A área de ocorrência das formações Tatuí e Irati, na região centro-leste do Estado de São Paulo, entre as cidades de Leme e Rio das Pedras é objeto desta pesquisa. São detalhadas as ocorrências destas duas formações, através de seções estratigráficas, caracterizando e analisando as sucessões de litotipos, conteúdo fossilífero, tafonomia dos fósseis, além de enfocar hipóteses paleoecológicas e paleoambientais. Na FormaçãoTatuí foram identificadas quatro fácies, a inferior de arenitos finos e paleoambiente incerto, duas refletindo contexto não marinho e a de topo com influência marinha. As duas fácies do contexto predominantemente não marinho são respectivamente siltitos arenosos com fósseis de água doce e arenitos grossos ou conglomeráticos, fácies Ibicatu, localmente com lenhos. A fácies de topo é caracterizada por depósitos de arenitos finos, ocasionalmente com grandes estratificações cruzadas, estratificações \"hummockies\", apropriado para um grande corpo d\'água salino. O conteúdo fóssil da Formação Tatuí inclui três tipos de icnofósseis em três fácies diferentes (fácies basal do estudo, Ibicatu, e no topo), grandes caules vegetais (pteridófitas e espermatófitas) na fácies Ibicatu, crustáceos (conchostráceos e fragmentos indeterminados) ocorrem na fácies síltica, escamas, dentes e partes ósseas de peixes ósseos na fácies siltica e topo da Formação Tatuí. O Membro Taquaral é reconhecido por duas fácies e dois paleoambientes de salinidade variável. A fácies basal, composta de arenitos finos a conglomeráticos, granulometria irregular horizontal e verticalmente e com ictiofósseis, é interpretada como depositada em ambiente raso dominado por ondas. A segunda fácies, folhelhos sílticos, é típica de paleoambientes mais calmos, provavelmente com menor salinidade. Os fósseis da base arenosa do Membro Taquaral são peixes, representados por Chondrichthyes sob a forma de dentes cladodontes, espinhos de Euselachii (Amelacanthuse Iratiacanthus), espinhos Ctenacanthiformes (Sphenacanthus sanpauloensis eS. sp.), dentes de Xenacanthiformes, Diplodoselachidae (Taquaralodus albuquerquei) e Xenacanthidae, dentes de Orodontiformes, (Orodus ipeunaensis), Petalodontiformes (Itapyrodus punctatus eI. sp.) e Holocephali indeterminados. A fauna de Osteichthyes é a mais abundante em número de espécimes, sendo composta, predominatemente, de dentes e escamas paleoniscóides, raras escamas de Coelacanthimorpha, partes ósseas e dentes labirintodontes, estes atribuídos a Osteolepiformes e a tetrápodes Temnospondyli. Os fósseis estão normalmente dispersos e desarticulados e os elementos ósseos fragmentados e desgastados. O conteúdo fóssil da fácies folhelho síltico do Membro Taquaral é raro, os mais comuns são crustáceos, principalmente do gênero Clarkecaris, e restos muito fragmentados de Coelacanthimorpha e Palaeonisciformes. / The following Paraná Basin, Late Paleozoic lithoestratigraphic units, the upper part of the Tatuí Formation, located under the lower partof the Irati Formation, Taquaral Member are cropping out at center-eastern State of São Paulo, Brazil, between Rio das Pedras and Leme. The lithologies, fossil contents and taphonomy ofthese units are studied through stratigraphic sections, allowing the formulations of paleoecological and paleoenvironmental hypothesis. Four facies were recognized at the top of the Tatuí Formation stratigraphic sections which were interpreted as following; the basal an uncertain paleoenvironment of deposition, two paleoenvironmental contexts; mostly continental and one under deposits marine influence. The two facies interpreted as mostly continental are respectively, sandy-siltstones facies with freshwater fossils and coarse to conglomeratic sandstone, Ibicatu facies, locally with log plants. The top facies, interpreted as under a marine influence, is characterized by deposits of fine sandstones, occasionally with large cross beds, hummockies, and, locally, tidal deposits, suited for a large body, of saline water. The fossil content of Tatui Formation include three kinds of trace fossils in three different facies (basal, Ibicatu and top respectively), large stem plants (Pterydophyta and Spermatophyta) in the Ibicatu deposit, with indeterminated fragments of crustaceans and conchostraceans, found out in the siltstone facies and scales, teeth and bone pieces, found out in siltstone and of the top facies. Two facies were recognized at the Taquaral Member. The basal are fine to conglomeratic sandstone with irregularly grain size both horizontal and vertically, with ichthyofossils. Itis interpreted as laid down in a salty shallow water dominated by waves. The second are silty shale laid down in low saline water. The fossils of the sandy facies are Chondrichthyes: cladodontes teeth, Euselachii finspines (Amelacanthus and Iratiacanthus santamariaensis), Ctenacanthiformes finspines (Sphenacanthus sanpauloensisand S.sp.), Xenacanthiformes teeth, Diplodoselachidae (Taquarodus albuquerquei) and Xenacanthidae, Orodontiformes: Orodus ipeunaensis, Petalodontiformes (Itapyrodus punctatus andI. sp.) and undetermined Holocephali. The fauna of Osteichthyes, the most abundant in number of specimens are predominantly paleoniscoid teeth and scales, rare Coelacanthimorpha scales, labyrinthodonts bones and teeth, assigned to Osteolepiformes and tetrapods Temnospondyli. The fossils are usually scattered, disorganized, fragmented and worn. The fossil content of the Taquaral silty-shale facies is meager, the most common are crustaceans, mainly of the genus Clarkecaris, and very fragmented remains of Coelacanthimorpha and Palaeonisciformes.

O clado de Passeriformes denominado, atualmente, Furnariida é endêmico da região Neotropical e muito diversificado; ele é representado por cerca de 623 espécies alocadas em 134 gêneros, distribuídas nas seguintes famílias: Furnariidae, Dendrocolaptidae, Thamnophilidae, Formicariidae, Conopophagidae e Rhinocryptidae. As aves deste grupo são, em geral, encontradas em bandos mistos de espécies e/ou podem seguir formigas de correição, fenômenos que são conspícuos entre aves de florestas tropicais. Os representantes de Furnariida são considerados insetívoros, embora possam consumir, ocasionalmente, pequena quantidade de frutos ou sementes e pequenos vertebrados. Este trabalho teve como objetivo descrever a dieta de espécies representantes dos Furnariida que ocorrem em diferentes regiões da Amazônia, além de estimar o número de presas e de biomassa bruta consumida. Para tal, foi analisado o conteúdo estomacal de 476 espécimes de aves Furnariida, dos quais 51 pertencem à família Furnariidae, 139 à Dendrocolaptidae, 280 à Thamnophilidae, 3 à Formicariidae e 3 à Conopophagidae. Foram utilizados dois métodos diferentes para avaliar a contribuição da biomassa de presas consumidas pelos Dendrocolaptidae. O método da biomassa parcial apresentou-se muito incerto e, neste estudo, considerou-se a biomassa estimada como o método mais confiável para comparar o número total de itens e sua biomassa correspondente. As principais presas consumidas por estes pássaros foram Coleoptera, Orthoptera e Araneae. No entanto, Orthoptera foi o item que contribuiu com a maior biomassa ingerida, seguido de Coleoptera e Vertebrata. A alta biomassa de Orthoptera no ambiente poderia explicar o maior consumo, ou preferência desses insetívoros por tal item. Os vertebrados foram consumidos por alguns espécimes de Dendrocolaptidae e de Thamnophilidae e a maior parte do material ingerido pelos dendrocolaptídeos corresponde a Gonatodes humeralis, um pequeno lagarto escansorial; já os vertebrados consumidos pelos tamnofilídeos não foram identificados. A predação de vertebrados pode ser ocasional e, em geral, é considerada oportunística. Nas famílias de Furnariida, com número representativo de espécimes, Orthoptera e Araneae tiveram maior frequência de ocorrência em Furnariidae, enquanto Coleoptera e Orthoptera em Thamnophilidae e Coleoptera em Dendrocolaptidae, o que pode estar relacionado aos hábitos de forrageamento das espécies nelas incluídas / The clade Furnariida of the Passeriformes is endemic to the Neotropical region, and is very diverse: it is represented by around 623 species in some 134 genera distributed in the following families: Furnariidae, Dendrocolaptidae, Thamnophilidae, Formicariidae, Conopophagidae e Rhinocryptidae. Commonly the birds of this group are found in mixed-species flocks and/or as army-ant-followers, features that are common amongst birds of the tropical forests. Members of the Funariida are considered to be insectivores although they may occasionally eat small quantities of fruit or seeds, or small vertebrates. The objective of this study was to describe the diet of representative species of the Funariida that occur in different Amazonian regions, and also estimate the numbers of prey and total biomass consumed. To do this the stomach contents of 476 specimens of the Furnariida were analyzed, of which, 51 belonged to the family Funariidae, 139 to the Dendrocolaptidae, 280 to the Thamnophilidae, and 3 each to the Formaricariidae and Conopophagidae. Two methods were used to evaluate the contribution of the biomass of the preys consumed by the Dendrocolaptidae. The partial biomass method was found to be very unreliable and so, in this study, the estimated biomass method was found to be the most appropriate to compare the total number of items in the corresponding biomass. The main types of prey eaten by these birds were Coleoptera, Orthoptera and Araneae. Nevertheless, Orthoptera were the group that made the biggest contribution to the ingested biomass, followed by Coleoptera and Vertebrata. The high biomass of Orthoptera in the environment would explain the high consumption and preference for these insects as prey. The vertebrates were consumed by some specimens of Dendrocolaptidae and Thamnophilidae, and in the case of the dendrocolaptids these were all the small scansorial lizard Gonatodes humeralis; those consumed by the thamnophilids were not identified. Predation on vertebrates seems to be occasional and is probably opportunistic. In the families of the Furnariida, represented by numbers of specimens, Orthoptera and Aranae had the highest frequency of occurrence in the Funariidae, with Coleoptera and Orthoptera in the Thamnophilidae, and Coleoptera in the Dendrocolaptidae, which can be related to the foraging habits of the species in these families

The human prefrontal cortex (PFC) is associated with complex cognitive behaviors such as planning for the future, memory for serial order, social information processing and language. Understanding how the PFC has changed through time is central to the study of human neural evolution. Here we investigate the expansion of the PFC by measuring relative surface area of the PFC in Pan troglodytes and Homo sapiens. Magnetic resonance images (MRI's) from 8 preserved chimpanzee brains (3 male and 5 female adults) were segmented and measured. The results of this study indicate that there are gross anatomical differences between the chimpanzee and human prefrontal cortex beyond absolute size. The lower surface area to volume ratio in PFC of the chimpanzee when compared to a human indicates less gyral white matter in this region and thus, less associative connectivity. This anatomical evidence of a difference corresponds with the lesser cognitive complexity observed in chimpanzees. / by Ian D. George. / Thesis (M.A.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web.

O presente projeto representa uma extensão dos paradigmas que criamos com estudos de simulação molecular para compreender as frequentes mudanças de estrutura e função das Aldeído Desidrogenases (ALDHs) durante a evolução. As ALDHs formam uma superfamília de proteínas que catalisam a oxidação de vários aldeídos, mas as origens evolutivas das preferências pelos seus substratos são pouco conhecidas. Apesar de possuírem uma elevada identidade sequencial, duas destas ALDHs, a ALDH1 e a ALDH2, exibem distintos papéis funcionais de sinalização celular e detoxicação, respectivamente. Através de prévia análise computacional e logenética, identicamos que, curiosamente, as ALDH1s de organismos invertebrados, Branchiostoma oridae e Ciona intestinalis apresentam características estruturais mais semelhantes às de suas ALDH2s do que das ALDH1 típicas. Isto sugere que essas ALDH1s divergentes podem ter evoluído na direção da atividade de degradação de aldeídos pequenos e tóxicos, que parecem representar a função ancestral das ALDH2s eucarióticas. Nossa análise identicou três assinaturas de aminoácidos localizadas na área interna do canal de entrada do substrato (CES) que distinguem as ALDH1 das ALDH2. Desta forma, constatamos que as ALDH1s possuem um CES amplo e desobstruído, consistente com o fato destas enzimas catalisarem aldeídos de cadeia longa como o retinaldeído, que é um precursor de vias de sinalização por retinóides. Em contraste, as ALDH2s possuem o CES pouco volumoso e constrito, consistente com sua função na degradação de pequenos aldeídos tóxicos e reativos, como o acetaldeído. Neste projeto o nosso objetivo é analisar a correlação funcional e estrutural entre as ALDH1 e ALDH2 presentes em B. oridae e C. intestinalis para desvendar e compreender seus papéis funcionais e evolutivos em cordados. Especicamente, testaremos a hipótese de que as três assinaturas descritas constituem o núcleo fundamental da preferência por substratos, e que sua inversão por mutações sitio-dirigidas entre ALDH1 e ALDH2 modicará a preferência de substrato de acordo com a origem da assinatura. Se conrmado experimentalmente, este será um exemplo pioneiro de reversão evolutiva molecular, que terá impacto direto sobre as interpretações atuais sobre controversa lei de Dollo da irreversibilidade evolutiva. / This project represents an extension of the paradigms that we created from our molecular simulation studies to understand the frequent structure and function changes of aldehyde dehydrogenases (ALDH) during evolution. The ALDHs form a superfamily of proteins that catalyze the oxidation of several aldehydes, but the evolutionary origins of their substrate preference are unknown. Despite having a high sequence identity, two of these ALDHs, the ADLH1, and ALDH2, exhibit distinct functional roles of cellular signaling and detoxication, respectively. Through previous computational and phylogenetic analysis, we found that, interestingly, the ALDH1s of invertebrate organisms (Branchiostoma oridaeand Ciona intestinalis) show structural features more similar to their ALDH2s than the typical ALDH1. It suggests that these divergent ALDH1sevolved to provide small aldehydes detoxication pattern, what seems to represent the ancestral eukaryotic ALDH2s function. Our analysis also identied three aminoacidsignatures, located internally in the substrate entry channel (SEC), that distinguishes the ALDH1 from ALDH2. Thus, we nd that ALDH1s have a wide, open and unobstructed SEC, consistent with the fact that these enzymes catalyze bulky long-chainaldehydes, like retinaldehyde, a precursor of important signaling pathways. In contrast, the ALDH2s have a small and constricted SEC, consistent with the degradation function of small aldehydes, like the toxic metabolite acetaldehyde. In this project, our objective is to understand the functional and structural correlation between ALDH1 and ALDH2 found in B. oridaeand C. intestinalisto discover and comprehend their functional and evolutionary roles in chordates. Specically, we will test the hypothesis that the three signatures described above are the fundamental core of the substrate preference, based on the signature origin. If conrmed experimentally, this will be a pioneeringexample of evolutionary molecular reversion, impacting directly on the current interpretations of the controversial Dollos Law of Irreversibility.

In 2005, Atlantic salmon (Salmo salar L.) migrating to the United Kingdom exhibited swollen, haemorrhagic vents, symptoms not previously recorded. The condition was latterly termed Red Vent Syndrome (RVS), and subsequently observed across the North Atlantic. RVS has been pathognomonically associated with one of the most abundant parasites within the marine environment, the ascaridoid nematode Anisakis simplex, which also causes Anisakiasis in humans. Although A. simplex is commonly found in Atlantic salmon, heavy infestation of the vent region is novel, and the expression of RVS has not been prevalent in other fish species. Red Vent Syndrome has been well studied, however, the causes of the condition, and the reasons driving the novel site of infestation exhibited by A. simplex, have not been clarified. The aim of this PhD therefore, is to provide new information regarding the underlying factors of the infestation of the vent region by A. simplex, and the emergence of RVS. This study therefore: i) assessed the relationship between nematode burdens within the viscera and musculature, in comparison to the vent in 117 adult Atlantic salmon; ii) compared the genetic structure of A. simplex present in the vent region and the viscera using the entire nuclear internal transcribed spacer (ITS) region; iii) investigated migratory route and feeding ground of Scottish salmon populations using stable isotope analysis of dorsal muscle tissue and parasite component communities and, iv) assessed the expression of the cytokine TNF-α1 within vent muscle tissue using (q)RT-PCR, in relation to RVS severity. Phylogenetic analyses have shown that it is A. simplex sensu stricto infesting the vent region. The results show that there is a significant positive relationship between the nematodue burden in the body (viscera and musculature) and in the vent region. Isotopic signatures of salmon populations showed no significant differences, however, A. simplex intensities between populations on the East and North coasts of Scotland suggest geographical differences in A. simplex transmission pathways. Finally, the expression of TNF-α1 is not significantly different between RVS severity, and nematode burden. Out of the four studied factors, increasing nematode intensities in Atlantic salmon populations, and the significant positive relationship of nematode intensities between the body (viscera and musculature) and the vent, are likely to explain the infestation of the vent by A. simplex. The underlying causes of RVS however remain uncertain and require further research. With incidences of RVS observed across a number of populations over a large spatial area, regional and global effectors such as warming sea surface temperatures, and the North Atlantic Oscillation are expected to play key roles in its aetiology.

Localidades contendo tetrápodes fósseis do Permiano são conhecidas para a Formação Rio do Rasto (FRR) no sul do Brasil desde a década de 1970. Posteriormente, elas foram agrupadas em três “faunas locais”, correlacionáveis com as ocorrências de tetrápodes do Guadalupiano e do Lopingiano da África do Sul e da Rússia. Contudo, os fósseis de tetrápodes no Brasil ocorrem em afloramentos dispersos, isolados e discontínuos, de maneira que a maioria deles não possui dados precisos referentes ao seu posicionamento estratigráfico no sítio de coleta. Sugere-se que seja suspenso o uso do termo “fauna local” para as localidades contendo tetrápodes da FRR, pois elas provavelmente agrupam táxons que não são contemporâneos. A presente tese reconheceu dez localidades contendo tetrápodes nesta formação, mas apenas em quatro delas há o registro de terápsidos (Serra do Cadeado-EFCP, Fazenda Fagundes, Fazenda Boqueirão e Tiarajú-Barro Alto). Até o momento, terápsidos permianos são reportados na América do Sul apenas na FRR e compreendem anomodontes e dinocefálios. Aqui são relatadas duas novas ocorrências de terápsidos para esta unidade. O espécime UFRGS-PV-0487P foi identificado como um Tapinocephalidade indeterminado (Dinocephalia) e provém da localidade Serra do Cadeado-EFCP. Comparação com outros Tapinocephalidae indicam que UFRGS-PV-0487P é um espécime juvenil ou sub-adulto, semelhante a Moschops e Moschognathus da Zona de Assembleia (ZA) de Tapinocephalus da África do Sul. A segunda ocorrência de terápsido reportada aqui é baseada no espécime UNIPAMPA-PV-317P, reconhecido como um novo gênero e espécie de anomodonte (especificamente um dicinodonte). Características diagnósticas do novo táxon incluem cristas bem desenvolvidas (em norma ventral) a partir da placa mediana do pterigoide e ao longo dos ramos anteriores do pterigoide, ângulo marcado da porção posterior dos ramos do pterigoide, presença de pequenas presas caniniformes a partir de uma pequena incisura levemente posterior a cada processo caniniforme e presença de um processo retro-articular bem desenvolvido e em forma de bulbo na mandíbula. Não está claro ainda se o tamanho reduzido das presas caniniformes é devido à ontogenia, patologia ou a dimorfismo sexual. A análise filogenética indicou que UNIPAMPA-PV-317P é o membro mais basal de Bidentalia, um clado cosmopolita que inclui a maioria dos dicinodontes permianos e triássicos. Em relação às correlações bioestratigráficas possíveis para as localidades contendo tetrápodes na FRR, não é possível correlacionar estas localidades com apenas uma das ZAs da África do Sul ou mesmo da Plataforma Russa no momento, por que a FRR parece abrigar múltiplas assembleias de tetrápodes, das quais um retrato muito tendenciado é conhecido. Apenas a localidade de Aceguá Sítio 1 indica um pequeno refinamento, visto que os níveis abaixo da ocorrência de Provelosaurus americanus (um pareiassaurídeo) foram datados com métodos radiométricos e indicaram ser mais recentes do que 265 Ma, demonstrando que este sítio é correlacionável a partir da ZA de Tapinocephalus. / Permian tetrapod-bearing localities have been recovered from the Rio do Rasto Formation (RRF) in southern Brazil since the 1970s. Posteriorly, they have been grouped into three ‘local faunas’, correlated with the Guadalupian and Lopingian tetrapods of South Africa and Russia. However, tetrapod findings in the Brazilian deposit occur in disperse, isolated and discontinuous outcrops and most specimens lack precise data regarding their stratigraphic provenance. We suggest that the term ‘local fauna’ be discontinued for the tetrapod-bearing localities of the RRF, since they may be grouping non-contemporaneous taxa. The present study recognized ten tetrapod-bearing localities in this formation, but only four of them bear therapsid remains (Serra do Cadeado-EFCP, Fagundes Farm, Boqueirão Farm and Tiarajú-Barro Alto). Until date, Permian therapsids in South America are only known from the RRF and comprise anomodonts and dinocephalians. Here we report two new therapsid occurrences for this unit. The specimen UFRGS-PV-0487P was identified as a Tapinocephalidae indet. (Dinocephalia), from the Serra do Cadeado-EFCP locality. Comparison with other tapinocephalids indicates that UFRGS-PV-0487P is a juvenile or sub-adult specimen, which most closely resembles the ‘moschopines’ Moschops and Moschognathus from the Tapinocephalus Assemblage Zone (AZ) of South Africa. The second occurrence is based on the specimen UNIPAMPA-PV-317P, recognized as a new genus and species of anomodont (namely a dicynodont). Diagnostic features of the new taxon include well-developed ridges extending from the crista oesophagea anteriorly along the pterygoid rami, strong posterior angulation of the posterior pterygoid rami, small tusks erupting from a short incisure slightly posterior to each caniniform process and well-developed bulbous retroarticular process of the articular. It is not clear whether the reduced size of the tusks represents pathology, an ontogenetic feature or sexual dimorphism. Phylogenetic analysis indicates that UNIPAMPA-PV-317P is the most basal member of Bidentalia, a cosmopolitan clade that includes most of the Permian and Triassic dicynodonts. It is not possible at the moment to constrain the time interval of the tetrapod-bearing localities of the RRF to only one biozone of South Africa or Russia because the RRF seems to bear incomplete but multiple faunal assemblages. Aceguá Site 1 age is better constrained due to radiometric dating, but it only indicates that the levels bearing the pareiasaurid Provelosaurus americanus are younger than 265 My and can be correlated with the Tapinocephalus AZ.

Traditional methods of teaching the laboratory course for Comparative Anatomy of the Vertebrates could be improved by applying current computer technology to construct an interactive, multimedial atlas of dissection. Five specimens used in comparative anatomy courses at most institutions were chosen as representative members of the Phylum Chordata: amphioxus, lamprey, dogfish shark, mud puppy, and cat. Specimens were dissected according to the modified method of Wischnitzer, 1993, and each stage was photographed with a Kodak DC120 digital zoom camera. These images were processed on a Power Macintosh 7600 computer with Adobe Photoshop v. 5.0. The atlas was constructed from these images using Macromedia Authorware v. 4.0.3. Each image contains a series of interactive objects that display a highlight and descriptive text as the cursor passes over each object.

Orientador: Cesar Martins / Coorientador: Ney Lemke / Banca: Antonio Sérgio Kimus Braz / Banca: José Luiz Rybarczyk Filho / Banca: Reinaldo Otávio Alvarenga Alves de Brito / Banca: Pedro Manuel Galetti Junior / Resumo: Atualmente os sistemas biológicos vem sendo abordados por diversas áreas de pesquisas, dentre elas a biologia de sistemas. Essa área tem centrado esforços para descrever e compreender as relações entre os componentes bióticos e abióticos desses sistemas, utilizando para isso a teoria de grafos. Uma forma de estudar esses sistemas, é avaliar as interações entre proteínas, que são as interações biomoleculares mais abundantes nas células. Nesse contexto, a presente tese focou no desenvolvimento de um algoritmo computacional capaz de predizer interações entre proteínas de qualquer espécie ou conjunto protéico. Para isso, foram utilizadas técnicas de aprendizado de máquina (sub-área da inteligência artificial) para a construção e aplicação desse preditor, o qual mostrou-se eficaz em predizer interações entre proteínas de mais de 80 espécies diferentes, incluindo interações entre proteínas de parasita e hospedeiro. Esse novo preditor foi aplicado no proteoma de zebrafish (Danio rerio) e humanos (Homo sapiens), gerando assim redes de interações proteicas para ambas as espécies. As interações obtidas foram avaliadas em um contexto geral e o foco das análises foi direcionado para a sub-rede relacionada com as vias de determinação e diferenciação sexual em vertebrados. Os resultados demonstraram uma relativa baixa conservação desses grafos ao longo da evolução dos vertebrados, tanto do ponto de vista global quanto da sub-rede relacionada com a determinação e diferenciação sexual em vertebrados. Além disso, foi possível observar ao menos um hub conservado entre as duas sub-redes, o qual representa um novo alvo a ser avaliado por pesquisas experimentais. Contudo, os dados demonstram que o preditor gerado possui um grande potencial para diversas áreas de estudos e é bastante útil para predição de interações em larga-escala. Além disso, os aspectos evolutivos aqui ... / Abstract: Nowadays the biological systems have been analyzed under several research foci, including the system biology. This area focus to describe and understand the relationship between biotic and abiotic factors using the graph theory. The protein interactions are target interactions to the system biology because they are the most abundant biomolecular interactions within a cell. Thus, this thesis reported the development of a computational algorithm to predict proteinprotein interactions for all species or protein sets. The machine learning technique (sub-area of artificial intelligence) were used to develop and apply this method, giving effective results to predict protein-protein interaction for more than 80 different species, including parasitehost associations. This new predictor was applied to the proteome set of zebrafish (Danio rerio) and humans (Homo sapiens), generating the protein-protein interactions for both species. Evolutionary aspects of the protein interactions were studied in a broad context and the focus was directed to the sub-network involved in the vertebrate sex determination and differentiation. The results reported a low conservation of those graphs across the evolution in a general view or for the sub-network related to the vertebrate sex determination and differentiation. Moreover, it was reported at least one conserved hub between both subnetworks, to be further evaluated by experimental procedures. Anyway, the data showed that the predictor here reported may be very useful for several research areas and it is desirable for large-scale prediction procedures. Furthermore, the evolutionary aspects discussed in this thesis open new perspectives concerning system biology and evolutionary pathways of vertebrate sex determination and differentiation / Doutor

Very few vertebrates survive extended periods of time without oxygen. Entry into metabolic depression is central to surviving anoxia, which is supported by overall suppression of protein synthesis, yet requires increased expression of specific proteins. Studying the rapid and complex regulation of gene expression associated with survival of anoxia may uncover new mechanisms of cellular biology and transform our understanding of cells, as well as inform prevention and treatment of heart attack and stroke in humans. Small non-coding RNAs (sncRNAs) have emerged as regulators of gene expression that can be rapidly employed, can target individual genes or suites of genes, and are highly conserved across species. There are diverse types of sncRNAs, some coopted from degradation of longer RNAs in the cell. The sncRNA revolution has yielded a large body of literature revealing the roles of sncRNAs in a myriad of biological processes, from development to regulation of the cell cycle and apoptosis, to responding to stress, including freezing, dehydration, ischemia, and anoxia. Given the regulatory complexity required to survive anoxia, examining sncRNAs in the context of extreme anoxia tolerance has the potential to expand our understanding of the role that sncRNAs may play in basic cell biology, as well as in response to stresses such as anoxia. A comparative model including anoxia-tolerant and anoxia-sensitive phenotypes allows us to better identify sncRNAs that likely play a critical role in anoxia tolerance. Embryos of A. limnaeus are the most anoxia tolerant vertebrate known and are comprised of a range of anoxia-tolerance phenotypes. These characteristics create a unique opportunity for comparative study of the role of sncRNAs in anoxia tolerance in phenotypes with a common genomic background. The overall goals of this project were to: (1) describe the sncRNA transcriptome and changes in its expression in response to anoxia in the embryos of A. limnaeus and in other anoxia-tolerant vertebrates, and (2) to identify specific sncRNAs of interest based on these sequencing projects and to follow-up on their biogenesis, localization, and function in A. limnaeus embryos and a continuous cell line derived from A. limnaeus embryos. Chapter 2 focuses on the identity and expression of sncRNAs in embryos of A. limnaeus in 4 embryonic stages that differ in their anoxia tolerance and physiology. Chapter 3 explores sncRNA expression in brain tissue (the most oxygen-sensitive organ) in other anoxia-tolerant vertebrates: the crucian carp, western painted turtle, leopard frog, and epaulette shark. This allows us to assess the similarities and differences in sncRNA biology in species that evolved anoxia independently, and put the findings from A. limnaeus in an evolutionary context. Chapter 4 describes the establishment of the AL4 anoxia-tolerant cell line derived from A. limnaeus embryos, which allows for more detailed study of particular sncRNAs of interest in Chapter 5. Using whole embryos of A. limnaeus and the AL4 cell line, Chapter 5 describes the expression, localization, and possible biogenesis and mechanism of action of mitochondria-derived sncRNAs, known as mitosRNAs. Chapter 6 summarizes the findings and discusses potential future directions. The work in this dissertation represents the first global survey of sncRNA expression in anoxia tolerant vertebrates. While many interesting patterns of expression were identified, the most interesting discovery is the expression of sncRNAs that are generated in the mitochondria, but have the potential to function in other compartments of the cell. This discovery could transform the way we view the role of the mitochondria in regulating gene expression in eukaryotic cells.

Humans have indirectly and directly contributed to the extinction of over 500 species within the past 500 years, a rate far higher than we have seen in the past. The high extinction rate and the fact that 18% of vertebrates may become extinct within the next century have pushed Earth into a biodiversity crisis. Understanding what makes species more at risk of extinction is needed to protect Earth’s biodiversity. Generally, it is expected that predators have greater extinction risk than omnivores and herbivores because predators are larger in body size, depend on other animal species for food, need large home ranges, and have fewer individuals within their populations. However, no study to date has actually tested the assumption that predators have the highest extinction risk. This question is important to understand because diet is associated with the ecological role a species plays in an ecosystem. We compared the extinction risk of species with different diets to determine species in which trophic level are proportionately more at risk of extinction. We classified each species’ diet, trophic level (i.e.,predator, omnivore, and herbivore), body size, habitat, geographic region, system, and associated threats. We focused our analyses on all mammals, birds, and reptiles assessed by the International Union for the Conservation of Nature. We then compared the expected and observed proportions of threatened species within each trophic level and diet group at global, system, habitat, and regional scales. We found that predators, except scavengers, fish-eating birds, and obligate mammal and bird eaters, were not more threatened than expected. On the other hand, herbivores consistently had greater proportions of threatened species than expected. Specifically within herbivores, fruit, grass, and leaf-eating species had high proportions of threatened species. When we separated large-bodied and small-bodied species, we found that most large-bodied species, regardless of their trophic level, had greater proportions of threatened species. When we looked at the regions and habitats where species were more often threatened, we found that herbivores were highly threatened in south and Southeast Asia, sub-Saharan Africa, and Oceania. In addition, herbivores were highly threatened in tropical forests, marine coasts, and sometimes grasslands. Overall, terrestrial herbivores and marine predatory birds were highly threatened. We found that these patterns may have resulted from overexploitation, habitat alteration, and pollution targeting herbivores and sometimes omnivores. These findings suggest that we should shift conservation focus from predators to include herbivores. The most threatened species, tropical herbivores, scavengers, and mammal, bird, and fish eaters should be of highest conservation priority.