Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2017-11-06T21:20:56Z No. of bitstreams: 1 WylquiMikaelGomesDeAndrade_DISSERT.pdf: 4821607 bytes, checksum: ca631cc1d1edb98183b539cabd333625 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2017-11-21T00:04:51Z (GMT) No. of bitstreams: 1 WylquiMikaelGomesDeAndrade_DISSERT.pdf: 4821607 bytes, checksum: ca631cc1d1edb98183b539cabd333625 (MD5) / Made available in DSpace on 2017-11-21T00:04:51Z (GMT). No. of bitstreams: 1 WylquiMikaelGomesDeAndrade_DISSERT.pdf: 4821607 bytes, checksum: ca631cc1d1edb98183b539cabd333625 (MD5) Previous issue date: 2017-07-24 / O ?xido n?trico (NO) ? uma mol?cula gasosa que exerce papel de neurotransmissor, regulando eventos sin?pticos e participando de fun??es neurais como mem?ria e aprendizado. No sistema nervoso, o NO ? catalisado pela ?xido n?trico sintase neuronal (nNOS). Por ser uma mol?cula gasosa, o NO pode se difundir livremente atravessando a membrana das c?lulas, desta forma agindo como um neurotransmissor retr?grado, geralmente considerado um moderador de a??o local. NO e nNOS s?o mol?culas altamente conservadas entre as esp?cies e est?o presentes no sistema nervoso de diversos vertebrados. N?s realizamos imunoistoqu?micas anti-nNOS e histoqu?micas para revela??o de NADPH-diaforase com o objetivo de investigar a distribui??o de c?lulas nitr?rgicas no compartimento subcortical do telenc?falo de moc? (Kerodon rupestris). Os dados mostram uma distribui??o heterog?nea de neur?nios imunorreativos a nNOS ou com atividade NADPH-diaforase ao longo de todo o compartimento subcortical. Observou-se neur?nios imunorreativos a nNOS no n?cleo accumbens, associando o NO a mecanismos de v?cio e recompensa; nos n?cleos da am?gdala e no hipocampo, podendo estar associados a aprendizado e mem?ria; no n?cleo intersticial da estria terminal, associado a comportamentos de defesa, analgesia e fun??es cardiovasculares; e nos n?cleos da base, sugerindo papel neuroprotetor e de regula??o neural do movimento, associando-se ainda a doen?as neurodegenerativas nessas regi?es. A distribui??o de NO no telenc?falo subcortical de moc? ? ampla, heterog?nea e complexa, mas guarda muitas semelhan?as com a distribui??o em outros roedores, o que pode significar um amplo papel do NO nas fun??es cerebrais desta esp?cie. Al?m disso, o mapeamento da distribui??o de nNOS est? sendo importante para a defini??o morfol?gica de certas ?reas encef?licas de moc?, em compara??o com outras esp?cies de roedores e outros mam?feros. / Nitric oxide (NO) is a gaseous molecule that acts as a neurotransmitter, regulating synaptic events and participating in neural functions such as memory and learning. In the nervous system, NO is catalysed by neuronal nitric oxide synthase (nNOS). As a gaseous molecule, NO can diffuse freely trespassing the cells membrane. Because of this NO can act as a retrograde neurotransmitter and is usually treated as a local moderator. NO and nNOS are highly conserved among species and are present in the nervous system of many vertebrates. We performed immunohistochemical anti-nNOS and histochemical for NADPH-diaphorase in order to investigate the distribution of nitrergic cells in the subcortical compartment of the rock cavy (Kerodon rupestris) telencephalon. The data show a heterogeneous distribution of neurons immunoreactive to nNOS or with NADPH-diaphorase activity throughout the subcortical compartment. Neurons immunoreactive to nNOS were observed in the nucleus accumbens, associating NO with mechanisms of addiction and reward; in the nuclei of the amygdala and in the hippocampus, that are associated with learning and memory; in the bed nucleus of the stria terminalis, associated to defense behaviors, analgesia and cardiovascular functions; and in the basal nuclei, suggesting a putative neuroprotector role and neural regulation of the movement, being still associated with neurodegenerative diseases in these regions. The distribution of NO in the subcortical telencephalon of the rock cavy is broad, heterogeneous and complex, suggesting a broad role of NO in the cerebral functions of this species. In addition, the mapping of nNOS distribution is being important for the morphological definition of the rock cavy's brain areas in comparison with other species of rodents and other mammals.

Made available in DSpace on 2014-06-11T19:27:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-03-13Bitstream added on 2014-06-13T20:35:43Z : No. of bitstreams: 1 pereira_acb_me_sjrp.pdf: 828257 bytes, checksum: de1b44b38dfac1b95be8ef5a683e7543 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O lenho estriado de rupestris ou cascudo (Rupestris stem pitting – RSP), um dos componentes do Complexo do lenho rugoso (“Rugose wood” - RW), é considerado uma das doenças de videira transmitidas por enxertia de grande relevância econômica para a viticultura. O Rupestris stem pitting associated virus – RSPaV foi associado com a doença do lenho estriado ou cascudo, sendo classificado como espécie do gênero Foveavirus, pertencente a família Flexiviridae. No presente trabalho, descrevem-se o sequenciamento do gene da proteína capsidial (CP) de um isolado brasileiro do RSPaV (RSPaV-SP), sua expressão em Escherichia coli, purificação da proteína capsidial recombinante e a produção de anti-soro policlonal em coelho. O sequenciamento do gene resultou em uma seqüência de 780 nucleotídeos e 259 aminoácidos deduzidos com massa molecular estimada de 28 kDa. A análise filogenética, entre a seqüência correspondente à CP do RSPaV-SP e outras variantes do mesmo vírus, evidenciou a formação de 4 grupos distintos, sendo o isolado brasileiro incluído no grupo da variante BS do RSPaV. A proteína capsidial recombinante foi purificada em coluna de afinidade e apresentou massa molecular estimada de 32kDa (4kDa da seqüência do vetor e 28kD da CP do RSPaV-SP). O anti-soro produzido apresentou-se específico na detecção da proteína capsidial recombinante purificada por “Western-blot”, sem reação com proteína heteróloga a partir da diluição 1:4000. Nesta diluição, o anti-soro foi efetivo na detecção do vírus em extratos de plantas infectadas, sendo que nenhuma reação foi observada com extratos de plantas sadias. Considerando-se que este vírus apresenta variações de concentração na planta durante as estações do ano, e que, os testes sorológicos foram realizados durante a estação de baixa concentração do vírus, os resultados... / Rupestris stem pitting (RSP), a component of the rugose wood (RW) complex, is one of the most graft-transmissible grapevine virus diseases with great economic importance for viticulture . Rupestris stem pitting-associated virus (RSPaV), genus Foveavirus within the family Flexiviridae, has been associated with this disease. This work reports the sequencing of the coat protein (CP) gene of a brazilian an isolate of RSPaV (RSPaV-SP), its expression in Escherichia coli, purification of the recombinant coat protein and production of a polyclonal antiserum in rabbit. CP gene was found to be 780nt long, with a 256 deduced amino acid sequence encoding a predicted protein of 28 kDa. In filogenetic analysis, with RSPaV-SP and other variants of the virus, four groups were found and the sequence of RSPaV-SP showed the highest identity with the variant RSPaV-BS. The recombinant coat protein was purified by affinity chromatography and showed a molecular weight of 32kDa (4 kDa from a small vector sequence plus 28 kDa for the CP of RSPaV-SP). The antiserum proved specific for detection of the recombinant protein by Western Blot, and did not react with heterologous proteins starting at a dilution of 1:4000. At this dilution, the antiserum was effective in the virus detection of leaf extracts of infected plants and no reaction was observed with extracts from healthy grapevines. Considering that the virus is found at low concentrations in the plants during the seasons of the year, the results obtained so far were highly satisfactory for RSPaV detection. Serological methods have advantages over the biological indexing method, since they are cheaper and can be used in large-scale tests such as ELISA. Experiments using the ELISA technique were not successful. Purification of the native recombinant protein would be an alternative more efective to detect the virus using these technique.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2017-03-21T18:32:42Z No. of bitstreams: 1 LucimarioThiagoFelixDeAraujo_DISSERT.pdf: 1666805 bytes, checksum: 491f0cadf9aec790018979edc6e49605 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2017-03-27T21:53:05Z (GMT) No. of bitstreams: 1 LucimarioThiagoFelixDeAraujo_DISSERT.pdf: 1666805 bytes, checksum: 491f0cadf9aec790018979edc6e49605 (MD5) / Made available in DSpace on 2017-03-27T21:53:05Z (GMT). No. of bitstreams: 1 LucimarioThiagoFelixDeAraujo_DISSERT.pdf: 1666805 bytes, checksum: 491f0cadf9aec790018979edc6e49605 (MD5) Previous issue date: 2016-12-21 / ?xido n?trico (NO) ? uma mol?cula gasosa importante em processos intra e extracelular, est? presente em v?rios tecidos, exercendo um papel importante no sistema imune, na regula??o da press?o sangu?nea, no relaxamento do m?sculo liso e na vasodilata??o via nervos perif?ricos. Por ser um g?s o NO atravessa livremente as membranas celulares. Portanto, na parte central do sistema nervoso age como um neurotransmissor em circuitos locais, distribuindo-se em curtas dist?ncias, difundindo-se de c?lula em c?lula participando de v?rias fun??es, como aprendizado e mem?ria, podendo mediar respostas excitat?rias a certos amino?cidos. O NO est? presente em v?rios n?cleos distribu?dos por todo o sistema nervoso e tem sido descrito em diversas esp?cies animais atrav?s da express?o de sua enzima de s?ntese, a NOS. Utilizando as t?cnicas de imunoistoqu?mica contra NOS e de histoqu?mica para marcar a atividade enzim?tica da NADPH diaforase, a NADPHd, n?s mapeamos a distribui??o de NO no tronco encef?lico de um roedor end?mico da caatinga brasileira que habita ?reas rochosas e tem h?bitos crepusculares, o moc? (Kerodon rupestris). Diversas regi?es e n?cleos do tronco encef?lico apresentaram imunorreatividade ao NOS ou atividade NADPHd. O presente trabalho mostra que em moc?, entre outras regi?es, NO est? em n?cleos do sistema visual prim?rio como os n?cleos pr?-tectais e col?culo superior; n?cleos do sistema auditivo como o complexo olivar, col?culo inferior e n?cleo coclear; em diversas subdivis?es da subst?ncia cinzenta periaquedutal, estrutura envolvida em comportamentos defensivos, nocicep??o e ansiedade, assim como o locus cer?leos onde NO tamb?m foi encontrado; subst?ncia negra, onde NO est? relacionado a encefalopatia hep?tica e com a doen?a de Parkinson em outros roedores. O grande n?mero de n?cleos nitr?rgicos e seu padr?o de distribui??o no tronco encef?lico de moc? foi semelhante ao observado em outras esp?cies de mam?feros, nos levando a concluir que a proximidade filogen?tica das esp?cies ? mantida na distribui??o de NO no tronco encef?lico de moc?. / Nitric oxide (NO) is a gas very important in intra and extracellular process. It is present in many tissues, having an important role in the immunological system, regulation of blood pressure, relaxation of the smooth muscle and vasodilatation through peripheral nervous system. As a gas, NO can pass freely through cell membranes. Therefore, it acts as a neurotransmitter of local action in the central nervous system, reaching short distances, diffusing from cell to cell. It has many functions as learning and memory and modulation of excitatory responses to aminoacids. NO is present in many areas throughout the brain and has been described in many animal species by the expression of its enzyme of synthesis, the NOS. Using immunohistochemistry against NOS and NADPH diaphorase histochemistry we described the distribution of NO in the brainstem of a rodent typical from the Brazilian caatinga, that inhabits rocky areas and has crepuscular habits, the rock cavy (Kerodon rupestris). Several brainstem areas and nuclei presented immunorreactivity to NOS or NADPHd activity. Some of them showed a high density of immunostained neurons, for example the periaqueductal gray, the magnocellular nucleus of the posterior commissure and the interpeduncular nucleus. Others nuclei presented a moderated, as the posterior pretectal nucleus, olivary pretectal nucleus, layers of the superior colliculus and cuneate nucleus. Several showed a low density as the posterior commissure nuclei, paranigral nucleus external cortex of the inferior colliculus and the inferior oliva. Finally, there is nuclei with a very low density, for example the reticular part of the substantia nigra, the pararubral nucleus, the dorsal raphe nucleus, the gracile nucleus and interstitial nucleus of the medulla. The great number of nitrergic nuclei and its pattern of distribution in the rock cavy's brainstem is similar to the other mammals, leading us to conclude that the phylogenetic proximity between species is kept in the brainstem. The present work shows that among other regions the NO is in nuclei of the primary visual system as the pretectal nuclei and the superior coliculum; nuclei of the auditory system as the olivar complex, inferior coliculum and the coclear nuclei; it is in several divisions of the periaqueductal grey matter, strutucture involved in defensive behavior, nociception and anxiety, like the locus coeruleus, where NO also was find; the substantia nigra, where the NO has been related to hepatic encephalopatia and Parkinson's disease in other rodents.The great number of nitrergic nuclei and its pattern of distribution in the rock cavy's brainstem looked alike what is seen in other mammals, leading us to conclude that the philogenetic proximity of the species is mantained in the distribution of NO in the rock cavy's brainstem.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2017-03-21T18:43:42Z No. of bitstreams: 1 MariaEmanuelaMartinsDosReis_DISSERT.pdf: 5769860 bytes, checksum: 74ddebdf2f9b77f3786b50ef1260466c (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2017-03-28T00:21:34Z (GMT) No. of bitstreams: 1 MariaEmanuelaMartinsDosReis_DISSERT.pdf: 5769860 bytes, checksum: 74ddebdf2f9b77f3786b50ef1260466c (MD5) / Made available in DSpace on 2017-03-28T00:21:34Z (GMT). No. of bitstreams: 1 MariaEmanuelaMartinsDosReis_DISSERT.pdf: 5769860 bytes, checksum: 74ddebdf2f9b77f3786b50ef1260466c (MD5) Previous issue date: 2016-12-20 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq) / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES) / O ?xido n?trico (NO) ? uma mol?cula muito simples (N=O), gasosa, com propriedades qu?micas de um radical livre e at? meados da d?cada de 1980 era considerado apenas membro de uma fam?lia de poluentes ambientais indesej?veis e carcin?genos potenciais. Desde sua descoberta no sistema nervoso, NO tem sido implicado em diversas fun??es, o que condiz com sua ampla distribui??o no enc?falo. NO tamb?m tem sido descrito no enc?falo de diversas esp?cies animais, mas ainda n?o foi descrito em moc? (Kerodon rupestris), um roedor end?mico da caatinga brasileira que habita ?reas rochosas e tem h?bitos crepusculares. Devido a estas caracter?sticas interessantes objetivamos descrever a distribui??o do NO do dienc?falo do moc?. Atrav?s das t?cnicas de imunoperoxidase padr?o contra a ?xido n?trico sintase (NOS), enzima de s?ntese de NO, e histoqu?mica para NADPH-diaforase pudemos identificar de forma indireta a presen?a de neur?nios nitr?rgicos ao longo de todo dienc?falo. O hipot?lamo apresentou uma densidade alta de neur?nios imunorreativos a NOS (NOS-IR) em v?rios n?cleos, dentre eles alguns como o n?cleo supra?ptico, decussa??o supra?ptica e a parte lateral da ?rea retroquiasm?tica. Com densidade moderada temos a ?rea pr?-?ptica lateral, o n?cleo pr?-?ptico magnocelular, a parte parvocelular anterior e a parte parvocelular medial do n?cleo paraventricular do hipot?lamo, o n?cleo ventrolateral do hipot?lamo, a parte peduncular da ?rea hipotal?mica lateral e o n?cleo posterior do hipot?lamo. A divis?o anterior do n?cleo ventromedial do hipot?lamo e a ?rea hipotal?mica dorsal apresentaram densidade baixa, e a parte lateral do n?cleo pr?-?ptico medial apresentou densidade muito baixa. No t?lamo, neur?nios NOS-IR estiveram presentes no n?cleo geniculado ventral com densidade alta. Na parte lateral do n?cleo habenular lateral, o n?cleo tal?mico posterodorsal ventral e a parte mediocaudal do n?cleo tal?mico posterior com densidade moderada. O n?cleo paraventricular do t?lamo, zona incerta e o n?cleo tal?mico parafascicular, apresentaram densidade baixa. Comparando nossos resultados com o descrito em outros animais podemos dizer que o sistema nitr?gico ? um sistema de neurotransmissor evolutivamente bem conservado. / Nitric oxide (NO) is a simple molecule (N=O), a gas with a free radical property whose until the 80s was considered a member of a family of environmental pollutants and a potential carcinogen. Since its discovery in the nervous system, NO has been implicated in several functions, what suits with its wide distribution in the brain. NO has been described in the brain of many animal species, but it was not described in the brain of the rocky cave (Kerodon rupestris), an endemic rodent of the Brazilian caatinga that inhabits rocky areas and have crepuscular habits. Due to these interesting characteristics we aim to describe the NO distribution of the rocky cavy diencephalon. Using standard immunoperoxidase against nitric oxide synthase (NOS), the NO synthesis enzyme, and histochemistry for NADPH-diaphorase, we were able to indirectly identify the presence of nitrergic neurons throughout the entire diencephalon. The hypothalamus showed a high density of NOS-IR neurons in several nuclei, among them the supraoptic nucleus, supraoptic decussation and the lateral part of the retrochiasmatic area. With moderate density we have the lateral pre-optic area, the preocular magnocellular nucleus, the anterior parvocellular part and the medial parvocellular part of the paraventricular nucleus of the hypothalamus, the ventrolateral nucleus of the hypothalamus, the peduncular part of the lateral hypothalamic area and the posterior nucleus of the hypothalamus. The anterior division of the ventromedial nucleus of the hypothalamus and the dorsal hypothalamic area presented low density, and the lateral part of the medial pre-optic nucleus presented very low density. In the thalamus, NOS-IR neurons were present in the ventral geniculate nucleus with high density. In the lateral part of the lateral habenular nucleus, the ventral posterodorsal thalamic nucleus and the mediocaudal part of the posterior thalamic nucleus with moderate density. The paraventricular nucleus of the thalamus, zona incerta and the parafascicular thalamic nucleus, presented low density. Comparing our results with those described in other animals we can say that the nitric system is an evolutionarily well-conserved neurotransmitter system.

A movement protein Potato virus X (PVX) chimera virus (PVX.GFP(CH3)) bearing the grapevine virus Grapevine rupestris stem pitting-associated virus (GRSPaV) triple gene block proteins (TGB) (denoted P1, P2 and P3) instead of the PVX TGB was delivered into N. benthamiana and other related species by agro-inoculation. This movement protein PVX chimera virus was found to be unable to support the local and systemic movement of PVX in cis. Local and systemic movement of this PVX chimera virus was restored in trans by the dianthovirus Red clover necrotic mosaic virus (RCNMV) movement protein and by a PVX TGB rescue virus that replaced the GRSPaV TGB with the PVX TGB (PVX.GFP(Rescue)). However, a PVX TGB hybrid chimera virus (PVX.GFP(HY2)) containing PVX P1 and the GRSPaV TGB had limited cell-to-cell, but not systemic, movement.

Made available in DSpace on 2014-12-17T15:36:35Z (GMT). No. of bitstreams: 1 SebastiaoFS.pdf: 2551917 bytes, checksum: 3538250a323b39c32585d41d316bcb6a (MD5) Previous issue date: 2009-09-08 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico / The primary and accessory optic systems comprise two set of retinorecipient neural clusters. In this study, these visual related centers in the rock cavy were evaluated by using the retinal innervations pattern and Nissl staining cytoarchigtecture. After unilateral intraocular injection of cholera toxin B subunit and immunohistochemical reaction of coronal and sagittal sections from the diencephalon and midbrain region of rock cavy. Three subcortical centres of primary visual system were identified, superior colliculus, lateral geniculate complex and pretectal complex. The lateral geniculate complex is formed by a series of nuclei receiving direct visual information from the retina, dorsal lateral geniculate nucleus, intergeniculate leaflet and ventral lateral geniculate nucleus. The pretectal complex is formed by series of pretectal nuclei, medial pretectal nucleus, olivary pretectal nucleus, posterior pretectal nucleus, nucleus of the optic tract and anterior pretectal nucleus. In the accessory optic system, retinal terminals were observed in the dorsal terminal, lateral terminal and medial terminal nuclei as well as in the interstitial nucleus of the superior fasciculus, posterior fibres. All retinorecipient nuclei received bilateral input, with a contralateral predominance. This is the first study of this nature in the rock cavy and the results are compared with the data obtained for other species. The investigation represents a contribution to the knowledge regarding the organization of visual optic systems in relation to the biology of species. / Os sistemas visual prim?rio e ?ptico acess?rio compreendem dois conjuntos de grupamentos neurais, que recebem proje??o direta da retina. Nesse estudo, estes dois sistemas foram avaliados com rela??o a citoarquitetura e padr?o de inerva??o retiniana, usando como tra?ador neural anter?grado, a subunidade B da toxina col?rica revelada por imunoistoqu?mica para detectar este tra?ador em terminais sobre grupamentos neuronais (alvos) no enc?falo do moc? (Kerodon rupestris), um roedor nativo do Nordeste Brasileiro. Os resultados permitiram identificar os componentes do sistema visual prim?rio o complexo geniculado lateral, o complexo pr?-tectal e o col?culo superior. O complexo geniculado lateral cont?m o n?cleo geniculado lateral dorsal, o n?cleo geniculado lateral ventral e o folheto intergeniculado. Todos recebem fibras da retina com predomin?ncia contralateral, menos intensa para o folheto intergeniculado. O complexo pr?-tectal cont?m os n?cleos pr?-tectal anterior, pr?-tectal medial, pr?-tectal posterior, olivar pr?-tectal e n?cleo do trato ?ptico, os quais recebem proje??o retiniana predominantemente contralateral. Do mesmo modo, o col?culo superior recebe fibras da retina contralateral nas camadas superficiais. Tamb?m foi identificado o sistema ?ptico acess?rio completo no moc?, constitu?do pelos n?cleos terminal medial, terminal lateral, terminal dorsal e intersticial do fasc?culo superior posterior. Esses n?cleos recebem inerva??o retiniana com forte predomin?ncia contralateral, sendo que o n?cleo terminal medial, embora preserve a predomin?ncia contralateral, exibe uma evidente inerva??o ipsolateral.

It appears to be unanimous that alien species in island environments tend to cause considerably more negative than positive impacts. To assess the potential level of threat aliens may pose to the native environment, understanding a species’ population structure and dynamics is of ultimate importance. Assessing both impacts and consequences of management interventions to alien species is likewise only possible through the comprehension of its population structure and dynamics. This can be achieved by estimating the number of individuals in the study site, as well as other population parameters through time, applying population models such as capture-recapture to the collected datasets. Nonetheless, alien species that have low capture rates, such as small mammals, might present a considerable obstacle for conservation, as available capturerecapture models need a relatively large dataset to precisely and accurately estimate population parameters. To improve accuracy and precision of estimates that use sparse datasets, the present study developed an integrated concurrent marking-observation capture-recapture model (C-MOM). The model proposed here, contrary to the commonly available mark-recapture and mark-resight models, allows for two different datasets (i.e. a capture-recapture and a population count) to be integrated, as well as for marking and observation (recapture) data to be collected simultaneously. While few models can integrate different datasets, no model is known to allow for concomitant capture-markobservation activities. To assess the performance of the C-MOM when estimating population parameters for sparse datasets, a virtual ecology study was carried out. The population dynamics of a small rodent, the rock cavy (Kerodon rupestris), as well as capture-recapture and population count datasets, were simulated under different scenarios. The sampled datasets were then analyzed by the C-MOM, and by two other established statistical models: a classical mark recapture (CMR) (based on the Jolly-Seber model), and a zero-truncated Poisson log-normal mixed effects (ZPNE), the only integrated mark-resight model that allows for recapture sampling with replacement. Estimates of population parameters provided by the three models were then compared in terms of bias, precision and accuracy. C-MOM and ZPNE models were afterwards applied to real data collected on a rock cavy colony in the island of Fernando de Noronha. The estimated parameters were used to extrapolate the number of individuals in the rock cavy colony to the whole population in the island. Subsequently, these results were used to develop a risk assessment for the species by modelling historical and management scenarios, simulating both the establishment of the species in the island, and the consequences of different management interventions applied to it. The virtual ecology study showed that, in comparison to the CMR and the ZPNE, the C-MOM presented improved accuracy without overestimating the precision of population parameter’s estimates. The last also presented reduced amplitude of the calculated credible interval at 95% when applied to real data in comparison to the ZPNE. While the extrapolation of C-MOM estimates suggests that the rock cavy population in Fernando de Noronha is 6,652 ± 1,587, ZPNE estimates are of 5,854 ± 3,269 individuals. In the risk assessment, historical simulation models demonstrated that even though different combinations of uncertainty in reproductive parameters of the rock cavy might be possible for the species, these did not interfere significantly in either establishment or spread of the rock cavy population in the island. Moreover, historical yearly mortality has most likely been under 30%. Regarding the species’ management simulations, the most effective management interventions to achieve population extinction were spaying and neutering of both sexes, although harvest effort presented the highest influence on this populations’ extirpation. Nonetheless, the relative influence of female and both sexes’ based interventions did not differ significantly regarding the frequency of extinction of stochastic replicates’. Moreover, none of the management interventions guaranteed the population extinction within the time span and harvest effort proposed for the management program. Neutering of both sexes was most inversely influential on time to extinction of this population, followed by removal of both sexes. Briefly, the C-MOM has proven to be a resourceful and precise model to estimate population parameters when low capture rates result in sparse datasets. Moreover, the rock cavy is well established in the island and likely at carrying capacity. In general, the risk assessment showed that the management interventions in the time span and harvest effort simulated in the present study were ineffective to extinguish the rock cavy population in Fernando de Noronha. Considering this, as well as the importance of investigating other vital factors to decide in favour of or contrary to the management of this species, it is recommended that both an impact assessment of the rock cavy and a cost-effectiveness analysis of the management interventions should be performed to complement the current study.:Acknowledgement III Abstract IV Zusammenfassung VI Resumen IX Table of Contents XII List of Tables and Figures XIV List of Abbreviations XIX 1. Introduction 1 1.1. Invasive alien species and their consequences 1 1.2. Population dynamics analysis 2 Capture-recapture models 3 Observation models 4 Integrated population models 5 Software 7 Model analysis 8 1.3. Fernando de Noronha and the rock cavy 10 1.4. Objectives 12 Overall Objectives 12 Specific Objectives 13 2. Study Framework 15 3. Methods 19 3.1. Study area 19 3.2. Study case species 21 3.3. Research Steps 24 RESEARCH STEP I: Comparing the C-MOM to established models – does this concurrent marking-observation model produces accurate estimates of population parameters for sparse datasets? 24 RESEARCH STEP II: C-MOM application to a real case study 40 RESEARCH STEP III: The rock cavy population in Fernando de Noronha 45 RESEARCH STEP IV: The colonization and eradication of the rock cavy in Fernando de Noronha 47 4. Results 63 4.1. RESEARCH STEP I: Comparing the C-MOM to established models – does this concurrent marking-observation model produces accurate estimates of population parameters for sparse datasets? 63 4.2. RESEARCH STEP II: C-MOM application to a real case study 72 4.3. RESEARCH STEP III: The rock cavy population in Fernando de Noronha 73 4.4. RESEARCH STEP IV: The colonization and eradication of the rock cavy in Fernando de Noronha 74 Sensitivity analysis 74 Simulation experiments 80 5. Discussion 83 5.1. Bias, precision and accuracy of population dynamic models for sparse datasets 85 Simulated data 85 Study case 90 5.2. Advantages and disadvantages of the C-MOM approach 93 5.3. Development and applications of the integrated models and the C-MOM 96 5.4. The reversed use of the PVA software Vortex to simulate AS and IAS populations’ extinction 97 5.5. Status of the rock cavy population in the island of Fernando de Noronha 100 The colonization of the rock cavy in Fernando de Noronha 101 Management of the rock cavy in Fernando de Noronha 104 Study case limitations and future researches 112 6. Conclusion 116 References 118 Appendices 124 APPENDIX I – Assessment of biological invasions 124 APPENDIX II – Population dynamics simulation and dataset sampling 125 APPENDIX III – CMR and C-MOM model codes in R 134 APPENDIX IV – ZPNE model code in R 138 APPENDIX V – C-MOM model used for real datasets 143 APPENDIX VI – Rock cavy colony sizes and number of individuals in Fernando de Noronha 145 APPENDIX VII – Parameter’s ranking of C-MOM, CMR and ZPNE models 148 APPENDIX VIII – Bias, precision and accuracy table 149

Thesis (MSc (Genetics))--University of Stellenbosch, 2010. / Includes bibliography. / ENGLISH ABSTRACT: The first aim of this study was to reliably and rapidly detect Grapevine rupestris stem pittingassociated virus (GRSPaV) in grapevine. This was achieved by screening 94 grapevines using crude plant extracts in both quantitative and conventional reverse transcription polymerase chain reaction (RT-PCR). The second aim was to establish a technique capable of differentiating GRSPaV sequence variants. The application of this technique is for the largescale screening of diseased vines to associate sequence variants of GRSPaV with disease symptoms. Nested quantitative polymerase chain reaction and high resolution melting assays (qPCR-HRM) were developed for three regions of the GRSPaV genome (coat protein, RNAdependant RNA-polymerase and triple gene block movement protein). The qPCR-HRM technique using the high saturation dye, EvaGreen™, and the Rotor-Gene™ 6000 analyzer was validated with a panel of sixteen sequence-characterized viral isolates. Diluted RT-PCR products and cloned cDNA gave the most consistent amplification plots and dissociation profiles. RT-PCR products generated from total RNA extracts were used as template for qPCR-HRM assays and for direct sequencing of sixteen samples in the three aforementioned regions. The average amplification efficiency for qPCR was 1.52±0.04. Auto-calling of userdefine genotypes was performed at a confidence interval of 70%. Phylogenetic analysis of the three regions of the GRSPaV genome was performed with published GenBank sequences to confirm the HRM data. The dominant sequence variants found in the South African sample set radiated with Group II, reference full-length variant GRSPaV-SG1. GRSPaV-infected samples can in future be subjected to qPCR-HRM assays developed during this study. This can be performed to establish similarity to known genotypes and therefore phylogenetic groups. Mixed infection of sequence variants and quasi-species were a common occurrence. The assay will be useful in establishing correlation of specific genotypes to different phenotypical expression of viral disease. This could provide insight into the etiology of diseases associated with GRSPaV. / AFRIKAANSE OPSOMMING: Die eerste doel van hierdie studie was om die virus wat met Rupestris-stamverpitting (Grapevine rupestris stem pitting-associated virus of “GRSPaV”) in wingerd verbind is, vinnig en betroubaar op te spoor. Dit is bereik deur 94 wingerdstokke vir die teenwoordigheid van die virus te toets met beide kwantitatiewe en konvensionele trutranskripsie polimerase kettingreaksies (RT - PCR) vanaf ongesuiwerde plant-ekstraksies. Die tweede doel was die daarstelling van ’n tegniek om onderskeid te tref tussen variante van GRSPaV met verskillende nukleotiedvolgordes. Hierdie tegniek kan op groot skaal gebruik word om ge-affekteerde wingerdstokke te toets om sodoende siektesimptome met spesifieke variante van GRSPaV te verbind. Ge-neste kwantitatiewe polimerase-kettingreaksies (qPCR) en hoë-resolusie smelt-analises (HRM) is ontwikkel vir drie streke van die GRSPaV-genoom (mantelproteïen, RNS-afhanklike RNS-polimerase en trippelgeenblok bewegingsproteïen). Die tegniek van qPCR-HRM met die hoë-versadingingskleurstof EvaGreen™ en die Rotor- Gene™ 6000 ontleder se geldigheid is bevestig deur vergelyking met ’n paneel van sestien virus-isolate waarvan die volgorde reeds bepaal is. Verdunde RT-PCR-produkte en gekloneerde DNS het die mees konsekwente amplifikasie-uitstipping en dissosiasieprofiele opgelewer. RT-PCR-produkte wat vanuit totale RNS-ekstrakte verkry is, is as templaat vir qPCR-HRM-analises gebruik. Dieselfde produkte is ook gebruik, om die volgorde van sestien monsters in drie streke direk te bepaal. Die gemiddelde amplifikasiedoeltreffendheid van die qPCR was 1.52±0.04. Gebruiker-gedefinieerde genotipes is deur middel van outooproeping teen ’n vertroue-interval van 70% uitgevoer. Filogenetiese analises vir drie streke van die GRSPaV-genoom is uitgevoer met gepubliseerde GenBank-volgordes om die HRMdata te bevestig. Die dominante volgorde-variante in die stel Suid-Afrikaanse monsters het ooreengestem met Groep II, vollengte-verwysingsvariant GRSPaV-SG1. Monsters wat met GRSPaV besmet is kan in die toekoms onderwerp word aan die qPCR-HRM-analises wat in hierdie studie ontwikkel is. Dit kan uitgevoer word om ooreenkomste met bekende genotipes te bepaal, en dus ook met filogenetiese groepe. Die besmetting van plante met meer as een volgorde-variant het algemeen voorgekom. Die kwasi-spesies populasie-struktuur van die virus het ook gedurig na vore gekom. Die toets sal nuttig wees in die bepaling van korrelasies tussen spesifieke genotipes en verskillende fenotipiese voorkomste van virussiektes. Dit kan insig verleen in die etiologie van siektes wat met GRSPaV verbind word.

Made available in DSpace on 2014-12-17T15:36:32Z (GMT). No. of bitstreams: 1 ExpeditoSNJ.pdf: 2182833 bytes, checksum: 1d14b6b7f5a8b99dccd3ec09fd418133 (MD5) Previous issue date: 2007-12-07 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / In this study, two circadian related centres, the suprachiasmatic nucleus (SCN) and the intergeniculate leaflet (IGL) were evaluated in respect to their cytoarchitecture, retinal afferents and chemical content of major cells and axon terminals with a tract tracer and immunohistochemical techniques in the rock cavy (Kerodon rupestris), a Brazilian caviidae rodent species. The rock cavy SCN is innervated in its ventral portion by terminals from the predominantly contralateral retina. It also contains neurophisin and vasoactive intestinal polypeptide immunoreactive cell bodies and neuropeptide Y and enkephalin immunopositive fibres and terminals and is marked by intense GFAP immunoreactivity. The IGL receives a predominantly contralateral retinal projection, contains neuropeptide Y and nitric oxide synthase producing neurons and enkephalin immunopositive terminals and is characterized by dense GFAP immunoreactivity. This is the first report examining the neural circadian system in a crepuscular rodent species for which circadian properties have been described. The results are discussed comparing with what has been described for other species and in the context of the functional significance of these centres / O sistema de temporiza??o circadiana compreende um conjunto de estruturas neurais diferenciadas, que incluem um marcapasso central, o qual produz ritmicidade na aus?ncia de est?mulos externos; vias de entrada, incluindo as afer?ncias retininas, que permitem a sincroniza??o dos ritmos aos ciclos ambientais; e vias de sa?da, que conectam o marca-passo aos efetores comportamentais. Entre os componentes centrais do sistema de temporiza??o circadiana de mam?feros, destaca-se o n?cleo supraquiasm?tico (NSQ) do hipot?lamo, at? o presente o ?nico marca-passo circadiano formalmente comprovado, e o folheto intergeniculado (FIG) do complexo geniculado lateral do t?lamo, que atua como modulador do marca-passo. Neste estudo, estes dois centros foram avaliados com rela??o a sua citoarquitetura, padr?o de inerva??o retiniana e conte?do neuroqu?mico de c?lulas e terminais ax?nicos, usando um tra?ador neural e t?cnicas imuno-histoqu?micas no moc? (Kerodon rupestris), um roedor nativo do Nordeste Brasileiro, cuja atividade locomotora exibe um padr?o circadiano predominantemente crepuscular. O NSQ do moc? ? inervado em sua por??o ventrolateral por terminais da retina predominantemente contralateral. O NSQ ? dotado de neur?nios contendo neurofisina (NPH) e polipept?deo intestinal vasoativo (VIP) e as prote?nas ligantes de c?lcio calbindina (CB) e cal-retinina (CR), terminais imunorreativos a neuropept?deo Y (NPY) e encefalina (ENK) e ? tamb?m marcado por imunorreatividade ? prote?na ac?dica fibrilar glial (GFAP). O FIG recebe uma proje??o retiniana predominantemente contralateral, cont?m neur?nios produtores de NPY, CB e CR, terminais positivos para ENK e ? marcado por imunorreatividade a GFAP. Este ? o primeiro trabalho a examinar o sistema de temporiza??o circadiana (STC) numa esp?cie de roedor crepuscular, para o qual as propriedades formais dos ritmos circadianos tenham sido descritas. Os resultados s?o comparados com resultados previamente descritos em outras esp?cies diurnas e noturnas e discutidos no seu contexto funcional