<p>alpha-actinin is a ubiquitous protein found in most eukaryotic organisms. The ability to form dimers allows alpha-actinin to cross-link actin in different structures. In muscle cells alpha-actinin is found at the Z-disk of sarcomeres. In non-muscle cells alpha-actinin is found in zonula adherens or focal adhesion sites where it can bind actin to the plasma membrane.</p><p>alpha-actinin is the shortest member of the spectrin superfamily of proteins which also includes spectrin, dystrophin and utrophin. Several hypotheses suggest that alpha-actinin is the ancestor of this superfamily.</p><p>The structure of alpha-actinin in higher organisms has been well characterized consisting of three main domains: an N-terminal actin-binding domain with two calponin homology domains, a central rod domain with four spectrin repeats and a C-terminal calcium-binding domain. Data mining of genomes from diverse organisms has made possible the discovery of new and atypical alpha-actinin isoforms that have not been characterized yet.</p><p>Invertebrates contain a single alpha-actinin isoform, whereas most of the vertebrates contain four. These four isoforms can be broadly classified in two groups, muscle isoforms and non-muscle isoforms. Muscle isoforms bind actin in a calcium independent manner whereas non-muscle isoforms bind actin in a calcium-dependent manner.</p><p>Some of the protozoa and fungi isoforms are atypical in that they contain fewer spectrin repeats in the rod domain. We have purified and characterized two ancestral alpha-actinins from the parasite Entamoeba histolytica. Our results show that despite the shorter rod domain they conserve the most important functions of modern alpha-actinin such as actin-bundling formation and calcium-binding regulation. Therefore it is suggested that they are genuine alpha-actinins.</p><p>The phylogenetic tree of alpha-actinin shows that the four different alpha-actinin isoforms appeared after the vertebrate-invertebrate split as a result of two rounds of genome duplication. The atypical alpha-actinin isoforms are placed as the most divergent isoforms suggesting that they are ancestral isoforms. We also propose that the most ancestral alpha-actinin contained a single repeat in its rod domain. After a first intragene duplication alpha-actinin with two spectrin repeats were created and a second intragene duplication gave rise to modern alpha-actinins with four spectrin repeats.</p>

Pineacea is the largest family of conifers that includes 51 species of Abies which is the second largest genus after Pinus. There are six native taxa in Turkey belonging to this genus. Four of these taxa (Abies cilicica subsp. isaurica, Abies nordmanniana subsp. bornm&uuml / lleriana, Abies nordmanniana subsp. equi-trojani, Abies x olcayana) are endemic and considered as low risk (LR) species according to the IUCN criteria. To determine the phylogenetic relationship in Abies spp. in Turkey, 18 populations of different taxa were collected from their natural distribution areas in Turkey. The matK gene regions of chloroplast DNA (cpDNA) were studied comparatively to reveal the genetic relationship among Turkish fir species. The available sequences from the NCBI database for the matK region of the other Abies species in the world were also investigated v comparatively with the sequences from Turkish firs. With the matK sequence data, a phylogenetic tree was constructed for the fir species and the molecular diversity parameters such as conserved and variable sites, nucleotide diversity, and evolutionary divergence were estimated using the MEGA software. The results indicated that there are no variable sites among Turkish firs with regard to matK regions of cpDNA. It appears that the matK region of cpDNA for Turkish firs is highly conserved. Since sequence data for all matK regions were not available from the NCBI data base, the phylogentic analysis with the sequence data of matK were comparatively analyzed in all firs including Turkish firs. According to matK1 region, the results showed that there were three major clades. One of the clades included all Turkish fir taxa and one species from European firs, A.numidica / however, A.holopylla, A.firma, A.veitchii, A.sachalinensis, A.nephrolepis, A.lasiocarpa, A.koreana, A.homolephis, A.fraseri, A.fargesii, A.sibirica and A.fabri formed in another clade. In addition to this, A.mariesii, A.hidalgensis, A.bracteata, A.alba formed in different major clade. According to matK1 region the results showed that Turkish firs and European firs are closer to each other. Furthermore, based on matK2 region, the results indicated that Turkish firs formed a monophyletic group.The other fir species, with respect to matK2 regions, formed different clades from Turkish firs. The results based on matK region suggest that all Turkish firs may have evolved from single ancestral fir species and the matK gene region appears to be highly conserved region in fir species.

alpha-actinin is a ubiquitous protein found in most eukaryotic organisms. The ability to form dimers allows alpha-actinin to cross-link actin in different structures. In muscle cells alpha-actinin is found at the Z-disk of sarcomeres. In non-muscle cells alpha-actinin is found in zonula adherens or focal adhesion sites where it can bind actin to the plasma membrane. alpha-actinin is the shortest member of the spectrin superfamily of proteins which also includes spectrin, dystrophin and utrophin. Several hypotheses suggest that alpha-actinin is the ancestor of this superfamily. The structure of alpha-actinin in higher organisms has been well characterized consisting of three main domains: an N-terminal actin-binding domain with two calponin homology domains, a central rod domain with four spectrin repeats and a C-terminal calcium-binding domain. Data mining of genomes from diverse organisms has made possible the discovery of new and atypical alpha-actinin isoforms that have not been characterized yet. Invertebrates contain a single alpha-actinin isoform, whereas most of the vertebrates contain four. These four isoforms can be broadly classified in two groups, muscle isoforms and non-muscle isoforms. Muscle isoforms bind actin in a calcium independent manner whereas non-muscle isoforms bind actin in a calcium-dependent manner. Some of the protozoa and fungi isoforms are atypical in that they contain fewer spectrin repeats in the rod domain. We have purified and characterized two ancestral alpha-actinins from the parasite Entamoeba histolytica. Our results show that despite the shorter rod domain they conserve the most important functions of modern alpha-actinin such as actin-bundling formation and calcium-binding regulation. Therefore it is suggested that they are genuine alpha-actinins. The phylogenetic tree of alpha-actinin shows that the four different alpha-actinin isoforms appeared after the vertebrate-invertebrate split as a result of two rounds of genome duplication. The atypical alpha-actinin isoforms are placed as the most divergent isoforms suggesting that they are ancestral isoforms. We also propose that the most ancestral alpha-actinin contained a single repeat in its rod domain. After a first intragene duplication alpha-actinin with two spectrin repeats were created and a second intragene duplication gave rise to modern alpha-actinins with four spectrin repeats.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2018-05-15T11:01:10Z No. of bitstreams: 2 Dissertação - Tharlley Rodrigo Eugenio Duarte - 2018.pdf: 3238895 bytes, checksum: 4372ea2b66d739dd3a82a02b57e2b24a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-05-15T12:24:47Z (GMT) No. of bitstreams: 2 Dissertação - Tharlley Rodrigo Eugenio Duarte - 2018.pdf: 3238895 bytes, checksum: 4372ea2b66d739dd3a82a02b57e2b24a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-05-15T12:24:47Z (GMT). No. of bitstreams: 2 Dissertação - Tharlley Rodrigo Eugenio Duarte - 2018.pdf: 3238895 bytes, checksum: 4372ea2b66d739dd3a82a02b57e2b24a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-04-26 / Brazil is the largest arbovirus granary in the world and presents the largest endemic area of yellow fever (YF). The Ministry of Health reported in 1170 suspected cases of yellow fever, of which 847 are under investigation, 93 were discarded and 230 were confirmed, being in the states of Minas Gerais (201), Espírito Santo (25) and São Paulo (4). Of the total number of cases reported, 186 died, 104 of which remained in the investigation, 79 deaths were confirmed and 3 were discarded. The case fatality rate among confirmed cases was 34.3%. For YF there is no specific treatment, however, vaccination is effective being the only and best way of prevention. Precisely because of this factor and others involved the diagnosis of YF is not made in the health system except by a relevant suspicion. The problem is that in many cases viruses go unnoticed in cases of Dengue virus infection because of cross reactivity between members of the genus Flavívirus or because of non-specific symptoms. The present study analyzed 118 samples that were screened for suspected Dengue Virus infections (VDEN) for the year 2011 to 2013, but discarded for this virus because they gave negative results to the viral agent through serological and molecular tests in the municipality of Goiânia, Goiás. Samples were sent to the Virology Laboratory of the Federal University of Goiás Regional Jataí and analyzed by molecular methods such as RT-PCR and Nested-PCR followed by verification of the amplicon by agarose gel electrophoresis. Among the 118 negative samples for the DENV virus, three of the samples were positive for the Yellow Fever Virus (YVF) according to the production of amplicons of 253 bp of the NS5 region and confirmation of the identity of the amplicon by nucleotide sequencing. The sequences obtained were submitted to BLAST for identity confirmation. The translated sequence was analyzed by MEGA software version 7.0. For phylogenetic analysis, the best model was previously determined and then the tree was constructed with 53 sequences of all Yellow Fever viruses present in databases for a comparative analysis. The sequences found were compared to sequences from the VFA recorded in the Genbank database and were identified as referring to a portion of the NS5 nonstructural protein, position 216 to 296 of this protein, conferring 81 amino acids. The representative tree demonstrated that the sequences submitted were directly related to Senegal taxa. The robustness of the phylogenetic method was by Bootstrap 2000 replicates using the best JTT + G model, Maximum Likelihood. The Tajima test applied yielded a value of D = 1.159570, thus demonstrating that there was no population expansion of the taxa analyzed, considering that they have a significant degree of conservation during evolution. From the results obtained in the study, it can be affirmed that there was already an YFV circulation in the year 2013, at least of patients seen in the central region of Brazil, even before the last outbreak in 2017. / O Brasil é o maior celeiro de arbovírus do mundo e apresenta a maior área endêmica de febre amarela (FA). O Ministério da Saúde notificou, em 2017, 1170 casos suspeitos de febre amarela, sendo que desses 847 estão em investigação, 93 foram descartados e 230 foram confirmados, sendo nos estados de Minas Gerais (201), Espírito Santo (25) e São Paulo (4). Do total de casos notificados, 186 evoluíram para óbito, sendo que 104 óbitos permanecem em investigação, 79 óbitos foram confirmados e 3 foram descartados. A taxa de letalidade entre os casos confirmados foi de 34,3%. Para FA não há tratamento específico, no entanto, a vacinação é eficaz sendo a única e melhor maneira de prevenção. Justamente por esse fator e outros envolvidos o diagnóstico da FA não é feito no sistema de saúde a não ser por uma suspeita relevante. O problema é que em muitos casos os vírus passam despercebidos em casos de infecção pelo vírus Dengue por apresentar reatividade cruzada entre membros do gênero Flavívirus ou por apresentar sintomas inespecíficos. O presente estudo analisou 118 amostras que foram triadas para infecções suspeitas de Vírus da Dengue (VDEN) referentes ao ano de 2011 a 2013, porém descartadas para esta virose por terem dado resultados negativos para o agente viral através de testes sorológicos e moleculares no município de Goiânia, Goiás. As amostras foram encaminhadas para o Laboratório de Virologia da Universidade Federal de Goiás Regional Jataí e analisadas por métodos moleculares, como o de RT-PCR e Nested-PCR seguida da verificação do amplicon por eletroforese em gel de Agarose. Dentre as 118 amostras negativas para os vírus DENV, três das amostras foram positivas para o Vírus da Febre Amarela (VFA) conforme produção de amplicons de 253 pb da região NS5 e confirmação da identidade do amplicon por sequenciamento nucleotídico. As sequências obtidas foram submetidas ao BLAST para confirmação da identidade. A sequência traduzida foi analisada pelo software MEGA versão 7.0. Para análise filogenética foi determinado previamente o melhor modelo e em seguida a árvore foi construída com 53 sequências de todos os vírus da Febre Amarela presentes em bancos de dados para uma análise comparativa. As sequências encontradas foram comparadas com sequências do VFA registradas no banco de dados Genbank e identificouse que se refere a uma porção da proteína não estrutural NS5, posição 216 a 296 desta proteína, conferindo 81 aminoácidos. A árvore representativa demonstrou que as sequências submetidas estavam diretamente relacionadas com táxons do Senegal. A robustez do método filogenético foi por Bootstrap 2000 réplicas utilizando o melhor modelo JTT+G, Maximum Likelihood (Máxima probabilidade). O teste D de Tajima aplicado gerou um valor de D= 1.159570, demonstrando assim que não houve expansão populacional dos táxons analisados, considerando que os mesmos possuem significativo grau de conservação durante a evolução. A partir dos resultados obtidos no estudo, pode-se afirmar que já havia circulação do VFA no ano de 2013, pelo menos de pacientes atendidos na região central do Brasil, antes mesmo do último surto em 2017.

The phylogenetic reconstruction has noted great development in recent decades. The development of computers and device for sequencing biopolymers have been an enormous amount od phylogenetic data from different sources and different types. The scientists are trying to reconstruct a comlet tree of life from these data. The phylogenetic supertree are theoretically this option because a supertree alow a combination of all information gathered so far – in contras to the phylogenetic trees. This thesis present the method of reconstruction supertrees using average konsensus method.

The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.

<div>Model-based clustering, with its flexibility and solid statistical foundations, is an important tool for unsupervised learning, and has numerous applications in a variety of fields. This dissertation focuses on nonparametric Bayesian approaches to model-based clustering under structural restrictions. These are additional constraints on the model that embody prior knowledge, either to regularize the model structure to encourage interpretability and parsimony or to encourage statistical sharing through underlying tree or network structure.</div><div><br></div><div>The first part in the dissertation focuses on the most commonly used model-based clustering models, mixture models. Current approaches typically model the parameters of the mixture components as independent variables, which can lead to overfitting that produces poorly separated clusters, and can also be sensitive to model misspecification. To address this problem, we propose a novel Bayesian mixture model with the structural restriction being that the clusters repel each other.The repulsion is induced by the generalized Matérn type-III repulsive point process. We derive an efficient Markov chain Monte Carlo (MCMC) algorithm for posterior inference, and demonstrate its utility on a number of synthetic and real-world problems. <br></div><div><br></div><div>The second part of the dissertation focuses on clustering populations with a hierarchical dependency structure that can be described by a tree. A classic example of such problems, which is also the focus of our work, is the phylogenetic tree with nodes often representing biological species. The structure of this problem refers to the hierarchical structure of the populations. Clustering of the populations in this problem is equivalent to identify branches in the tree where the populations at the parent and child node have significantly different distributions. We construct a nonparametric Bayesian model based on hierarchical Pitman-Yor and Poisson processes to exploit this, and develop an efficient particle MCMC algorithm to address this problem. We illustrate the efficacy of our proposed approach on both synthetic and real-world problems.</div>

In the Western United States, the Great Basin is a geographic feature that is home to a variety of unique species, including Great Basin bristlecone pine (Pinus longaeva, PILO). P. longaeva is well known for the age of some of the trees, some of which are over 4000 years old. In this study 17 microsatellite markers (simple sequence repeat, SSR) are identified and used to genotype a selection of 480 individuals spread across 24 PILO populations and 60 individuals divided equally between 2 outgroup species, Pinus aristata and Pinus flexilis. One population of PILO, HMW, shows more genetic similarity with P. aristata, and is included with outgroup species in the analysis. The population structure of PILO is examined and found to be weakly related to the geographic distance between populations. The population statistics Fst, Gst, Rst, Dest and an AMOVA analysis suggest that there is a substantial amount of admixture at the individual level, similar to some other species of pines. Phylogenetic trees computed using the neighbor-joining method based on the average population genetic distance and based on individual genetic distance support the population structure results and show further evidence that most of the species variation is concentrated at the individual level, rather than inside of or between species. It is possible that gene flow is still occurring, or that gene flow has occurred recently enough that the separated populations have not yet diverged from each other in a measurable way.

Limnephilidae is a large family within Trichoptera, consisting of 4 subfamilies (Dicosmoecinae, Ecclisomyiinae, Limnephilinae, and Philocascinae), 98 genera, and 1178 species. It is among the most diverse families within Trichoptera. It is also ecologically diverse, occupying more habitats than any other family in the order. There are currently no published generic phylogenies of Limnephilidae based on molecular data. Here we used anchored hybrid enrichment to capture and sequence 922 loci for 57 species taken from what have been considered the full range of genera in the family. We expanded the taxon sampling by adding supplementary species with DNA barcodes, 28S sequences, or containing both from other sources. We present a favored tree from the collected data. We examine the evolutionary patterns associated with larval habitat transitions and highlight instances where our preferred evolutionary tree is incongruent with current limnephilid classification.

這一篇論文是說明矩陣中的元素如果滿足熱帶格雷斯曼就可以將它用樹型圖表示。第二章簡述熱帶數學的基本運算和介紹超曲面，作為熱帶格雷斯曼的先備知識。第三章介紹演化樹，在第二節中用兩種方法重建演化樹，第一種方法UPGMA是要在特定的條件下所建造的演化樹才會正確，第二種方法是利用矩陣中兩個物種間的距離假設的樹型配置圖，解聯立方程組得到各段距離，第三節中先介紹代數幾何中的格雷斯曼再聯結到熱帶幾何中的格雷斯曼。第四章是將第二種方法寫成Python程式，輸入矩陣中的元素，如果滿足熱帶格雷斯曼，就可以顯示它可能的樹型圖以及算出距離。