This research project is an ongoing project in collaboration with colleagues in the Department of Biology at the University of the Pacific. The main purpose of this project was to separate and identify the female-attracting substance secreted by male frog by developing chromatography methods for the male and female aqueous extracts. Three methods were used to concentrate the samples: sample lyophilization,..solid phase extraction (SPE), and direct sample loading. Different parameters such as the type and concentration of the phase modifier, wavelength for UV-detection, composition of the mobile phase, flow rate, and gradient elution were studied to achieve the required separation. The optimal method was determined as: direct sample loading, 0.01% (v v) formic acid in in mobile phase A (water) and mobile phase B (acctonitrile), 200 nm, 0.60 mL/min, and gradient method. The chromatograms of male and female skin gland water samples were compared and the fractions specific to male frog were collected and lyophilized for bio-activity testing and mass spectrometry analysis. Three different mass spectrometer systems, JEOL LCMate (ES+), Micromass Q-Tof Ultima™ Global (ES-). Voyager-DE™ STR Biospectromelry™ Workstation (MALDI-TOF), and Varian Mercury 300 MHz FT-NMR were utilized to investigate the structure of the fractions collected through HPLC. Only Micromass Q-Tof Ultima™ Global (ES+) gave some potential results. After analysis, the proposed protonated molecular ion peak was determined to be at m/z 779 by analyzing the abundance and relationship among the peaks at higher m/z values. The detail structure was inconclusive. vi

Maternally inherited poly(A)+ RNAs are important for directing early development in many animal species. This thesis investigates the regulation of maternal mRNA in the South African clawed frog, Xenopus laevis. The first portion of this thesis examines an unusual class of maternal RNA, interspersed poly(A)+ RNA, which is composed of co-linear repeat and single copy sequences. A cDNA clone, called pXR, contains the repeat portion of an interspersed RNA that hybridizes to several different oocyte transcripts of diverse size that persist until the neurula stage. DNA sequence analysis of the cDNA and hybrid selection of the oocyte transcripts followed by in vitro translation show that molecules of this repeat family are not translatable. This data, combined with the developmental profile of XR containing RNAs, indicate that members of this repeat family are not likely to be maternal messenger RNAs. The second part of this thesis investigates the expression of a class of maternal mRNAs that are regulated by cytoplasmic polyadenylation during progesterone induced oocyte maturation. One particular mRNA G10, is stored as a polyadenylated RNA in the cytoplasm of stage VI oocytes until maturation when the process of poly(A) elongation stimulates its translation. Injection of mutant and wild-type mRNAs, synthesized in vitro, revealed that two sequence elements, UUUUUUAUAAAG and AAUAAA, were both necessary and sufficient for polyadenylation and polysomal recruitment of G10. Maturation promoting factor and cyclin as well as progesterone can induce polyadenylation but in each case protein synthesis is required. Extracts from oocytes and unfertilized eggs were employed to identify factors that may be responsible for maturation-specific polyadenylation. An 82 kd protein that binds to the UUUUUUAUAAAG in egg, but not oocyte extracts, was identified by UV crosslinking. This data suggests that p82 is a good candidate for a developmentally regulated protein that controls the expression of maternal messenger RNAs in early Xenopus development.

Neuronal nicotinic acetylcholine receptors (nAChRs) are expressed in both the periperhal and central nervous systems, and are involved in pre-, post-, and non-synaptic control of neuronal activation. In the brain, these receptors play an important role in a variety of physiological processes such as cognition, development, learning, and memory formation. Malfunction of these receptors have been implicated in neurodegenerative diseases like Alzheimer's disease (AD), schizophrenia, and Parkinson's disease. To date, 17 different nAChR subunits, including α2-α7 and β2-β4, have been cloned that can form homo- and/or hetero-pentameric ionotropic receptors. The unique combinations of subunit pentamers manifest in distinct functional receptors. Using single-cell real-time quantitative RT-PCR, we identified the individual expression rates and co-expression rates of the different nAChR subunits in rat CA1 hippocampal interneurons in efforts to characterize functional receptors involved in learning and memory. The two-way combination of subunits with highest expression in hippocampal interneurons was α3β2. Moreover, this combination was expressed in ratios near 1:3 or 3:1 α3 to β2 respectively. To investigate the functionality of α3β2 receptors in different stoichiometries, we injected human α3 and rat β2 subunit mRNA in 1:3, 1:1, and 3:1 ratios into Xenopus laevis oocytes for expression. Two-electrode voltage clamp was then performed with the application of different concentrations of ACh to produce full dose-response curves and channel kinetics data. Distinct α3β2 functional channels were identified from the different expression ratios based on significant differences in channel kinetics (i.e.- peak current rise times, peak current decay times, steady state current in forced desensitization) Dose-response curves produced no significant difference in EC50 values in the different expression groups. However, there was a trend to greater agonist sensitivity with increased α3 expression relative to β2. α3β2 receptors were further characterized through forced desensitization of the receptors and generation of IV plots. The findings from this study elucidate the neuronal nAChR subunit combinations that form functional channels in hippocampal interneurons.

<p>Per- and polyfluoroalkyl substances (PFAS) are a group of emerging global contaminants used in a variety of industrial processes and consumer products, such as personal care products and fast-food wrappers. However, due to their carbon-fluorine bonds, these chemicals resist degradation and persist in the environment. PFAS toxicity is driven by a compound’s functional group and chain length with perfluorooctane sulfonate (PFOS), perfluorohexane sulfonate (PFHxS), perfluorooctanoic acid (PFOA), and hexafluoropropylene oxide dimer acid (GenX) being of focal concern due to their toxicity to wildlife and presence in the environment. Despite growing concern regarding these contaminants, inadequate attention has been given to evaluating what organismal characteristics influence uptake and depuration of these chemicals, such as life stage and sex. <em>Xenopus laevis</em> tadpoles are a useful model to assess the influence of sex on PFAS kinetics since they have a life history that includes a gill to lung transition. Previous studies have shown that air-breathing organisms depurate PFAS more slowly than water-breathing organisms, but this relationship has never been directly tested. Sex has been shown to be an important factor in the depuration of PFOA for rats, with female rats depurating PFOA in four hours while males depurate in four days. The early portion of bioaccumulation curves are also understudied even though tadpoles accumulate PFAS rapidly, reaching steady state within 48 hours of exposure. <em>Xenopus laevis</em> are used to study multiple endpoints for endocrine disrupting chemicals including PFAS. Despite this, toxicity reference values (TRVs) have not been described for the uptake and elimination of PFAS using <em>X. laevis</em>. To address these gaps in knowledge, I first developed TRVs for <em>X. laevis</em> tadpoles exposed to PFOA throughout metamorphosis and evaluated the influence of sex on phenotypic endpoints. Results showed a no observed effect concentration (NOEC) of 11.1 ppm for body mass at day 14 and no effect of sex on apical endpoints. Next, I described the early bioaccumulation of four PFAS with differing structure (chain lengths and functional groups). PFOS was the only chemical to bioaccumulate with a log bioconcentration factor (BCF) at 10 and 1,000 ppm of 1.33 and 1.18, respectively. PFHxS, PFOA, and GenX had BCFs less than 0. Finally, I examined the impact of life-stage and sex on <em>X. laevis</em> tadpole and juvenile depuration rates. Larval tadpoles depurated four times faster than juveniles, indicating a significant effect of life stage on elimination rates. Sex had no influence on elimination rates. These are the first studies conducted evaluating the significance of life stage and sex in toxicokinetics of PFAS in amphibians.</p>

Gastrulation is a fundamental process that reorganizes the primary germ layers to shape the internal and external features of an early embryo. Morphogenetic movements underlying this process can be classified into a variety of different types of cellular movements. I will focus on investigating in this thesis two types of cell movements in the dorsal mesoderm; mediolateral cell intercalation and convergence and extension. During gastrulation, mesoderm cells send protrusions to gain traction on neighboring cells and the surrounding extracellular matrix; a process called mediolateral cell intercalation. Mesoderm cells use this type of cell movement to converge and extend the dorsal mesoderm tissue during gastrulation; a process called convergence and extension. These morphogenetic movements are essential to form the early embryo and are important for later development. There are a number of different proteins involved in regulating the morphogenetic movements during gastrulation. The Planar Cell Polarity Signaling Pathway helps establish individual cell polarity and is activated in dorsal mesoderm cells undergoing convergence and extension. In addition, dorsal mesoderm cells migrate by using integrin receptors and the surrounding extracellular matrix to correctly position the mesoderm in the embryo. I will focus my efforts on analyzing the function of ADAM proteins during Xenopus laevis gastrulation. The ADAM family of metalloproteases is important for a variety of biological processes. ADAM proteins function as ectodomain sheddases by cleaving membrane bound proteins involved in signal transduction, cell-cell adhesion, and cell-extracellular matrix adhesion. I will focus on investigating the roles of two ADAM family members; ADAM13 and ADAM19 during gastrulation. Both ADAM13 and ADAM19 are expressed in the dorsal mesoderm during gastrulation. Throughout early embryonic development, ADAM13 is expressed in the somitic mesoderm and cranial neural crest cells. ADAM19 is expressed in dorsal, neural and mesodermal derived structures such as the neural tube, notochord, the somitic mesoderm, and cranial neural crest cells. Since ADAM13 and ADAM19 are expressed in similar tissues, I investigated if both proteins functionally interacted. I show that a loss of ADAM13 protein in the embryo reduces the level of ADAM19 protein by 50%. In the opposite experiment, a loss of ADAM19 protein in the embryo reduces the level of ADAM13 protein by 50%. This suggests that both ADAM13 and ADAM19 are required to maintain proper protein levels in the embryo. This might be explained through their physical interaction in a cell. The ADAM19 Proform binds to the ADAM13 Proform in cultured cells. Through domain analysis, I show that ADAM19 binds specifically to the cysteine-rich domain of ADAM13. When co-overexpressed in a cell, the level of Mature ADAM13 (compared to the Proform) is reduced suggesting a complex form of regulation. I propose a few hypothetical models that discuss how ADAM19 may function as a chaperone to stabilize and regulate the further processing of ADAM13 protein. Some of the unpublished work discussed in this thesis focuses on the roles of ADAM13 and ADAM19 in the dorsal mesoderm during gastrulation. Specific emphasis is made on investigating the axial mesoderm during notochord formation. I show that ADAM19 affects gene expression important for the A-P polarity of the notochord while ADAM13 does not. The changes in gene expression can be partially rescued by the EGF ligand Neuregulin1β, a known substrate for ADAM19 in the mouse. ADAM13 and ADAM19 are important for convergence and extension movements of the axial mesoderm during gastrulation. Specifically, a loss of ADAM13 or ADAM19 causes a delay in mediolateral cell intercalation resulting in a significantly wider notochord compared to control embryos. These defects occur without affecting dishevelled intracellular localization or the activation of the PCP signaling pathway. However, a loss of ADAM13 or ADAM19 reduces dorsal mesoderm cell spreading on a fibronectin substrate through α5β1 integrin. To conclude, the work presented in this thesis focuses on the similarities and differences of ADAM13 and ADAM19 in the early embryo. Although ADAM13 and ADAM19 are required for normal morphogenetic movements during gastrulation, my data suggests they have different functions. ADAM13 appears to function in regulating cell movements while ADAM19 appears to function in regulating cell signaling. I propose a few hypothetical models that discuss how each ADAM metalloprotease may function in the dorsal mesoderm and contribute to convergence and extension movements during gastrulation.>

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Gene duplications can facilitate genetic innovation, reduce pleiotropy and catalyze reproductive incompatibilities and speciation. Therefore, the molecular and transcriptional fate of duplicate genes plays an important role in the evolutionary trajectory of entire genomes and transcriptomes. Using the polyploid African clawed frog Xenopus, I have investigated mechanisms that promote the retained expression of duplicate genes (paralogs) after whole genome duplication. The studies herein estimated molecular evolution and characterized expression divergence of thousands of duplicate genes and a singleton ortholog from a diploid outgroup. In this thesis, I have discussed the multiple mechanisms for the retention of duplicate genes in a polyploid genome and examined the potential effects that gene characteristics before duplication have on the odds of duplicate gene persistence. I have also explored the use of microarrays for comparative transcriptomics between duplicate genes, and between diverged genomes. The main objectives of my thesis were to better understand the genetic mechanisms that promote the retained expression of gene duplicates. My research utilized the duplicated genome from the allopolyploid clawed frog Xenopus. Genome duplication in clawed frogs offers a compelling opportunity to study factors that influence the genetic fates of gene duplicates because many paralogs in these frogs are of the same age, permitting one to control for the influence of time when evaluating the impact of duplication. My work has major impacts on several biological fronts including evolutionary genomics and comparative transcriptomics, and also on technical aspects of using microarrays. I have provided among the most comprehensive studies of its kind, in terms of examining molecular and regulatory aspects of thousands of expressed duplicates of the same age, and exploring various alternative hypotheses to explain how these genes are retained. / Thesis / Doctor of Philosophy (PhD)

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