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Color vision can affect our assumptions of an animals’ natural history. It can be determined by testing sensory or perception ability, which was employed here. Two Asian small-clawed otters (Aonyx cinerea), of opposite sexes, housed at ZooAtlanta, were trained via operant conditioning to discriminate stimuli within 7 tasks, primarily in a two-choice fashion. Varying shades of the colors blue, green and red were tested against varying greys, all which differed in intensity, served as the stimuli for the first 4 tasks. The remaining 3 tasks, the colors were tested against each other. The male reached criterion for the first 6 tasks, indicating an ability to discriminate the stimuli based on color. The female however participated only in 2, and could not achieve criterion as set, though there were indications of discrimination ability. Taken together with sensory work on two related otter species, Asian small-clawed otters possess color vision.

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)

<p>Repetitive elements, including tandem repeats and transposable elements (TE), are genetic features of all plant and animal genomes. Despite their abundance and the phylogenetic breadth of host genomes, factors that control the genome-wide distribution of repetitive elements are not well understood. Here we have evaluated the correlation between various genomic predictor variables such as gene expression level, distance from genes, and GC content, with the presence of TEs and non-TE repeats in two kilobase windows of the complete genome sequence of the Western Clawed Frog (<em>Silurana tropicalis</em>). We found that the distributions of different classes of TEs and repeats have distinct correlations with these predictor variables, including a generally strong negative correlation with proximity to exons and GC content. We also found that DNA transposons, but not retrotransposons, are preferentially inserted or preferentially retained near germline-expressed genes. Retrotransposons and simple repeats are found more often in or near conserved regions than expected by chance. These results offer insights into various models that have been proposed to account for heterogeneity in the genomic distribution of repetitive elements, most notably for the “gene disruption model” which posits that TE insertion and repeat presence near or in genes imposes costs to host fitness. In general, multiple lines of evidence suggests that the nature of natural selection on TE and other repetitive element evolution in this frog appears to be similar to that acting on TE and other repetitive elements in the human genome. This is possibly related to the similar size and level of complexity of the genomes of both of these species.</p> / Master of Science (MSc)

Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Endocrine disrupting contaminants (EDCs) coming from households, industrial parks, wastewater (sewage) treatment and agricultural areas have been shown to pollute our freshwater systems. These contaminants may disrupt early development and reproductive systems in freshwater organisms (fish, frogs and crocodile species) as well as humans. Agricultural pesticides are shown as a large contributor to endocrine disruption activity in water catchment areas through spray drift, runoff, and/or groundwater leeching. Although South Africa is recognized as the largest consumer of agricultural pesticides in Africa, few studies have been undertaken to assess the prevalence and impact of endocrine disorders activities of pesticides in local freshwater systems. Recent studies have suggested that various agricultural pesticides, especially fungicides, might have adverse effects on the male endocrine system. There is therefore a need to test for a wider range of endocrine disrupting activities (mechanisms) in environmental waters other than conventional estrogenic (feminising) activities. Furthermore, there is a need to establish biomarkers in endemic species (bio-indicators) to show endocrine disruption in vertebrates (therefore also apply to humans). The specific objectives of the study were to: (1) describe and confirm the use of androgen-controlled breeding glands in male African clawed frogs (Xenopus laevis) as a biomarker for (anti)androgenic endocrine disruption activity (Chapter 2), (2) to investigate the premature development of breeding glands in X. laevis tadpoles (pre-metamorphic) and young froglets (post-metamorphic) (Chapter 2), (3) to investigate the disruption of male reproductive traits in adult X. laevis frogs by exposure to substances disrupting two different anti-androgenic endocrine disruption pathways (Chapter 3), (4) screen for (anti)androgenic activity of individual and binary mixtures of pesticides, which are regularly used in agricultural areas in the Western Cape Province of South Africa (Chapter 4), and (5) to test for (anti)androgenic and estrogenic endocrine disrupting activities by making use of in vitro assays as well as adult male X. laevis frogs collected from selected ponds surrounded by vineyards and fruit orchards in the Stellenbosch Winelands. The present study confirmed that male breeding glands can serve as biomarkers for (anti)androgenic endocrine disruption and that male reproductive and secondary sexual characteristics can be disrupted through two different biochemical control pathways. The study also confirmed that the expression of androgen-regulated breeding glands can be stimulated in pre-metamorphic tadpoles and immature, post-metamorphic frogs, and can thus be used for (anti)androgenic testing. The rapid testing and predictive value of an in vitro recombinant yeast screen for androgen receptor binding inhibition of selected individual or binary mixtures of pesticides was also confirmed. However, the current study showed that the predicted in vitro (anti)androgenic activity did not always correspond with in vivo (anti)androgenic biomarker outcomes. This It also confirmed that single-cell in vitro assays can be used as a first-level prediction for (anti)androgenic activities of individual or mixtures of agricultural pesticides. This study provides a better understanding for potential mixture interactions of commonly used agricultural pesticides, the hormonal control of secondary sexual characteristics in male frogs and the use of reproduction biomarkers to study long-term effects of endocrine disruptors in local water supplies. / AFRIKAANSE OPSOMMING: Endokriene versteurings-kontaminante (EVKe) wat vanaf huishoudings, industriële parke, afvalwater(riool)-behandeling en landbougebiede kom, besoedel ons varswaterstelsels. Hierdie kontaminante mag versteuring van vroeë ontwikkeling- en voorplantingstelsels in varswater-organismes (vis-, padda- en krokodil-spesies) sowel as die mens inhou. Landbou-plaagdoders word uitgesonder as ’n bydraer van endokriene versteuring-aktiwiteite in wateropvangs-gebiede deur spuitnewel, afloop-water en/of grondwater-deurvloei. Hoewel Suid-Afrika erken word as die grootste verbruiker van landbou-plaagdoders in Afrika, word min studies onderneem om die voorkoms en impak van endokriene versteurings-aktiwiteite van plaagdoders in plaaslike varswaterstelsels te ondersoek. Onlangse studies het voorgestel dat verskeie landbou-plaagdoders, veral swamdoders, nadelige uitwerkings kan hê op die manlike endokriene stelsel. Daar bestaan dus 'n behoefte om te toets vir 'n wyer verskeidenheid van endokriene versteurings-aktiwiteite (meganismes) in omgewingswater anders as konvensionele estrogeniese (vervroulikings) aktiwiteite. Verder bestaan daar ’n behoefte om biomerkers in endemiese spesies te gebruik as bio-indikators van endokriene versteuring in werweldiere (daarom ook van toepassing op die mens). Die spesifieke doelwitte van die studie het ingesluit om: (1) die gebruik van androgeen-beheerde parings- velkliere (“breeding glands”) in manlike platannas (Xenopus laevis) as 'n biomerker vir (anti)androgeniese endokriene versteuring-aktiwiteit te beskryf en bevestig (Hoofstuk 2); (2) ondersoek in te stel na die voortydige ontwikkeling van parings-kliere in X. laevis paddavisse (pre-metamorfose) asook jong paddas (post-metamorfose) as biomerkers van androgeniese (vermanlikheids) aktiwiteite (Hoofstuk 2); (3) ondersoek in te stel na die versteuring van manlike geslags-eienskappe in volwasse X. laevis paddas deur middel van blootstelling aan stowwe wat twee verskillende androgeniese endokrien reaksie-weë verteenwoordig (Hoofstuk 3); (4) toets vir (anti)androgeniese aktiwiteit van individuele en binêre mengsels van landbou-plaagdoders wat gereeld in die Westelike Provinsie van Suid Afrika gebruik word (Hoofstuk 4) en (5) te toets vir (anti)androgeniese en estrogeniese endokriene versteurings aktiwiteite deur gebruik te maak van in vitro toetse asook volwasse manlike X. laevis paddas wat uit geselekteerde damme (omring deur wingerde en vrugte boorde in die Stellenbosch wynland distrik) versamel was. Die huidige studie het bevestig dat die manlike parings-velkliere as biomerkers vir (anti)androgeniese versteuring kan dien en dat manlike voortplanting en sekondêre geslagskenmerke deur twee verskillende biochemiese beheer-weë ontwrig kan word. Die studie het verder bevestig dat die uitdrukking van androgeen-gereguleerde parings-velkliere voortydig gestimuleer kan word in pre-metamorfose paddavissies asook onvolwasse, post-metamorfose paddas. Die vinnige toetsing en voorspellingswaarde van 'n rekombinante in vitro gis toets om binding-inhibisie van die androgeen reseptor deur geselekteerde individuele of binêre mengsels van plaagdoders aan te toon is ook bevestig. Alhoewel, die huidige studie het getoon dat die voorspelde in vitro (anti)androgeniese aktiwiteit nie altyd ooreenstem met in vivo (anti)androgeniese biomerker uitkomstes nie. Hierdie studie bevestig dat enkel-sel in vitro toetse aangewend kan word as eerste vlak- en voorspelling-toetse vir (anti)androgeniese aktiwiteite van enkel of mengsels van landbou-plaagdoders. Sodoende is 'n beter begrip verkry vir potensiële mengsel-interaksies van algemeen-gebruikte landbou plaagdoders, die hormonale beheer van sekondêre geslagskenmerke in manlike paddas asook die aanwending van voortplantingsbiomerkers om langtermyn effekte van endokriene versteurders in plaaslike waterbronne te ondersoek.

Il existe peu d’études sur les effets physiologiques et pharmacologiques du médicament anesthésiant le plus utilisé chez les anoures, la tricaïne méthanesulfonate, et son utilisation chez la grenouille Xenopus laevis. Notre premier objectif était d’évaluer l’effet de bains d’immersion de 20 minutes de 1 et 2 g/L de tricaïne méthanesulfonate sur la fonction cardiorespiratoire, l’analgésie et les réflexes ainsi que d’étudier la pharmacocinétique. Nos résultats démontrent que des bains de 1 et 2 g/L produisent une anesthésie chirurgicale de 30 et 60 minutes respectivement, sans effet significatif sur le système cardiorespiratoire. À la suite d’une immersion à 2 g/L, on note une demi-vie terminale de 3,9 heures. Cette dose ne produit aucun effet sur l’histologie des tissus 24 heures après l’immersion. Dans une deuxième expérience, nous avons évalué les effets d’une surdose de tricaïne méthanesulfonate en bain d’immersion sur les systèmes cardiorespiratoire et nerveux central grâce à l’électroencéphalographie ainsi que l’effet d’une injection de pentobarbital sodique après 2 heures d’immersion. L’EEG montre un effet dépresseur sur le SNC avec l’utilisation de la tricaïne méthanesulfonate sans voir un arrêt de signal d’EEG sur la période de 2 heures d’enregistrement. Les surdoses à 1 g/L et 3 g/L n’ont pas d’effet significatif sur le rythme cardiaque, et l’injection de pentobarbital suite au bain d’immersion de tricaïne méthanesulfonate est nécessaire pour induire l’euthanasie. Nous avons démontré que le bain de tricaïne méthanesulfonate peut produire une anesthésie de 30 à 60 minutes avec dépression du SNC sans effet cardiovasculaire chez les Xenopus laevis. / Very few studies exist on the physiological and pharmacological effects of the most commonly used anesthetic agent used in amphibians, tricaine methanesulfonate, in Xenopus laevis frogs. Our first goal was to measure the effects of 20 minutes bath immersions of 1 and 2 g/L tricaine methanesulfonate on cardiorespiratory system, analgesia and reflexes. We also studied the pharmacokinetic of tricaine methanesulfonate following an immersion in a 2 g/L bath. Our results show that both 1 and 2 g/L baths produce surgical anesthesia during 30 and 60 minutes respectively, without significant effect on the cardiorespiratory system. Following the immersion in a 2 g/L bath, the tricaine methanesulfonate has a terminal half-life of 3,9 hours and no effect on tissue histology is observed 24 hours after anesthesia. In a second experiment, we evaluated the effects of tricaine methanesulfonate overdose on cardiorespiratory system and on central nervous system using electroencephalography. Moreover, we evaluated the effect of sodium pentobarbital injection after 2 hours of immersion. A significant EEG depression of central nervous system activity occurred with the use of tricaine methanesulfonate following 2 hours of recording and the pentobarbital injection was necessary to induce euthanasia. We showed that tricaine methanesulfonate can produce safe anesthesia of 30 to 60 minutes with reduction of CNS activity and without cardiorespiratory effect in Xenopus laevis.

Il existe peu d’études sur les effets physiologiques et pharmacologiques du médicament anesthésiant le plus utilisé chez les anoures, la tricaïne méthanesulfonate, et son utilisation chez la grenouille Xenopus laevis. Notre premier objectif était d’évaluer l’effet de bains d’immersion de 20 minutes de 1 et 2 g/L de tricaïne méthanesulfonate sur la fonction cardiorespiratoire, l’analgésie et les réflexes ainsi que d’étudier la pharmacocinétique. Nos résultats démontrent que des bains de 1 et 2 g/L produisent une anesthésie chirurgicale de 30 et 60 minutes respectivement, sans effet significatif sur le système cardiorespiratoire. À la suite d’une immersion à 2 g/L, on note une demi-vie terminale de 3,9 heures. Cette dose ne produit aucun effet sur l’histologie des tissus 24 heures après l’immersion. Dans une deuxième expérience, nous avons évalué les effets d’une surdose de tricaïne méthanesulfonate en bain d’immersion sur les systèmes cardiorespiratoire et nerveux central grâce à l’électroencéphalographie ainsi que l’effet d’une injection de pentobarbital sodique après 2 heures d’immersion. L’EEG montre un effet dépresseur sur le SNC avec l’utilisation de la tricaïne méthanesulfonate sans voir un arrêt de signal d’EEG sur la période de 2 heures d’enregistrement. Les surdoses à 1 g/L et 3 g/L n’ont pas d’effet significatif sur le rythme cardiaque, et l’injection de pentobarbital suite au bain d’immersion de tricaïne méthanesulfonate est nécessaire pour induire l’euthanasie. Nous avons démontré que le bain de tricaïne méthanesulfonate peut produire une anesthésie de 30 à 60 minutes avec dépression du SNC sans effet cardiovasculaire chez les Xenopus laevis. / Very few studies exist on the physiological and pharmacological effects of the most commonly used anesthetic agent used in amphibians, tricaine methanesulfonate, in Xenopus laevis frogs. Our first goal was to measure the effects of 20 minutes bath immersions of 1 and 2 g/L tricaine methanesulfonate on cardiorespiratory system, analgesia and reflexes. We also studied the pharmacokinetic of tricaine methanesulfonate following an immersion in a 2 g/L bath. Our results show that both 1 and 2 g/L baths produce surgical anesthesia during 30 and 60 minutes respectively, without significant effect on the cardiorespiratory system. Following the immersion in a 2 g/L bath, the tricaine methanesulfonate has a terminal half-life of 3,9 hours and no effect on tissue histology is observed 24 hours after anesthesia. In a second experiment, we evaluated the effects of tricaine methanesulfonate overdose on cardiorespiratory system and on central nervous system using electroencephalography. Moreover, we evaluated the effect of sodium pentobarbital injection after 2 hours of immersion. A significant EEG depression of central nervous system activity occurred with the use of tricaine methanesulfonate following 2 hours of recording and the pentobarbital injection was necessary to induce euthanasia. We showed that tricaine methanesulfonate can produce safe anesthesia of 30 to 60 minutes with reduction of CNS activity and without cardiorespiratory effect in Xenopus laevis.

L'eugénol (2-methoxy-4-(2-propenyl) phénol), produit dérivé du clou de girofle (Eugenia aromatica), fut tout d’abord utilisé en application topique à des fins d’analgésie dentaire. Il produit également une anesthésie chirurgicale lorsque administré en immersion chez les poissons. L’eugénol agit sur les récepteurs vanilloïdes, sensibles à la chaleur, aux protons et à certaines molécules lipidiques. Ces récepteurs jouent un rôle important dans le mécanisme de l’inflammation et de l’hyperalgésie. L’eugénol pourrait également produire ses effets par antagonisme des récepteurs glutamaergiques (NMDA) et par son activation des récepteurs GABAergiques. Considérant que l’eugénol produit des effets analgésiques et anesthésiques, des études de pharmacocinétique et de pharmacodynamie furent réalisées chez la grenouille (Xenopus laevis), le poisson (Oncorhynchus mykiss) et le rat (Rattus norvegicus). Les résultats démontrent que l’eugénol administré par immersion à une dose efficace permet d’atteindre une anesthésie chirurgicale chez les grenouilles (350 mg/L) et les poissons (75 mg/L). Suite à des analyses plasmatiques par LC/MS/MS, la pharmacocinétique des grenouilles, des poissons et des rats montre que la drogue est éliminée et qu’il pourrait y avoir une recirculation entérohépathique plus importante chez la grenouille et le rat. La longue demi-vie chez le rat suggère aussi une accumulation dans les tissus après des administrations répétées. Suite à l’administration intraveineuse d’une dose de 20 mg/kg chez le rat, l’eugénol induit une anesthésie chirurgicale pour une très courte période de temps variant autour de 167 s. Les résultats de sensibilité thermique confirment l’efficacité de l’eugénol pour réduire l’hyperalgésie induite chez des rats neuropathiques. L’effet pharmacologique de l’eugénol a démontré une augmentation progressive constante de l’analgésie sur une période de cinq jours de traitements journaliers. En conclusion, l’eugénol possède des propriétés analgésiques et anesthésiques chez la grenouille africaine à griffes (Xenopus laevis), le poisson (Oncorhynchus mykiss) et le rat (Rattus norvegicus). / Eugenol (2-methoxy-4-(2-propenyl) phenol), derived from cloves, was first used as a topical agent for dental analgesia by dentistry practitioners, and subsequently to induce surgical anaesthesia by immersion in fish. Eugenol binds to vanilloid receptors, which are sensitive to heat, protons and certains lipid molecules. These receptors also play an important role in the mechanisms of inflammation, as well as hyperalgesia (Kanai 2005, and Crotright 2004). Eugenol could also produce its effects via its antagonistic interactions with glutamaergiques receptors (NMDA), and agonistic interactions with GABAergic receptors. Considering that eugenol has analgesic and anesthetic effects, pharmacokinetic and pharmacodynamic studies were performed in frogs (Xenopus laevis), fish (Oncorhynchus mykiss) and rats (Rattus norvegicus). Results show that a surgical anesthetic dose was observed for frogs (350 mg/L) and fish (75 mg/L) with a eugenol solution. Pharmacokinetics were evaluated following LC/MS/MS plasma analysis of frogs, fish and rats. Results show that eugenol was eliminated in all species and that an enterohepathic recirculation was apparent for frogs and rats. The long half-life in rats suggests an accumulation in tissues following repeated administrations. Following an intravenous administration 20 mg/kg of eugenol, a surgical anesthesia of approximately 167 sec was observed in rats. Hargreave’s test results, evaluating hyperalgesia, show that eugenol reduced pain perception in a rat model of neuropathic pain. This pharmacological effect showed an increasing progression of the analgesia over the 5 days of daily treatments. In conclusion, eugenol has analgesic and anesthetic properties in African clawed frogs (Xenopus laevis), trout (Oncorhynchus mykiss) and rats (Rattus norvegicus).

L'eugénol (2-methoxy-4-(2-propenyl) phénol), produit dérivé du clou de girofle (Eugenia aromatica), fut tout d’abord utilisé en application topique à des fins d’analgésie dentaire. Il produit également une anesthésie chirurgicale lorsque administré en immersion chez les poissons. L’eugénol agit sur les récepteurs vanilloïdes, sensibles à la chaleur, aux protons et à certaines molécules lipidiques. Ces récepteurs jouent un rôle important dans le mécanisme de l’inflammation et de l’hyperalgésie. L’eugénol pourrait également produire ses effets par antagonisme des récepteurs glutamaergiques (NMDA) et par son activation des récepteurs GABAergiques. Considérant que l’eugénol produit des effets analgésiques et anesthésiques, des études de pharmacocinétique et de pharmacodynamie furent réalisées chez la grenouille (Xenopus laevis), le poisson (Oncorhynchus mykiss) et le rat (Rattus norvegicus). Les résultats démontrent que l’eugénol administré par immersion à une dose efficace permet d’atteindre une anesthésie chirurgicale chez les grenouilles (350 mg/L) et les poissons (75 mg/L). Suite à des analyses plasmatiques par LC/MS/MS, la pharmacocinétique des grenouilles, des poissons et des rats montre que la drogue est éliminée et qu’il pourrait y avoir une recirculation entérohépathique plus importante chez la grenouille et le rat. La longue demi-vie chez le rat suggère aussi une accumulation dans les tissus après des administrations répétées. Suite à l’administration intraveineuse d’une dose de 20 mg/kg chez le rat, l’eugénol induit une anesthésie chirurgicale pour une très courte période de temps variant autour de 167 s. Les résultats de sensibilité thermique confirment l’efficacité de l’eugénol pour réduire l’hyperalgésie induite chez des rats neuropathiques. L’effet pharmacologique de l’eugénol a démontré une augmentation progressive constante de l’analgésie sur une période de cinq jours de traitements journaliers. En conclusion, l’eugénol possède des propriétés analgésiques et anesthésiques chez la grenouille africaine à griffes (Xenopus laevis), le poisson (Oncorhynchus mykiss) et le rat (Rattus norvegicus). / Eugenol (2-methoxy-4-(2-propenyl) phenol), derived from cloves, was first used as a topical agent for dental analgesia by dentistry practitioners, and subsequently to induce surgical anaesthesia by immersion in fish. Eugenol binds to vanilloid receptors, which are sensitive to heat, protons and certains lipid molecules. These receptors also play an important role in the mechanisms of inflammation, as well as hyperalgesia (Kanai 2005, and Crotright 2004). Eugenol could also produce its effects via its antagonistic interactions with glutamaergiques receptors (NMDA), and agonistic interactions with GABAergic receptors. Considering that eugenol has analgesic and anesthetic effects, pharmacokinetic and pharmacodynamic studies were performed in frogs (Xenopus laevis), fish (Oncorhynchus mykiss) and rats (Rattus norvegicus). Results show that a surgical anesthetic dose was observed for frogs (350 mg/L) and fish (75 mg/L) with a eugenol solution. Pharmacokinetics were evaluated following LC/MS/MS plasma analysis of frogs, fish and rats. Results show that eugenol was eliminated in all species and that an enterohepathic recirculation was apparent for frogs and rats. The long half-life in rats suggests an accumulation in tissues following repeated administrations. Following an intravenous administration 20 mg/kg of eugenol, a surgical anesthesia of approximately 167 sec was observed in rats. Hargreave’s test results, evaluating hyperalgesia, show that eugenol reduced pain perception in a rat model of neuropathic pain. This pharmacological effect showed an increasing progression of the analgesia over the 5 days of daily treatments. In conclusion, eugenol has analgesic and anesthetic properties in African clawed frogs (Xenopus laevis), trout (Oncorhynchus mykiss) and rats (Rattus norvegicus).