A associação simbiótica entre a diatomácea cêntrica Chaetoceros coarctatus e o ciliado peritríquio Vorticella oceanica é amplamente conhecida e registrada em diversos estudos, porém nunca havia sido analisada sob o ponto de vista de suas implicações para o movimento destes organismos. A fim de contribuir com novos dados acerca desta associação simbiótica, o presente trabalho analisou a relevância ecológica da simbiose entre Chaetoceros e Vorticella, por meio de um estudo comportamental do deslocamento destes organismos na coluna de água. As associações foram coletadas em águas costeiras de Ubatuba, São Paulo, onde sua ocorrência foi observada em elevada abundância, particularmente durante o verão. Utilizando técnicas de imagem de alta frequência em um sistema óptico tridimensional foi possível descrever os padrões de deslocamento desta associação e avaliar as implicações ecológicas deste comportamento. De acordo com as análises realizadas neste trabalho, pode-se sugerir que o comportamento de deslocamento realizado pela associação Chaetoceros-Vorticella na coluna de água resulta em vantagens tanto para o epibionte quanto para o hospedeiro. Em termos de submesoescala, este estudo sugere que o deslocamento realizado pela associação Chaetoceros-Vorticella pode contribuir para a formação de camadas finas, levando à formação de hotspots de atividade biogeoquímica e interações tróficas no ecossistema pelágico. / The symbiotic association between the centric diatom Chaetoceros coarctatus and the peritrich ciliate Vorticella oceanica is widely known and reported in several studies, but its implications for the movement of these organisms have never been analyzed. In order to contribute with new data about this symbiotic association, the present study investigated the ecological relevance of the Chaetoceros-Vorticella association by recording displacement parameters of these organisms in the water column. The associations were collected in coastal waters of Ubatuba, São Paulo, where their occurrence was observed in high abundance, particularly during the summer. Using high-resolution imaging techniques in a three dimensional optical system it was possible to describe the displacement patterns of this association and to provide initial insights about the ecological implications of this behavior. It is suggested that the displacement behavior performed by the Chaetoceros-Vorticella association in the water column is beneficial for both the epibiont and the host. In terms of submesoscale processes, this study indicates that the displacement carried out by the Chaetoceros-Vorticella association may contribute to the formation of thin layers, leading to the formation of hotspots of biogeochemical activity and trophic interactions in the pelagic ecosystem.

A model for DNA recombination uses 4-valent rigid vertex graphs, called assembly graphs. An assembly graph, similarly to the projection of knots, can be associated with an unsigned Gauss code, or double occurrence word. We define biologically motivated reductions that act on double occurrence words and, in turn, on their associated assembly graphs. For every double occurrence word w there is a sequence of reduction operations that may be applied to w so that what remains is the empty word, [epsilon]. Then the nesting index of a word w, denoted by NI(w), is defined to to be the least number of reduction operations necessary to reduce w to [epsilon]. The nesting index is the first property of assembly graphs that we study. We use chord diagrams as tools in our study of the nesting index. We observe two double occurrence words that correspond to the same circle graph, but that have arbitrarily large differences in nesting index values. In 2012, Buck et al. considered the cellular embeddings of assembly graphs into orientable surfaces. The genus range of an assembly graph [Gamma], denoted gr([Gamma]), was defined to be the set of integers g where g is the genus of an orientable surface F into which [Gamma] cellularly embeds. The genus range is the second property of assembly graphs that we study. We generalize the notion of the genus range to that of the genus spectrum, where for each g [isin] gr([Gamma]) we consider the number of orientable surfaces F obtained from [Gamma] by a special construction, called a ribbon graph construction, that have genus g. By considering this more general notion we gain a better understanding of the genus range property. Lastly, we show how one can obtain the genus spectrum of a double occurrence word from the genus spectrums of its irreducible parts, i.e., its double occurrence subwords. In the final chapter we consider constructions of double occurrence words that recognize certain values for nesting index and genus range. In general, we find that for arbitrary values of nesting index [ge] 2 and genus range, there is a double occurrence word that recognizes those values.

Honors Project--Smith College, Northampton, Mass., 2010. / Includes bibliographical references (p. 18-21, 54-60).

Made available in DSpace on 2016-06-02T19:32:00Z (GMT). No. of bitstreams: 1 4173.pdf: 1140916 bytes, checksum: 20dfe79f655af716f14bb7ff0f256252 (MD5) Previous issue date: 2012-02-13 / Universidade Federal de Minas Gerais / Planktonic bacteria play important role in the organic matter decomposition, nutrient cycling and as food for organisms of higher trophic levels such as flagellates and ciliates, thus representing fundamental components in planktonic food webs. This study analyzed the microbial community structure and evaluated the importance of heterotrophic nanoflagellates (HNF) and ciliates bacterivory in a subtropical environment predominantly mesotrophic (Lobo-Broa reservoir, Brazil) by the quantification of their ingestion rates during one year period. The in situ experiments using fluorescently labelled bacteria (FLB) were conducted on the surface of two sampling points that have different trophic degrees. In parallel, physical, chemical and biological water variables were also evaluated. The ciliates showed a higher specific ingestion rate of bacteria (3,3 x 103 bact ind-1 h-1) than HNF (79,7 bact ind-1 h-1) due to differences in size and food acquisition among the two protozoans. The ingestion rates for both ciliates and HNF were always higher in the point 2 (P2) probably due to the higher water temperatures, which accelerate the protozoans metabolism, and higher bacterial densities. Concerning total protozoan bacterivory, the HNF populations had the greatest grazing impact (60%) on the reservoir bacterial community, especially the HNF smaller than 5 μm. The data showed that HNF grazing, in addition to regulation the bacteria abundance, probably also induced changes in the bacterial community structure, such as increasing bacterial filaments numbers and size. The ciliates contributed significantly to the bacterivory, especially in P2, where high densities and ingestion rates were verified. The main ciliate consumers of bacteria were from Spirotrichea, Peritrichia, Haptoria and Scuticociliatia groups. The bottom-up control was more important in the dry season and the top-down control was more important in the rainy one. Thus, in an annual basis, the resource availability and protozoan predation are equally important to the bacterial abundance regulation in the Lobo reservoir. / Bactérias planctônicas desempenham importante papel na decomposição da matéria orgânica, na reciclagem de nutrientes e como alimento para organismos de níveis tróficos superiores tais como flagelados e ciliados, representando, assim, componentes fundamentais nas teias alimentares. Este estudo analisou a estrutura da comunidade microbiana e avaliou a importância da bacterivoria por nanoflagelados heterotróficos (NFH) e ciliados em um ambiente subtropical predominantemente mesotrófico (reservatório do Lobo-Broa, Brasil) pela quantificação de suas taxas de ingestão durante o período de um ano. Os experimentos in situ utilizando bactérias marcadas fluorescentemente (FLB) foram realizados na superfície de dois pontos de coleta que apresentam graus de trofia diferentes. Em paralelo foram avaliadas variáveis físicas, químicas e biológicas da água. Os ciliados apresentaram taxa de ingestão individual de bactérias maior (3,3 x 103 bact ind-1 h-1) do que a dos NFH (79,7 bact ind-1 h-1) devido às diferenças de tamanho e forma de obtenção de alimento entre os dois protozoários. As taxas de ingestão, tanto para os ciliados quanto para os NHF, foram sempre maiores no ponto 2 (P2) devido provavelmente as maiores temperaturas da água, que aceleram o metabolismo dos protozoários, e as maiores densidades de bactérias. Em relação à bacterivoria total por protozoários, as populações de NFH causaram maior impacto de predação (60%) sobre a comunidade bacteriana do reservatório, principalmente os NFH menores que 5μm. Os dados indicaram que a predação por NFH, além de regular a abundância de bactérias, provavelmente também induziu modificações na estrutura da comunidade bacteriana, como o aumento do tamanho e da quantidade de filamentos bacterianos. Os ciliados contribuíram significativamente para a bacterivoria, principalmente no P2, onde apresentaram altas densidades e taxas de ingestão. Os principais grupos de ciliados consumidores de bactérias foram os Spirotrichea, Haptoria, Peritrichia e Scuticociliatia. O controle bottom-up teve maior importância no período seco e o controle top-down maior importância no período chuvoso. Assim, em uma base anual, a disponibilidade de recursos e a predação são igualmente importantes na regulação da abundância bacteriana no reservatório do Lobo.

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No. of bitstreams: 1 robertojuniopedrosodias.pdf: 16324224 bytes, checksum: d89ac49f5783a9ad6211a6e7c47c0824 (MD5) Previous issue date: 2007-02-26 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / No presente trabalho, foram estudados os aspectos da taxonomia e morfologia dos protistas ciliados encontrados no córrego São Pedro (Juiz de Fora, MG), bem como o potencial destes microorganismos como indicadores da qualidade da água e ainda os aspectos ecológicos das relações epibióticas entre os ciliados e alguns macroinvertabrados bentônicos. A presente dissertação está dividida em sete capítulos. No capítulo 1, foi realizado o inventário dos ciliados encontrados em cinco estações amostrais do córrego, durante um ano de estudo, e foi observada a sucessão destes protistas em laboratório. Foram identificadas 42 espécies de ciliados e caracterizou-se morfologicamente Apoamphisiella sp. nov. (Spirotrichea, Amphisiellidae). No capítulo 2, foi descrito um doublet do tipo imagem espelhada em Gastrostyla setifera (Spirotrichea, Oxytrichidae), obtida de amostras de água e sedimento de uma estação amostral do córrego São Pedro. O capítulo 3 registra a presença de Neobursaridium gigas (Oligohymenophorea, Neobursaridiidae) no córrego e apresenta uma revisão dos aspectos morfológicos, ecológicos e da distribuição geográfica deste ciliado. No capítulo 4, verificou-se a influência da poluição orgânica sobre a composição e a distribuição da taxocenose de protistas ciliados ao longo do córrego, com o objetivo de avaliar a qualidade da água deste sistema lótico. Durante o estudo de um ano, em cinco estações amostrais ao longo do córrego, foram encontradas 39 espécies de protistas ciliados, das quais 32 estão incluídas no sistema sapróbio e são consideradas bioindicadoras. A composição e a distribuição da taxocenose de protistas ciliados variaram espacial e temporalmente. O índice sapróbio e o índice de valência sapróbia foram utilizados para avaliar a qualidade da água das cinco estações amostrais e demonstraram o alto grau de poluição das estações 4 e 5. Os dados obtidos confirmam que, em águas correntes, a poluição orgânica parece ser um fator determinante, capaz de influenciar a composição, a distribuição e a estrutura trófica da taxocenose de protozoários ciliados. Os capítulos seguintes versam sobre as associações epibióticas dos protistas ciliados com moluscos, oligoquetas e larvas de insetos. No capítulo 5, foram registradas sete espécies de ciliados sobre as conchas de Pomacea figulina, sendo seis pertencentes à subclasse Peritrichia: Carchesium polypinum, Vorticella microstoma, Vorticella campanula, Epistylis plicatilis, Epistylis sp., Opercullaria sp. e uma pertencente à subclasse Suctoria: Hypophrya fasciculata. Os resultados são discutidos em termos das vantagens e desvantagens desta relação para os protistas ciliados e dos aspectos ecológicos envolvidos nesta associação. No capítulo 6, foram investigados o sítio de localização e o padrão de distribuição espacial e temporal de protistas ciliados peritríquios do gênero Rhabdostyla colonizando oligoquetas límnicos tubificídeos da espécie Limnodrilus hoffmeisteri (Oligochaeta, Tubificidae) nas cinco estações amostrais do córrego, ao longo de 11 meses de coleta. O padrão de ocorrência dos epibiontes sobre os oligoquetas apresentou heterogeneidade espacial e temporal. Os resultados são discutidos em termos das possíveis causas da localização dos ciliados preferencialmente na região posterior dos oligoquetas e dos fatores relacionados ao padrão de distribuição espacial e temporal heterogêneo. E finalmente, o capítulo 7 relata a ocorrência de Rhabdostyla chironomi (Ciliophora, Peritrichia) sobre larvas de Chironomus decorus (Diptera, Chironomidae) no córrego e reporta, ainda, os fatores envolvidos na localização dos ciliados sobre os túbulos abdominais dos hospedeiros e a possível utilização desta relação como indicadora da qualidade da água. / In the present study, both taxonomy and morphology aspects of the ciliate protists found in São Pedro stream (Juiz de Fora-MG), as well as their potential as water quality indicators were studied together with the ecological aspects of the epibiotic relation between the ciliate and some benthic macroinvertebrates. The present dissertation is divided into seven chapters. In chapter 1, the survey of ciliate protists was obtained from samples of water and sediment from the stream, during a hole year, and the succession of these protists was observed in laboratory. Forty-two ciliate species were identified and Apoamphisiella sp. n. (Spirotrichea, Amphisiellidae) was morfologically characterized. In chapter 2, mirror-image doublet was described in Gastrostyla setifera (Spirotrichea, Oxytrichidae), obtained from samples of water and sediment at the São Pedro stream. The Chapter 3 registers the presence of Neobursaridium gigas Balech, 1941 (Oligohymenophorea, Neobursaridiidae) in the stream and presents a revision of the morphological aspects of this ciliate, as well as its ecological and geographical distribution. In chapter 4, the influence of the organic pollution on both the composition and the distribution of the taxocenose of ciliate protists along the stream had the aim of evaluating the water quality of this lotic system. During the one year study, 39 ciliate protist species were found, 32 of which were included in the saprobic system and their potencial as indicators are considered. The composition and the distribution of the taxocenose of ciliate protist varied both spatial and seasonally. The saprobic index and the valency methods were used to evaluate the water quality at the five stations and they demonstrated the high degree of pollution on stations 4 and 5. Our results confirm that the organic load in watercourses may be a dominating factor capable of influencing the composition, distribution and trophic structure of the taxocenose of ciliate protist. The following chapters consider the epibiotic ciliate protist associations to mollusks, oligochates and insect larvae. In chapter 5, seven ciliate species were registered on the shells of Pomacea figulina, six of which belonging to the subclass Peritrichia: Carchesium polypinum, Vorticella microstoma, Vorticella campanula, Epistylis plicatilis, Epistylis sp., Opercullaria sp. and one belonging to the subclass Suctoria: Hypophrya fasciculata. Results are discussed in terms of the advantages and disadvantages of this relationship from the ciliate protist point of view, together with the ecological aspects involved in this association. In chapter 6, location ranch and both spatial and temporal distribution patterns of Rhabdostyla peritrichids were found colonizing limnic oligochaetes Tubificidae of the species Limnodrilus hoffmeisteri in the five amostral stations, during 11 months of collection. The occurrence pattern of the epibionts on the oligochaetes was spatial and seasonally heterogeneous. Results are discussed in terms of the possible causes for the site preference of the ciliates in the posterior region of the oligochaetes and factors related to the heterogeneous pattern of space and temporal distribution. Finally, chapter 7 registers the occurrence of Rhabdostyla chironomi (Ciliophora, Peritrichia) on Chironomus decorus larvae (Diptera, Chironomidae) in the stream and still it moderates the factors involved in the location of the ciliates on the ventral tubules of its hosts and the possible usage of this relationship as indicative of the water quality.

Patterns, sequences of variables, have traditionally only been studied when morphic images of them appear as factors in words. In this thesis, we initiate a study of patterns in words that appear as subwords of words. We say that a pattern appears in a word if each pattern variable can be morphically mapped to a factor in the word. To gain insight into the complexity of, and similarities between, words, we define pattern indices and distances between two words relative a given set of patterns. The distance is defined as the minimum number of pattern insertions and/or removals that transform one word into another. The pattern index is defined as the minimum number of pattern removals that transform a given word into the empty word. We initially consider pattern distances between arbitrary words. We conjecture that the word distance is computable relative the pattern αα and prove a lemma in this direction. Motivated by patterns detected in certain scrambled ciliate genomes, we focus on double occurrence words (words where every symbol appears twice) and consider recursive patterns, a generalization of the notion of a pattern which includes new types of words. We show that in double occurrence words the distance relative so-called complete sets of recursive patterns is computable. In particular, the pattern distance relative patterns αα (repeat words) and ααR (return words) is computable for double occurrence words. We conclude by applying pattern indices and word distances towards the analysis of highly scrambled genes in O. trifallax and discover a common pattern.

Au cours de son cycle sexuel, le cilié Paramecium tetraurelia procède à de massifs réarrangements programmés de son génome (RPG). Ils consistent, entre autres choses, en l’excision de 45 000 séquences précisément délimitées, appelées IES (Internal Eliminated Sequences). La transposase domestiquée Piggymac (Pgm) introduit les cassures double-brin (CDB) à l’extrémité des IES. La réparation très précise de ces dommages est réalisée par la voie de réparation des extrémités non-homologues (NHEJ). Un des acteurs de cette voie est l’hétérodimère Ku70/Ku80. Suite à des duplications globales du génome, la paramécie possède trois gènes KU80, Un seul de ces gènes est induit lors des RPG (KU80c) et une expérience d’ARN interférence (ARNi) contre KU80c montre une complète inhibition de l’introduction des CDB. De plus, des expériences de Co-IP en système hétérologue montrent que Ku70/Ku80c interagit avec Pgm. Ces résultats prouvent le rôle essentiel de Ku dans l’introduction des CDB lors des RPG et soulèvent la question du mécanisme impliqué. Au cours de ma thèse j’ai caractérisé le couplage entre Ku et Pgm en analysant des expériences d’immunofluorescence avec ou sans pré-extraction, permettant de déterminer les interdépendances de ces protéines pour leur localisation et pour leur stabilité nucléaire. Ces approches ont permis de démontrer que Pgm requiert la présence de Ku pour être stablement localisé dans les noyaux lors des RPG. Ku80c partage 74% de sa séquence protéique avec Ku80a. Des expériences de complémentations fonctionnelles surexprimant Ku80a lors des RPG ont montré que Ku80a n’est pas capable ni de se localiser stablement dans les noyaux ni de participer à la stabilisation nucléaire de Pgm. De plus, les RPG sont inhibés. Ces résultats montrent que Ku80c s’est spécialisé dans le couplage avec Pgm pour l’introduction des CDB lors des RPG. L’utilisation de protéines chimériques a permis de déterminer que la spécialisation de Ku80c est portée par son domaine N-terminal ∝-β. / During its sexual cycle, the ciliate Paramecium tetraurelia undergoes massive Programmed Genome Rearrangements (PGR). They consist, among others, in excision of 45,000 precisely delimited sequences, called IES (Internal Eliminated Sequences). A domesticated transposase, PiggyMac (Pgm), introduces double-strand DNA breaks (DSB) at IES ends. The Non Homologous End Joining pathway (NHEJ) handles highly precise repair of DSB. One of the actors of this pathway is the heterodimer Ku70/Ku80. In P. tetraurelia, the KU80 gene is present in three paralogous copies. Only KU80c is specifically expressed during PGR and RNA interferences against KU80c showed a complete inhibition of DNA cleavage. Furthermore, a Co-IP experiment in a heterologous system showed that both Ku70/Ku80c interact with Pgm. These results provide evidence that Ku is an essential partner of Pgm for DSB introduction; raising the question of the activating mechanism involved. During my PhD, I characterized the coupling between Ku and Pgm by analyzing immunofluorescence experiments, with or without pre-extraction, allowing the determination of inter-dependencies between those proteins for their nuclear localization and stability. Those methods demonstrated that Pgm requires the presence of Ku for a stable nuclear localization during the PGR. Ku80c shares 74% of the protein sequence with Ku80a. Functional complementation assays overexpressing Ku80a during the PGR showed that Ku80a is not capable to stably localize in nuclei nor to participate in Pgm nuclear stability. Furthermore, PGR are inhibited. Those results show that Ku80c has specialized for the DSB introduction during PGR. The use of chimeric proteins allowed to determine that Ku80c specialization was carried out by its N terminal domain.

A ciliate is a phylum of protozoa that has two types of nuclei, macronuclei and micronuclei. There may be more than one of each type of nucleus in the organism [1]. The macronucleus is the structure where protein synthesis and cell metabolism occur [1]. The micronucleus stores genetic information and is mobilized during a sexual reproduction process called conjugation [1]. The somatic macronucleus (MAC) is developed from the germ-line micronucleus (MIC) through genome rearrangement during a sexual reproduction process called conjugation [6, 8]. Segments of the MIC that form the MAC during conjugation are called macronuclear destined sequences (MDSs) [8]. During sequencing each MDS is given coordinates where the MDS sequences begin and end in the MIC. The orientation of a MDS in the MIC can be taken to be positive or negative. If the direction of the MDS in the MIC agrees with the direction in the MAC then the orientation is positive otherwise it is a negative orientation. In this thesis we analyze various aspects of the gene assembly during the rearrangment process of the ciliate Oxytricha trifallax that were recently sequenced [15]. Some of the properties analyzed include overlapping MDSs, orientation, MDSs starting and ending position in the MIC and the gaps of overlapping MDS pairs. A gap of an overlapping MDS pair is the order difference of two MDSs for a particular MAC contig that overlap in the MIC contig. We use 120 MAC contigs from [15] that have overlaps among their own MDSs. These 120 MAC contigs make up the data set we call D4. We explore the patterns of overlapping MDSs in the MIC in D4. To quantify such patterns, we associate a vector V (An) to each MAC contig An, where V (An) = (v1(An), v2(An), v3(An)) is a vector in R3. The first entry is the number of overlapping MDS pairs divided by the number of MDSs. The second entry is the sum of gaps of overlapping MDS pairs divided by the sum of all possible gaps. The final entry is the total number of overlapping base pairs divided by the total length of the MAC contig. We computed the distance matrixM = (dij) where dij is the Euclidean distance between V (Ai) and V (Aj). The MAC contig vectors and M were computed using Python. To analyze D4 we applied Topological Data Analysis (TDA). TDA uses topological constructs to assess shapes in data [3, 12]. From the data entries of the distance matrix M = (dij) we applied a Vietoris-Rips filtration to generate the barcodes of the persistent homology in dimensions 0, 1 and 2. The persistence barcode of 0-dimensional homology illustrates clusters of the data while the 1-dimensional homology represents non-trivial loops in the simplicial complex [3, 13]. The application of TDA on the ciliate Oxytricha trifallax identified ten MAC contig clusters at epsilon= 0.1 in D4 and several loops that were persistent for two or three epsilon values. Other TDA methods can be applied to the Vietoris-Rips filtration to further identify which MAC contigs appear in each cluster.

Ciliates are also of the most extensively studied and diverse groups of unicellular eukaryotes, and yet, their anaerobic representatives have been largely neglected; in part due to culturing difficulties. Although all main ciliate lineages contain anaerobes, their diversity and evolution of anaerobiosis are especially poorly understood and just starting to gain attention. In fact, Ciliophora is an excellent model group to study adaptations to life in anoxia, since it, apart from the aerobic majority, includes free-living and endobiotic obligately anaerobic lineages, facultative anaerobes, microaerophiles, and microaerotolerant species. The diversity of Metopida, the free-living order of obligately anaerobic class Armophorea, has been partially revised and significantly broadened during the past years, including numerous redescriptions using modern methods, as well as the description of novel families Tropidoatractidae and Apometopidae, several genera, and multiple species. Oxygen plays a crucial role in ATP production via oxidative phosphorylation that takes place in the mitochondrion in most known eukaryotes. Nevertheless, anaerobic ciliates, among many other eukaryotes that have adapted to low oxygen concentrations or even its absence, have modified their mitochondria and energetic metabolism to...

The IAC group (Armophorea: Metopida: Metopidae) includes both free-living and endosymbiotic anaerobic ciliates. The thesis focuses on the diversity of free-living representatives, the so-called metopids. First, the position of the IAC group in the system is explained and the history of the taxonomy of the core species Metopus is presented. Then the taxonomic confusion surrounding this group is depicted. For diversity research more than 30 isolates from the IAC group were obtained from various anaerobic habitats and localities. The phylogenetic analysis of the IAC group is based on the 18S rRNA gene and shows a rich diversity of new lineages. In addition to the IAC group, another newly-found lineage of metopids is presented. Light microscopy, including staining techniques and scanning electron microscopy, was used to establish morphological characteristics. In the work, a detailed description of one selected lineage at the species level is performed. In the discussion, the results are interpreted, the limitations of the selected methods are pointed out and the chaotic taxonomic and phylogenetic situation of the IAC group species described. Suggestions for the improvement of future taxonomic practices in the description of metopids are offered.