Thesis (Ph. D.)--University of Wisconsin--Madison, 1924. / Caption title. Reprinted from Ecology, v. 6, October, 1925. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references.

No description available.

Thesis advisor: Marc-Jan Gubbels / Toxoplasma gondii – an obligate intracellular parasite – has a complex multistep mechanism for host cell invasion with a pivotal role played by calcium signaling. However, the coordination amongst the players in all the key steps of this signaling pathway, essential for parasitic life cycle of Toxoplasma, is still not entirely known. Given the evolutionary relationship between ciliates and apicomplexans, this work evaluates the functions of three orthologous proteins in cell signaling of alveolates leading to calcium-dependent exocytosis of vesicles such as trichocysts and micronemes. The proteins investigated are calmodulin (CaM) which is a calcium sensor, calcineurin (CN), a protein phosphatase, and parafusin-related protein 1 (PRP1), the Toxoplasma ortholog of ciliate protein parafusin. In the ciliate, CaM activates CN upon rise in intracellular calcium. Activated CN then leads to the dephosphorylation of the secretory vesicle scaffolding protein called parafusin. Parafusin dephosphorylation dissociates it from the calcium-dependent secretory vesicles, which then discharge their contents. As expected upon conditional depletion, we found CaM to be essential for Toxoplasma tachyzoites and CN to be significant for the lytic cycle. Surprisingly, the microneme secretion remained normal in the CN depleted parasites, although there was significant reduction in the attachment of the parasite to the host cell. We also found that PRP1 is dispensable for Toxoplasma lytic cycle, despite its absence affecting the microneme secretion induced by the calcium ionophore, A23187. However the secretion defect is not uniform and remains comparable to the wild type when it is induced using other pharmacological agents like ethanol, zaprinast and propranolol. Therefore despite phylogenetic conservation of the three proteins in alveolates, this work demonstrates their involvement in distinct functional aspects in Toxoplasma compared to other ciliates. Alongside the limited understanding of the molecular mechanism, our knowledge about the cellular sensors in Toxoplasma is also scarce. Our laboratory has previously identified a double C2 (DOC2) domain containing protein called TgDOC2 and demonstrated its role in overall microneme secretion. However, TgDOC2 does not regulate the dosed microneme release associated with varied steps of the egress-invasion trajectory. In general, DOC2 domain containing proteins work in coordination with each other to execute their cellular function, mostly in calcium-dependent manner. We therefore, wanted to expand our knowledge of this domain containing proteins in the parasite. In this work, we investigated a conserved apicomplexan protein called FER2 containing multiple DOC2 domains. Conditional depletion of FER2 appeared detrimental due to significant loss of invasion and attachment of the parasites. FER2 depleted parasites have normal microneme secretion, which is currently the only known calcium-dependent secretory organelle in Toxoplasma, but abrogated the release of rhoptries, the second secretory organelle to be released during invasion. Altogether this work extends the importance of calcium signaling in Toxoplasma gondii and brings into light the novel aspects of some parasitic proteins which are significant in reconstructing our understanding of the signaling pathway in this parasite. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

The construction process of the functional macronucleus in certain types of ciliates is known as the ciliate gene assembly process. It consists of a massive amount of DNA excision from the micronucleus and the rearrangement of the rest of the DNA sequences (in the case of stichotrichous ciliates). While several computational models have tried to represent certain parts of the gene assembly process, the real process remains not completely understood. In this research, a new formal model called the Computational 2JLP model is introduced based on the recent biological 2JLP model. For justifying the formal model, a simulation is created and tested with real data. Several parameters are introduced in the model that are used to test ambiguities or edge cases of the biological model. Parameters are systematically tested from the simulation to try to find their optimal values. Interestingly, a negative correlation is found between a parameter (which is used to filter out scnRNAs that are similar to IES specific sequences from the macronucleus) and the outcome of the simulation. It indicates that if a scnRNA consists of both an MDS and IES, then from the perspective of maximizing the outcome of the simulation, it is desirable to filter out this scnRNA. The simulator successfully performs the gene assembly process whether the inputs are scrambled or unscrambled DNA sequences. It is desirable for this model to serve as a foundation for future computational and mathematical study, and to help inform and refine the biological model.

Microorganisms swimming in their natural habitat interact with debris and boundaries, which can modify their swimming characteristics. However, the boundary effect on swimming microorganisms have not been completely understood yet, and is one of most active areas of research. Amongst microorganisms, unicellular ciliates are the fastest swimmers and also respond to a variety of external cues. We choose Paramecium multimicronucleatum as a model system to understand the locomotion of ciliates. First, we explore the effects of boundaries on swimming modes of Paramecium multimicronu- cleatum by introducing them in 2D films and 1D channels. The geometric confinements cause the Paramecia to transition between: a directed, a meandering and a self-bending behaviors. During the self-bending mode the cell body exerts forces on the walls; which is quantified by using a beam bending analogy and measuring the elasticity of the cell body. The first inves- tigation reveals the complicated swimming patterns of Paramecium caused by boundaries. In the second study we investigate the directed swimming of Paramecium in cylindrical capillaries, which mimics the swimming of ciliates in the pores of soil. A finite-sized cell lo- comoting in extreme confinements creates a pressure gradient across its ends. By developing a modified envelop model incorporating the confinements and pressure gradient effects, we are able to predict the swimming speed of the organisms in confined channels. Finally we study how Paramecium can swim and feed efficiently by stirring the fluid around its body. We experimentally employ "-Particle Image Velocimetry to characterize flows around the freely swimming Parameicum and numerically use Boundary Element Method to quantify the effect of body shapes on the swimming and feeding process. Results show that the body shape of Paramecium (slender anterior and bulky posterior) is hydrodynamically optimized to swim as well as feed efficiently. The dissertation makes significant advances in both experimentally characterizing and the- oretically understanding the flow field and locomotion patterns of ciliates near solid bound- aries. / Ph. D.

Submitted by Caroline Falcao (caroline.rfalcao@ufpe.br) on 2017-05-25T17:27:38Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Dissertacao Alejandro.pdf: 2660688 bytes, checksum: 955f967f57cbed1266ae0f604a24c884 (MD5) / Made available in DSpace on 2017-05-25T17:27:38Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Dissertacao Alejandro.pdf: 2660688 bytes, checksum: 955f967f57cbed1266ae0f604a24c884 (MD5) Previous issue date: 2014-02-06 / A presente dissertação de mestrado é composta por três capítulos, cada um constituindo um artigo a ser submetido para publicação. O primeiro deles consiste de uma revisão do conhecimento que se tem a respeito dos ciliados tintinídeos de águas nordestinas brasileiras. Para isso se consultou trabalhos publicados ao longo das quatro ultimas décadas, e que possuíam alguma relação com os tintinídeos, mesmo não tendo esses ciliados como principal objeto de estudo. Assim foram levantadas todas as espécies de tintinídeos que já possuem registro de ocorrência publicado para a região Nordeste do Brasil. Além das fontes bibliográficas utilizadas, também foram realizadas análises de amostras coletadas em algumas regiões costeiras dos Estados da Paraíba, Pernambuco e Bahia, aumentando a lista de espécies registradas para a região. A partir da consulta dos trabalhos publicados, um total de 91 espécies de tintinídeos foi registrado em águas nordestinas do Brasil. Com a análise das amostras esse número aumentou para 111 espécies, pertencentes a 32 gêneros e 16 famílias. Neste primeiro capítulo é apresentada uma lista das espécies registradas, identificando as regiões nas quais elas ocorrem e os trabalhos utilizados como fonte bibliográfica. O segundo capítulo consiste de um trabalho desenvolvido a fim de se estudar a estrutura da comunidade dos tintinídeos em três áreas recifais na região de Abrolhos, no Estado da Bahia. Em cada área foram delimitados dois pontos de coleta, um sobre os recifes e outro a 1 km de distancia dos recifes. As coletas foram realizadas a cada 6 horas, ao longo de um período de 24 horas, totalizando 8 amostras por área e 3 dias de amostragens (um para cada área). Os tintinídeos foram coletados através de arrastos subsuperficiais de rede de plâncton (20 m de abertura de malha, 30 cm de diâmetro de boca e 2 m de comprimento). Três hipóteses foram testadas: i) a estrutura da comunidade dos tintinídeos varia entre os períodos diurno/noturno; ii) a estrutura da comunidade dos tintinídeos varia em uma escala espacial curta (diferentes pontos em uma mesma área recifal); e iii) a estrutura varia em uma escala espacial de grande extensão (entre as diferentes áreas recifais amostradas). Um total de 24 espécies foi encontrado, sendo todas de distribuição nerítica, típica de águas quentes e cosmopolitas. Apenas a hipótese relacionada com a variabilidade em uma maior escala espacial não foi rejeitada. Existem diferenças significativas entre essas áreas (ANOVA p = 0,017). A existência de duas comunidades distintas de tintinídeos ficou bem evidenciada através de análises de agrupamentos realizadas com amostras e espécies. Existe uma comunidade típica das áreas mais próximas à costa, composta basicamente por espécies de lorica aglutinante e de distribuição nerítica, e outra típica das áreas mais “oceânicas”, formadas basicamente por espécies de lorica hialina e de distribuição cosmopolita e de águas quentes. O grande fator influenciando a comunidade dos tintinídeos na região de Abrolhos é a distância em relação à costa. No terceiro capítulo se estudou a estrutura da comunidade dos tintinídeos na região de Tamandaré, no Estado de Pernambuco. As coletas foram realizadas em uma estação, a cada maré vazante, ao longo de um período de 26 dias. Dados de temperatura, salinidade, teor de clorofila-a e quantidade de material particulado em suspensão foram coletados. Os tintinídeos foram coletados através de arrastos horizontais subsuperficiais de rede de plâncton (20 m de malha). Com o desenvolvimento do estudo tentou se responder as seguintes perguntas: i) existe variação na comunidade dos tintinídeos em um curto intervalo de tempo (período diurno/noturno) na região de Tamandaré? ii) existe algum tipo de influência do ciclo lunar sobre a comunidade dos tintinídeos nessa região? iii) qual fator hidrológico possui mais influência sobre a comunidade desses ciliados? Um total de 20 espécies de tintinídeos foi identificado, sendo a maioria de distribuição nerítica e do gênero Tintinnopsis. A estrutura da comunidade dos tintinídeos não variou em uma escala de tempo curta. Foram detectadas diferenças significativas entre as amostras das diferentes fases do ciclo lunar (Kruskal-Wallis p = 0,005), com as espécies respondendo de diferentes formas. Tintinnopsis nana, T. schotti e T.nucula apresentaram as variações mais pronunciadas. O material particulado em suspensão foi o parâmetro hidrológico de maior influência sobre a comunidade dos tintinídeos, tendo sido encontrada correlação negativa. Por outro lado, foi encontrada correlação positiva entre o material particulado em suspensão e o teor de clorofila-a presente na água. Contudo, o aumento da clorofila-a está associado a uma resposta de organismos fitoplanctônicos a maior atenuação da luz na água e não a um aumento na produtividade. Dessa forma, existe aumento no teor de clorofila, sem que haja aumento na disponibilidade de alimento para os tintinídeos, podendo chegar a haver diminuição nessa disponibilidade, o que levaria a redução da comunidade desses ciliados. / The following master thesis is composed of three chapters; each one of them is a complete scientific paper which is going to be submitted for publication. The first one consists of a review of the knowledge related to the tintinnid ciliates in Brazilian northeastern waters. We consulted not only papers directly focused on the tintinnid ciliates, but also papers related to the microzooplankton, but that mentioned the tintinnids in the results. These papers were published during the last four decades. We assembled all the tintinnid species that had been registered in these papers, as well as worked with samples collected in some coastal regions in the State of Paraíba and Pernambuco, in addition to samples collected in the region of Abrolhos, in the State of Bahia. Through the published papers, we found a total of 91 registered tintinnid species in the northeastern region of Brazil. With the analysis of the samples, this number was raised to 111 species, belonging to 32 genera and 16 families. In this first chapter we present a list of the registered species, providing also the regions where they were found and the papers used as the bibliographical source. The second paper consists of a work developed in order to study the tintinnid community structure in the Abrolhos region, in the State of Bahia. Three reef areas in the Abrolhos region were sampled. In each area, we delimited two sampling points; one located directly above the coral reefs, and the other nearly 1 km away from the reefs. The samplings were performed in each 6 hours, during 24 hours, totalizing 8 samples per area, and three days of field work (one for each area). The tintinnids were collected through subsurface hauls of a plankton net (20 m mesh-size, 30 cm of mouth diameter, and two meters of length). Three hypotheses related to possible variations in the community structure of these ciliates were tested: i) the tintinnid community structure varies in a short temporal scale (between diurnal and nocturnal periods); ii) the community structure varies in a short spatial scale (between different points within a same area); and iii) the community structure varies in a broad spatial scale (between different sampled areas). A total of 24 species was found. All the species was of neritic, warm-water and cosmopolitan distribution. Only the hypothesis related to the variation in a broader spatial scale was not rejected. There are significant differences between the three studied areas (ANOVA p = 0,017). A continent-ocean gradient was highlighted by the clustering of the samples and species. There is a community typical of the areas closer to the coast, which is composed mainly by neritic species of agglutinated loricae, and other community typical of the “more oceanic” areas, which is composed mainly by warm-water and cosmopolitan species of hyaline loricae. The main factor influencing the tintinnid community in the Abrolhos region is the distance from the coast. In the third chapter we studied the tintinnid community structure in the Tamandaré region, Pernambuco State. The samplings were performed each 12 hours in a fixed point during 26 days. Temperature, salinity, chlorophyll-a content and the quantity of particulate material in suspension were evaluated. The tintinnids were collected through horizontal subsurface plankton net (20 m mesh width) hauls. We tried to answer the following questions in the present study: i) Is there any degree of variation in the tintinnid community in a temporal short scale (diurnal and nocturnal periods) in the region of Tamandaré? ii) Does the lunar cycle influence the tintinnid community in some way in this region? iii) Which is the main hydrologic parameter influencing the tintinnid community structure in the Tamandaré region? A total of 20 tintinnid species was identified. Most of them are of neritic distribution, and belongs to the genus Tintinnopsis. No variation in the tintinnid community under a temporal short scale was detected. We found significant differences in the tintinnid community structure in relation to different stages of the lunar cycle (Kruskal-Wallis p = 0,005). The species present different patterns of variation following the lunar cycle. Tintinnopsis nana, T. schotti and T. nucula displayed the most noticeable variations. We found a negative correlation between the tintinnid and the particulate material in suspension; it was the hydrologic parameter with the strongest effect on the tintinnid community. We also found a positive correlation between the particulate material in suspension and the chlorophyll-a content in the water. The increase in the chlorophyll-a content is associated with a response of the phytoplanktonic organisms to the increased light attenuation, and is not related with an increase in production. There is then an increase in chlorophyll-a content, without any increase in the food availability for the tintinnids; a reduction in the food availability is also possible, what could lead to the biomass reduction of the tintinnid community.

Dissertação(mestrado) - Universidade Federal do Rio Grande, Programa de Pós–Graduação em Oceanografia Biológica, Instituto de Oceanografia, 2011 / Submitted by Cristiane Gomides (cristiane_gomides@hotmail.com) on 2013-12-16T03:06:44Z No. of bitstreams: 1 Priscila da Fonseca Teixeira.pdf: 335923 bytes, checksum: 69841da63959745c00a7a0e8b7859194 (MD5) / Approved for entry into archive by Sabrina Andrade (sabrinabeatriz@ibest.com.br) on 2013-12-18T18:10:59Z (GMT) No. of bitstreams: 1 Priscila da Fonseca Teixeira.pdf: 335923 bytes, checksum: 69841da63959745c00a7a0e8b7859194 (MD5) / Made available in DSpace on 2013-12-18T18:10:59Z (GMT). No. of bitstreams: 1 Priscila da Fonseca Teixeira.pdf: 335923 bytes, checksum: 69841da63959745c00a7a0e8b7859194 (MD5) Previous issue date: 2011 / Na aqüicultura, o sistema sem trocas de água é eficiente e sustentável, permite manejar o balanço entre carbono e nitrogênio, e o desenvolvimento de microorganismos que contribuem na boa qualidade da água, alimentação e sobrevivência do organismo alvo do cultivo. No presente estudo, a composição e densidade de fitoplâncton e protozooplâncton em conjunto com variáveis físico-químicas foram avaliados em viveiros de cultivo de camarão Litopenaeus vannamei (Boone) em sistema sem troca de água em dois tratamentos, com e sem a adição de melaço como fertilizante de carbono. As amostras de água foram coletadas por um período de 70 dias (janeiro a abril de 2009) e os tratamentos apresentaram diferença significativa para o teor dos nutrientes fosfato, silicato e clorofila <20 μm. A clorofila foi dominada pela fração <20μm (>80%) nos dois tratamentos e alcançou os maiores valores (~400 μg L-1) no final do experimento. No viveiro com melaço houve um maior crescimento de cianobactérias filamentosas (Pseudoanabaena spp. e Spirulina sp.), de diatomáceas especialmente Pleurosigma sp. e de ciliados, além da presença de Oxyrrhis marina Dujardin e de Anabaena sp.. No viveiro sem melaço os flagelados e dinoflagelados, especialmente Protoperidinium sp. e outros da ordem Peridiniales foram mais freqüentes e abundantes. Em ambos os tratamentos foi observada uma alta densidade de cianobactérias cocóides e de dinoflagelados (Gymnodiniales e Gyrodinium sp.). Apesar de não terem sido encontradas diferenças estatísticas entre os tratamentos, ficaram claras tendências distintas de composição e densidade do fitoplâncton e protozooplâncton entre os viveiros, indicando a influência da adição de melaço. / In aquaculture the zero water exchange system is efficient, sustainable, and allows the management to balance the carbon and nitrogen compounds through the development of microorganisms contributing to good water quality, feeding and survival of the target organism. In this study, the composition and density phytoplankton and protozooplâncton together with physical and chemical variables were evaluated in shrimp ponds (Litopenaeus vannamei Boone) without water exchange in two treatments with and without the addition of molasses as carbon fertilizer. Water samples were collected during 70 days (January- April 2009). The treatments differed significantly in dissolved inorganic phosphate, silicate and chlorophyll <20 μm. Chlorophyll, dominated by the fraction <20 μm (> 80%), reached the highest values (~400 μg L-1) at the end of the experiment in both treatments. In the pond with molasses, the filamentous cyanobacteria (Pseudoanabaena spp., Spirulina sp.), the diatom Pleurosigma sp. and ciliates reached highest density and the dinoflagellate Oxyrrhis marina Dujardin and the cyanobacteria Anabaena sp. were present. In the pond without molasses, flagellates, and dinoflagellates Protoperidinium sp. and other Peridiniales were more frequent and abundant. In both treatments coccoid cyanobacteria and dinoflagellates (Gyrodinium sp. and other Gymnodiniales) were abundant. Although the differences were not statistically significant, the composition and abundance of phytoplankton and protozooplankton differed over time in both treatments, indicating the influence of the molasses addition.

Aquatic microbial food webs are in general size structured. Phytoplankton, which constitute the base of the food web, are grazed by protozoa and mesozooplankton, which in turn are consumed by planktivorous fish. Food web efficiency (FWE) is a measure of how efficiently energy is transported up the food web. FWE is low if the phytoplankton is inedible by the grazers, while FWE is higher if the phytoplankton community is dominated by edible phytoplankton. Recently, the presence of microfungi in aquatic food webs have been suggested to facilitate energy transfer up the food web, via the “mycoloop”. The aim of the study was to set-up a model system of phytoplankton – zooplankton food chains, relevant to the Baltic Sea, and to test FWE in diatom and flagellate-based food webs. Further, I wanted to introduce microfungi in the system and observe their impact on FWE. After many phytoplankton and zooplankton species tests, I decided to perform grazing experiments using one grazer, the ciliate Tetrahymena pyriformis, and two phytoplankton species: a diatom (Skeletonema marinoi) and a flagellate (Rhodomonas baltica). I hypothesized that T. pyriformis would more efficiently feed on flagellates than on diatoms. I performed a grazing experiment where the increase in ciliate abundance was measured, the consumption of the phytoplankton monitored and the FWE estimated. The diatom-based food web led to 14 times higher FWE than the flagellate-based food web. The variation in FWE may be explained by a difference in initial abundances introduced in the experimental treatment, which created unequal grazer:prey ratio between treatments. Further, the swimming behaviour of the flagellate might have reduced the capture efficiency by the ciliate. Microfungi were introduce in an experiment, from a natural seawater sample, but fungal infection was not observed for any of the tested phytoplankton species. Further development is needed to test the effects of microfungi on marine FWE.

No description available.

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.