Thesis (Ph. D.)--University of Sydney, 2005. / Title from title screen (viewed 20 May 2008). Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy to the School of Biological Sciences, Faculty of Science. Degree awarded 2005; thesis submitted 2004. Includes bibliographical references. Also available in print form.

Thesis (M. Sc.), Memorial University of Newfoundland, 1999. / Bibliography: p. 78-85.

Undergraduate honors paper--Mount Holyoke College, 2005. Dept. of Biological Sciences. / Includes bibliographical references (leaves 59-61).

Würzburg, Universiẗat, Diss., 2004. / Erscheinungsjahr an der Haupttitelstelle: 2004.

Ribonuklease P (RNase P) ist eine essentielle Endonuklease, welche die 5'-Flanke von pre-tRNAs entfernt. Die RNase P RNA des Cyanobakteriums Prochlorococcus marinus ist in vitro katalytisch aktiv und bevorzugt in heterologen Prozessierungssystemen Substrate mit vollständigem 3’-CCA-Ende. Diese Substratspezifität widerspricht den Erwartungen, da tRNAs in P. marinus nicht mit dem CCA-Ende codiert sind und die RNase P RNA auch nicht das GGU-Bindungsmotiv für diese CCA-Enden aufweist. Um die Substratspezifität und Aufbau des Ribozym-Substrat-Komplex von P. marinus RNase P RNA im homologen System untersuchen zu können, wurden Transkriptionsklone für P. marinus pre- und mat-tRNAArgCCU konstruiert, mit denen nach entsprechender Restriktionshydrolyse Transkripte mit stufenweise verkürzten 3’-CCA-Ende synthetisiert werden können. Durch enzymkinetische Untersuchungen der Prozessierung durch P. marinus RNase P RNA wurde unter steady-state-Bedingungen für pre-tRNACCA eine Michaelis-Menten Konstante von 6,92 µM ermittelt. Die Entfernung von A76 und C75 des 3’-CCA-Endes führt zu einer Erhöhung der KM (7,13 µM bzw. 19,68µM). Diese Substrate werden folglich weniger stark gebunden, was sich auch in der freien Bindungsenthalpie von 0,02 und 0,65 kcal/mol ausdrückt. Die Entfernung des vollständigen 3’-CCA-Endes führt zu einer erheblichen Erniedrigung der KM (0,83µM) und zu einer energetisch begünstigten, stärkeren Substratbindung (–1,31 kcal/mol). P. marinus RNase RNase P RNA zeigt folglich bei der in vitro Prozessierung im homologen System unter steady-state-Bedingungen eine Substratspezifität für das Substrat mit deletiertem 3’-CCA-Ende. Durch die Methode des Crosslinking, die in dieser Arbeit etabliert und optimiert wurde, können RNA-Protein und RNA-RNA Interaktionen nachgewiesen werden. Mit ihr wurde die Bindung von Substrat und Produkt im Komplex mit der RNase P RNA untersucht. Durch interne Modifizierung der P. marinus RNase P RNA-Komponente mit dem photosensiblen Nukleotidanalogon s4U wurden Kontaktstellen in 5’-Flanke, Acceptor-Stamm, D-Stamm, D-Schleife, Anticodon-Schleife und in der variablen Schleife der P. marinus pre-tRNAArg identifiziert. Diese lokalisierten Kontaktstellen stehen denen in der 5’-Flanke, dem Acceptor-Stamm und der 3’-Flanke, wie sie für den Ribozym-Substrat-Komplex mit E. coli RNase P RNA identifiziert wurden, gegenüber. In P. marinus RNase P RNA werden folglich alternative Kontaktstellen zur Substratbindung benutzt. Mit Hilfe der hier überexprimierten E. coli Nukleotidyltransferase, konnte pre- und mat-tRNAArg durch eine neue Synthesestrategie am 3’-CCA-Ende mit dem Crosslink-Reagenz Azidophenacyl (APA) modifiziert werden. Durch die Positionierung von APA am 5’-Terminus von pre- und mat-tRNAArg wurden weitere modifizierte tRNAs synthetisiert. Durch Crosslink-Experimente im homologen P. marinus System mit diesen modifizierten pre- und mat-tRNAArg-Varianten wurden die selben Regionen des katalytischen Zentrums (J18/2, Region P15/P16, J5/15) der RNase P RNA identifiziert, wie sie von E. coli und B. subtilis RNase P RNA bekannt sind. Dies bedeutet, dass die 5’-Flanke, die Prozessierungsstelle und das 3’-CCA-Ende der tRNAs auf einer vergleichbaren Oberfläche positioniert werden wie in anderen Ribozymen. Durch die fehlende Fixierung des 3’-CCA-Endes über Basenpaarungen mit dem GGU-Bindungsmotiv werden die tRNAs in P. marinus RNase P RNA weniger starr an das Ribozym gebunden und das 3’-CCA-Ende besitzt eine flexiblere Positionierung im Komplex mit dem Ribozym. Die Existenz unterschiedlicher Crosslink-Muster in P6, P18, J5/15 und J3/4 zeigt, dass pre-tRNAs und reife tRNAs durch verschiedene Modi an das P. marinus Ribozym gebunden werden. Die Identifizierung von vernetzten Nukleotiden in P15, J15/16, P16 und J16/15, die mit vergleichbaren modifizierten tRNAs in E. coli RNase P RNA nicht gefunden wurden, belegen, dass in P. marinus RNase P RNA ein anderer Produkt-Bindungs-Modus existiert als in E. coli. Erstmals konnten in dieser Arbeit auch zu erwartende Interaktionen mit dem katalytischen Zentrum identifiziert werden, die in bisherigen Crosslink-Experimenten in E. coli und B. subtilis RNase P RNA nicht oder nur geringfügig auftraten. Um die erhaltenen Ergebnisse besser veranschaulichen zu können, wurde mit dem Programm ERNA 3D ein Raumstrukturmodell für P. marinus RNase P RNA und tRNAArg erstellt. Die RNase P RNA der Cyanellen von Cyanophora paradoxa, ist in vitro katalytisch inaktiv. Um zu klären, ob die fehlende Ribozym-Aktivität dieser RNase P RNA auf eine fehlerhafte Substratbindung zurückzuführen ist, sollten Crosslink-Experimente mit den modifizierten P. marinus tRNAArg durchgeführt werden. Es konnte gezeigt werden, dass 5’- und 3’-modifizierte pre-tRNAs in C. paradoxa in einem anderen Modus gebunden werden, als durch die katalytisch aktive P. marinus RNase P RNA. / Ribonuclease P (RNase P) is the essential endonuclease responsible for the removal of the 5’-flank of precursor tRNAs. The RNase P RNA from the cyanobacterium Prochlorococcus marinus shows in vitro catalytic activity and specificity for heterologous substrates containing the complete 3’-CCA end. This preference is in contrast to the fact that the P. marinus RNase P RNA does not possess the binding motif for the CCA terminus, which is not encoded in tRNA genes in this organism. To analyse the substrate specificity and architecture of the ribozyme-substrate-complex of P. marinus RNase P RNA in a homologous system, transcription clones for P. marinus pre- and mat-tRNAArg were generated to obtain different transcripts with stepwise shortened 3’-CCA ends. In the kinetic analysis of P. marinus RNase P RNA, the Michaelis constant (KM) for pre-tRNACCA was 6,92 µM, as determined under steady-state conditions. The subsequent deletion of A76 and C75 from the 3’-CCA end results in an increase of KM (7,13 µM and 19,69 µM, respectively). These substrates are bound less strongly, which is expressed in loss of binding energy (0,02 and 0,65 kcal/mol, respectively).The removal of the complete CCA end results in an considerable decrease of KM (0,83 µM) and an energetically favoured and stronger binding of substrate (–1,31 kcal/mol). In conclusion, in the homologous in vitro system, P. marinus RNase P RNA has a preference for substrate lacking the 3’-CCA end. The method of Crosslinking, which was established and optimised in this work, is generally used to determine RNA-protein and RNA-RNA interactions. This method was used to examine the binding of substrate and product in the complex composed with RNase P RNA. P. marinus RNase P RNA was internally modified with the photoinducible nucleotide analogue s4U. With this modified RNA, interactions of the 5’-flank, acceptor stem, D-stem and loop, anticodon loop and variable loop of pre-tRNAArg with RNase P RNA were detected. These contacts are in contrast to signals in the 5’-flank, acceptor stem and 3’-flank which have been identified in the ribozyme-substrate-complexes of E. coli RNase P RNA. Thus, in P. marinus RNase P RNA, alternative interactions are used for substrate binding. Using purified recombinant E. coli Nucleotidyltransferase, pre- and mat-tRNAArg were modified at the 3’-CCA end by a new strategy using the crosslink-reagent azidophenacyl (APA). Additional modified tRNAs were obtained by positioning the APA-reagent at the 5’-end. In the homologous P. marinus system, crosslinking experiments with the modified tRNAs identified the same regions of the catalytic centre (J18/2, region P15/P16, J5/15) which have been established in E. coli and B. subtilis RNase P RNA. This observation indicates that 5’-flank, cleavage site and 3’-CCA end are positioned on a similar surface, as in the other ribozymes. Due to the missing interaction between the GGU motif and the CCA end, tRNAs are bound less rigid to the ribozyme in P. marinus and the 3’-CCA end is more flexible in the complex. Different crosslink patterns in P6, P18, J5/15 and J3/4 indicate that pre-tRNAs and mat-tRNAs are bound in a different mode by P. marinus RNase P RNA. The identification of crosslinked nucleotides in P15, J15/16, P16 and J16/15 which are not observed with analogous modified tRNAs in E. coli RNase P RNA, show that a different mode of product binding exists in P. marinus RNase P RNA. For the first time, interactions within the catalytic centre could be identified which had been anticipated, but were only weakly detectable in the E. coli and B. subtilis RNase P RNAs. The crosslinks in P4, J3/4 and P3 are a distinctive feature, which is supported by mutational studies, phosphorothioate interference and NAIM analysis. To obtain a good visualization of the crosslinking results, a 3D-model of P. marinus RNase P RNA and tRNAArg was created with the program ERNA-3D. RNase P RNA from the cyanelles of Cyanophora paradoxa does not show catalytic activity in vitro. To establish whether the lack of substrate binding ability is the reason for the missing ribozyme activity, crosslinking experiments with the modified P. marinus tRNAArg were done. 5’- and 3’- modified pre-tRNAArg are bound by cyanelle RNase P RNA in a different mode than by the catalytically active P. marinus RNase P RNA.

The natriuretic peptides, atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP) and C-type natriuretic peptide (CNP) are members of a family of hormones that play an important role in mammalian fluid and electrolyte balance. In the periphery, natriuretic peptides reduce blood volume and subsequently blood pressure by increasing renal natriuresis and diuresis and relaxation of vascular smooth muscle. The actions of natriuretic peptides are mediated via two membrane-linked guanylate cyclase receptors (NPR-GC); natriuretic peptide receptor-A (NPR-A) which has a high affinity for ANP and BNP; and natriuretic peptide receptor-B (NPR-B)which has the greatest affinity for CNP. A third receptor not linked to guanylate cyclase, natriuretic peptide receptor-C (NPR-C) also exists, which binds to ANP, BNP and CNP with a relatively equal affinity, and is involved with clearance of the peptides from the circulation and tissues. The natriuretic peptides are present in the brain and are particularly predominant in cardiovascular and fluid and electrolyte regulating areas such as the anteroventral third ventricle (AV3V) region. This distribution has led to the suggestion natriuretic peptides play a neuromodulatory role in the central control of fluid homeostasis. Natriuretic peptides in the brain have been observed to inhibit the release of other fluid and electrolyte regulating hormones such as arginine vasopressin (AVP) and angiotensin II (AII). Natriuretic peptides have also been identified in the non-mammalian vertebrates although information regarding the distribution of the peptides and their receptors in the non-mammalian brain is limited. In amphibians, immunohistochemical studies have shown that natriuretic peptides are highly concentrated in the preoptic region of the brain, an area believed to be analogous to the A\T3\ region in mammals, which suggests that natriuretic peptides may also be involved in central fluid and electrolyte regulation in amphibians. To date, CNP is the only natriuretic peptide that has been isolated and cloned from the lower vertebrate brain, although studies on the distribution of CNP binding sites in the brain have only been performed in one fish species. Studies on the distribution of ANP binding sites in the lower vertebrate brain are similarly limited and have only been performed in one fish and two amphibian species. Moreover, the nature and distribution of the natriuretic peptide receptors has not been characterised. The current study therefore, used several approaches to investigate the distribution of natriuretic peptides and their receptors in the brain of the amphibian Bufo marinus. The topographical relationship of natriuretic peptides and the fluid and electrolyte regulating hormone arginine vasotocin was also investigated, in order to gain a greater understanding of the role of the natriuretic peptide system in the lower vertebrate brain. Immunohistochemical studies showed natriuretic peptides were distributed throughout the brain and were highly concentrated in the preoptic region and interpeduncular nucleus. No natriuretic peptide-like immunoreactivity (NP-IR) was observed in the pituitary gland. Arginine vasotocin-like immunoreactivity (AvT-IR) was confined to distinct regions, particularly in the preoptic/hypothalamic region and pituitary gland. Double labelling studies of NP-JR and AvT-IR showed the peptides are not colocalised in the same neural pathways. The distribution of natriuretic peptide binding sites using the ligands 125I-rat ANP (125I-rANP) and 125I-porcine CNP (125I-pCNP) showed different distributions in the brain of B. marinus. The specificity of binding was determined by displacement with unlabelled rat ANP, porcine CNP and C-ANF, an NPR-C specific ligand. 125I-rANP binding sites were broadly distributed throughout the brain with the highest concentration in pituitary gland, habenular, medial pallium and olfactory region. Minimal 125I-rANP binding was observed in the preoptic region. Residual 125I-rANP binding in the presence of C-ANF was observed in the olfactory region, habenular and pituitary gland indicating the presence of both NPR-GC and NPR-C in these regions. 125I-pCNP binding was limited to the olfactory region, pallium and posterior pituitary gland. All 125I-pCNP binding was displaced by C-ANF which suggests that CNP in the brain of B. marinus binds only to NPR-C. Affinity cross-linking and SDS-PAGB demonstrated two binding sites at 136 kDa and 65 kDa under reducing conditions. Guanylate cyclase assays showed 0.1 µM ANP increased cGMP levels 50% above basal whilst a 10-fold higher concentration of CNP was required to produce the same result. Molecular cloning studies revealed a 669 base pair fragment showing 91% homology with human and rat NPR-A and 89% homology with human, rat and eel NPR-B. A 432 base pair fragment showing 67% homology to the mammalian NPR-C and 58% homology with eel NPR-D was also obtained. The results show natriuretic peptides and their receptors are distributed throughout the brain of B. marinus which indicates that natriuretic peptides may participate in a range of regulatory functions throughout the brain. The potential for natriuretic peptides to regulate the release of the fluid and electrolyte regulating hormone AVT also exists due to the high number of natriuretic peptide binding sites in the posterior pituitary gland. At least two populations of natriuretic peptide receptors are present in the brain of B. marinus, one linked to guanylate cyclase and one resembling the mammalian clearance receptor. Furthermore, autoradiography and guanylate cyclase studies suggest ANP may be the major ligand in the brain of B. marinus, even though CNP is the only natriuretic peptide that has been isolated from the lower vertebrate brain to date.

Evolution can occur rapidly, along timescales that are traditionally regarded as 'ecological'. Despite growing acceptance among biologists of rapid evolution, a strong paradigm of contemporary evolution is still absent in many sub-disciplines. Here I apply a contemporary evolution viewpoint to conservation biology. Specifically, I examine the impact of cane toads (Bufo marinus) on Australian snakes. Toads were introduced into Australia in 1935, have spread rapidly and represent a novel, extremely toxic prey item to na�ve Australian predators (including snakes). Based on dietary preferences and geographic distributions I find that 49 species of Australian snake are potentially at risk from the invasion of the toad. Furthermore, examination of physiological resistance to toad toxin in 10 of these �at risk� species strongly suggests that most species of Australian snake are poorly equipped to deal with a likely dose of toad toxin. Even species that are highly resistant to toad toxin (such as the keelback, Tropidonophis mairii) face indirect fitness costs associated with consuming toads. Within a population of snakes however, the impact of toads is unlikely to be random. For example, the examination of several component allometries describing the interaction between snakes and toads revealed that, within a species, smaller snakes are more likely to ingest a fatal dose of toad toxin than are larger snakes. Further consideration of the interaction between snakes and toads suggests that toads will not only be exerting differential impact on snakes based upon morphology, but also exert non-random selection on prey preference and resistance to toad toxin in snake populations. To examine the possibility of a morphological response by snakes to toads, I examined changes in the body size and relative head size of four species of snake as a consequence of time since exposure to toads. Two of the species (green treesnakes and red-bellied blacksnakes) are predicted to face strong impacts from toads. These two species showed an increase in mean body size and a decrease in relative head size as a consequence of time since exposure to toads; both changes in an adaptive direction. In contrast, the other two species (keelbacks and swampsnakes) are predicted to face much lower impact from toads, and these two species showed little or no evidence of morphological change associated with time since exposure to toads. These results indicate an adaptive change in morphology at a rate that is proportional to the predicted level of impact for each species, strongly suggesting an evolved response. Red-bellied blacksnakes (a toad-vulnerable species) were further assessed for evolved responses in prey preference and toxin resistance. Comparisons between toad-exposed and toad-na�ve populations of blacksnakes revealed that snakes from toad-exposed populations exhibited slightly higher resistance to toad toxin and a much-reduced tendency to eat toads, when compared with toad-na�ve snakes. Na�ve snakes exhibited no tendency to learn avoidance of toxic prey, nor were they able to acquire resistance to toxin as a result of several sub-lethal doses, suggesting that the observed differences between populations is evolved rather than acquired. Together, these results strongly suggest that blacksnakes are exhibiting an evolved shift in prey preference and toxin resistance as a consequence of exposure to toads. Thus, it appears that snakes are exhibiting adaptation at multiple traits in response to exposure to toads. Given the high likelihood that these adaptive shifts have an evolved basis, it appears that the impact of toads will decrease with time in many snake populations. But what about toads? Because the outcome of the interaction between a toad and a snake is also mediated by the body size and relative toxicity of toads, it is important to understand how these traits vary in space and time. Exploratory analysis revealed that toads exhibit a decrease in body size and a decrease in relative toxicity as a consequence of time since colonisation, indicating that their impact on native predators decreases with time. Additionally, there appears to be meaningful spatial variation in toad relative toxicity, indicating that some populations of native predators are facing higher impact from toads than others. Overall, these results clearly indicate the importance of assessing the potential for rapid evolutionary response in impacted systems. Doing so may provide evidence that some species are in less trouble than originally thought. Additionally, and as more data accumulate, it may be possible to characterise certain categories of environmental impact by their potential for eliciting adaptive response from �impacted� species. This approach has strong implications for the way conservation priorities are set and the way in which conservation dependent populations are managed.

Thesis (Ph.D.)--Ohio University, November, 2009. / Release of full electronic text on OhioLINK has been delayed until December 1, 2014. Title from PDF t.p. Includes bibliographical references.

Evolution can occur rapidly, along timescales that are traditionally regarded as 'ecological'. Despite growing acceptance among biologists of rapid evolution, a strong paradigm of contemporary evolution is still absent in many sub-disciplines. Here I apply a contemporary evolution viewpoint to conservation biology. Specifically, I examine the impact of cane toads (Bufo marinus) on Australian snakes. Toads were introduced into Australia in 1935, have spread rapidly and represent a novel, extremely toxic prey item to na�ve Australian predators (including snakes). Based on dietary preferences and geographic distributions I find that 49 species of Australian snake are potentially at risk from the invasion of the toad. Furthermore, examination of physiological resistance to toad toxin in 10 of these �at risk� species strongly suggests that most species of Australian snake are poorly equipped to deal with a likely dose of toad toxin. Even species that are highly resistant to toad toxin (such as the keelback, Tropidonophis mairii) face indirect fitness costs associated with consuming toads. Within a population of snakes however, the impact of toads is unlikely to be random. For example, the examination of several component allometries describing the interaction between snakes and toads revealed that, within a species, smaller snakes are more likely to ingest a fatal dose of toad toxin than are larger snakes. Further consideration of the interaction between snakes and toads suggests that toads will not only be exerting differential impact on snakes based upon morphology, but also exert non-random selection on prey preference and resistance to toad toxin in snake populations. To examine the possibility of a morphological response by snakes to toads, I examined changes in the body size and relative head size of four species of snake as a consequence of time since exposure to toads. Two of the species (green treesnakes and red-bellied blacksnakes) are predicted to face strong impacts from toads. These two species showed an increase in mean body size and a decrease in relative head size as a consequence of time since exposure to toads; both changes in an adaptive direction. In contrast, the other two species (keelbacks and swampsnakes) are predicted to face much lower impact from toads, and these two species showed little or no evidence of morphological change associated with time since exposure to toads. These results indicate an adaptive change in morphology at a rate that is proportional to the predicted level of impact for each species, strongly suggesting an evolved response. Red-bellied blacksnakes (a toad-vulnerable species) were further assessed for evolved responses in prey preference and toxin resistance. Comparisons between toad-exposed and toad-na�ve populations of blacksnakes revealed that snakes from toad-exposed populations exhibited slightly higher resistance to toad toxin and a much-reduced tendency to eat toads, when compared with toad-na�ve snakes. Na�ve snakes exhibited no tendency to learn avoidance of toxic prey, nor were they able to acquire resistance to toxin as a result of several sub-lethal doses, suggesting that the observed differences between populations is evolved rather than acquired. Together, these results strongly suggest that blacksnakes are exhibiting an evolved shift in prey preference and toxin resistance as a consequence of exposure to toads. Thus, it appears that snakes are exhibiting adaptation at multiple traits in response to exposure to toads. Given the high likelihood that these adaptive shifts have an evolved basis, it appears that the impact of toads will decrease with time in many snake populations. But what about toads? Because the outcome of the interaction between a toad and a snake is also mediated by the body size and relative toxicity of toads, it is important to understand how these traits vary in space and time. Exploratory analysis revealed that toads exhibit a decrease in body size and a decrease in relative toxicity as a consequence of time since colonisation, indicating that their impact on native predators decreases with time. Additionally, there appears to be meaningful spatial variation in toad relative toxicity, indicating that some populations of native predators are facing higher impact from toads than others. Overall, these results clearly indicate the importance of assessing the potential for rapid evolutionary response in impacted systems. Doing so may provide evidence that some species are in less trouble than originally thought. Additionally, and as more data accumulate, it may be possible to characterise certain categories of environmental impact by their potential for eliciting adaptive response from �impacted� species. This approach has strong implications for the way conservation priorities are set and the way in which conservation dependent populations are managed.

Thesis (Ph.D.)--University of Western Australia, 2003.