yet to be explored in the context of glaucoma. PEA15 demonstrated protective function by decreasing levels of matrix metalloproteinase 2 (MMP2) and apoptosis. However, mechanical insult uncoupled the protective functions of PEA15 leading to increases in MMP2 and apoptosis. Phosphorylation of serine 104 on PEA15 was shown to be critical in uncoupling these protective functions as mutation of this residue rescued anti-apoptotic activity and suppression of MMP2. Overall glaucomatous mechanical insult appears to abrogate protective functions of PEA15 in apoptosis and ONH remodeling.
Microfluidic Bioprinter for Hydrogel Sheet Formation
Keywords: biopolymer
bioprinting
gelation
hydrogel
microfluidic

We present a microfluidic bioprinter that is compatible with a wide range of biopolymers and is able to continuously or periodically produce intact homogeneous or heterogeneous hydrogel sheets in Couette flow condition with different throughputs through different cross-linking mechanisms with control over the sheet geometries and mechanical properties. The printer includes a movable platform to achieve the automated production, collection and transportation of the hydrogel sheets, a microfabricated printing device that defines the geometry and composition of the printed hydrogel sheets, pressure controls upstream for introducing biomaterials with different flow rates, and temperature features to fulfill the thermal requirement during the material processing. According features can be enabled for different gelation mechanisms including ionic cross-linking gelation and thermal gelation. Using the concept of Couette flow with controls over printing parameters, homogenous and heterogeneous hydrogel sheets with different geometries and mechanical properties can be produced as predicted using the theoretical model.
Effect of Pulses in a Low Glycemic Index Diet on Renal Function in Participants with Type 2 Diabetes mellitus
Keywords: Dietary pulses
Glycemic index
Renal function
Type 2 diabetes mellitus

Dietary pulses are rich sources of protein, dietary fiber and are amongst the lowest glycemic index (GI) foods. We hypothesized that addition of pulses to a low GI (LGI-pulse) diet in participants with type 2 diabetes mellitus may be associated with improvement in renal markers resulting from replacement of animal by plant (pulse) protein. We attempted to develop a low GI pulse bread for use in therapeutic diets. The pulse bread had a low GI but lacked the required palatability. We determined the effect of increased plant protein intake on markers of renal function. We included 109 participants with type 2 diabetes mellitus who completed the diet. Pulses as part of a low GI diet in participants with type 2 diabetes mellitus did not adversely affect markers of renal function.
Fluid Dynamics and Biofilm Removal Generated by Syringe-delivered and Two Ultrasonic-assisted Irrigation Methods: A Novel Experimental Approach
Keywords: Biofilm
Irrigation
Root canal
Ultrasonic

Introduction: This study aimed to develop a standardized root canal model to study fluid/irrigation dynamics and biofilm elimination. Methods: A maxillary incisor with an instrumented canal was replicated in soft lithography-based models. Canals were irrigated using a syringe (SI) and two ultrasonic-assisted methods: intermittent (IUAI) and continuous (CUAI). Real-time fluid movement within the apical 3 mm of canals was imaged using micro-particle image velocimetry. Canals were inoculated with Enterococcus faecalis to grow 3-week-old biofilms. Biofilm reduction by irrigation was assessed. Results: CUAI generated the highest overall velocity and shear stress of all the groups in the apical 0-3 mm. Biofilm was significantly reduced compared to the control only by CUAI (p=0.005). Conclusions: CUAI exhibited the highest mechanical effects of fluid flow in the apical 3 mm, which correlated with significant biofilm reduction. The soft lithography-based models provided a novel model/method for study of root canal irrigation.
The Role of the ErbB2/Neuregulin Signaling Network in Regulating Acute or Chronic Nerve Regeneration and its Application to the Protection Provided by Side-to-side Nerve `Bridges'
Keywords: ErbB2
Herceptin
Nerve Regeneration
Neuregulin
Peripheral Nerve
Side-to-Side Nerve Bridges

Functional outcomes following peripheral nerve injuries are profoundly inhibited by the harmful consequences of chronic denervation. Surgical strategies that employ side-to-side nerve `bridges' can protect against chronic denervation. We hypothesize that this protection results from the activity of the Schwann cell mitogen Neuregulin-1 and its receptor ErbB2. A detailed histological assessment in the first series of experiments demonstrated typical patterns of axon regeneration, myelination and changes in Schwann cell phenotype, which implicate neuregulin signaling in directing Schwann cell behaviour in the `protected' denervated stump. The second and third experimental series examine regeneration following acute and chronic denervation in the presence of an inhibitor to the neuregulin receptor, ErbB2. Motoneuron and myelinated fiber regeneration is paradoxically enhanced in addition to increased cellular proliferation in the distal nerve. This effect may result from a newly described inhibitory association between ErbB2 and epidermal growth factor receptor (EGFR).
Palladium-catalyzed Carbohalogenation of Sterically Congested Alkynes: An Intramolecular Approach to the Synthesis of Vinyl Halides
Keywords: Carbohalogenation
Catalysis
Palladium
Steric Bulk

Pd catalyzed cross coupling reactions are extensively used to effect a multitude of organic transformations. The recent advent of carbon-halogen reversible oxidative addition has introduced C-X bond forming as a viable catalytic process. These carbohalogenation reactions are ideal because the reactive halide functionalities are retained in the products, however several limitations in the methodology still remain. Specifically, carbohalogenations using aryl bromides and chlorides and the formation of vinyl halide products are desirable transformations that have been elusive. Cyclopropene substrates were initially examined as intermolecular carbohalogenation coupling partners but these substrates were not found to be amenable to carbohalogenation. The focus shifted to using alkynes as intramolecular coupling partners. These substrates were found to successfully undergo cyclization, forming vinyl halide products. Additionally, aryl iodides, bromides and chlorides all react to form the corresponding vinyl halides. The reaction parameters were examined, a substrate scope was developed and mechanistic studies were performed.