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1
Bromley, Candice Leigh. "The chemistry of Algoa Bay ascidians." Thesis, Rhodes University, 2016. http://hdl.handle.net/10962/d1020606.
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This thesis investigates the chemistry of 25 ascidian species collected from Algoa Bay, South Africa with a concerted focus on metal accumulation by these ascidians and the possible interaction of these metals with ascidian metabolites. Chapter 2 details the screening techniques employed to establish the presence of nitrogenous metabolites (1H- 15N HMBC), hyper-accumulated metal ions (ICP-MS) and potential metal ion/ ascidian metabolite complexes (LC-ICP-MS/ESI-MS). Unfortunately, exhaustive attempts to detect intact metal ion/ascidian metabolite complexes through the use of liquid chromatography with parallel inductively coupled plasma mass spectrometry/electrospray mass spectrometry (LC-ICPMS/ ESI-MS) were unsuccessful. However, the LC-ICP-MS/ESI-MS data obtained for the crude organic extracts of six of the Algoa Bay ascidian species, Distaplia skoogi, Aplidium monile, Aplidium sp., Didemnum sp., Leptoclindines sp. and Polycitor sp. enabled identification of a number of ten halogenated metabolites, namely the indoles 2.28-2.30, and the tyramine and tyrosine derivatives (2.31-2.33, 2.41, 2.43, 2.44 and 2.46), within the ascidian extracts. This study confirmed that LC-ICP-MS/ESI-MS is a powerful tool for the dereplication of halogenated metabolites in complex mixtures especially where these compounds are present in very small amounts. This study is also the first report of these compounds (eight of which are known) in African ascidians. Compounds 2.32 and 2.46 have not been reported before from a marine source. Compounds 2.28-2.30 and 2.33 were present in sufficient amounts in the respective ascidian extracts to allow their isolation and structure elucidation using standard spectroscopic techniques Chapter 3 explores the ability of ascidians to accumulate a wide range of metal ions at concentrations which are often orders of magnitude higher than those of the surrounding sea water. Inductively coupled plasma mass spectrometry (ICP-MS) was used to determine the total ion concentrations of 24 metals in 25 Algoa Bay ascidian species. To the best of our knowledge this is the largest and most extensive investigation of metal concentrations in a group of different ascidians occurring in the same area. Hypotheisizing that the metal ion concentrations for each ascidian specimen screened may represent a unique fingerprint for each specimen principal component analysis (PCA) was used in an attempt to establish whether there were spatial, temporal or phylogenetic relationships associated with the metal concentration fingerprints of the ascidians that formed part of this study. The PCA results showed that there were no statistically significant relationships between ascidian metal ion concentrations and either the collection year or the collection site of the ascidians. However, species from the family Didemnidae provided the clearest statistical evidence supporting a phylogenetic relationship between these ascidians and their hyperaccumulated metal ion profiles. Furthermore, these results suggested that ascidian species are indeed actively concentrating metal ions from the surrounding sea water and are not simply sinks for passively accumulated metal ions. Interestingly, the concentration of vanadium in the set of ascidians studied did not appear to correlate with any of the other metals accumulated by these ascidians suggesting that there is possibly a unique method employed for the accumulation of vanadium by ascidians. Chapter 4 investigated this possibility further after the nucleosides 4.10, 4.11, 4.13, 4.15, 4.17 and 4.40 were isolated from the vanadium accumulating ascidian Aplidium monile. Studies into the interactions between nucleosides and vanadyl are unfortunately rare and usually qualitative in nature with limited information provided about the stability or structures of the complexes formed. The vanadyl accumulating aplousobranch ascidians e.g. Aplidium monile dominated our study of Algoa Bay ascidians therefore providing us with the rationale to investigate the relatively little studied binding ability and stability of vandyl-nucleoside complexes. Potentiometric studies were conducted to determine the stability constants of complexes formed between the oxovanadium ion vanadyl (VO2+) and the commercially available nucleosides 4.10-4.14. The data afforded by this analysis clearly confirmed the complexity of the vanadyl/nucleoside complexation and suggested that guanosine (4.12) formed the most stable complex with oxovanadium ions. We were also able to establish a third protonation constant for the hydroxyl moiety in 4.12 with a logK 8.87 which has not been previously reported. Finally, Chapter 5 revisited the cytoxicity two Algoa Bay ascidians, Clavelina sp. and Atriolum marinense the extracts from which produced promising bioactivity results in previous studies against oesophageal cancer cells. The HP-20 fractionated extracts of Clavelina sp. and Atriolum marinense proved to be similalrly cytotoxic to breast cancer cells. With the exception for the 100% acetone(aq)fractions the NMR data for both species suggested that most active non polar fractions were dominated by what appeared to be structurally unremarkable fatty acid glycerides and as such were not pursued further. Purification of the 100% acetone(aq)fraction of A. marinense resulted in the isolation of a styrene trimer, 5.1, common to both ascidian extracts. The NMR simulation software WIN-DAISY was employed to confirm the structure of 5.1. Attempts to establish if 5.1 was an isolation artefact or a product of marine pollution were inconclusive
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Parker-Nance, Shirley. "Aplousobranch ascidians (Tunicata: Ascidiacea) from Southern Africa." Thesis, University of Port Elizabeth, 2003. http://hdl.handle.net/10948/311.
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The ascidian (subphylum Tunicata: class Ascidiacea) fauna along the southern African coast constitutes an important component of the sessile benthic reef fauna. Little is known of the species composition, biodiversity and distribution of ascidians on southern African intertidal and subtidal reefs. Past research on the ascidian fauna of South Africa was sporadic and limited, with only about one hundred and seventy species recorded during the last one hundred and twenty years. This is the first taxonomic study undertaken by a South African resident scientist. The study focused on six genera in four families (Euherdmaniidae, Polyclinidae, Pseudodistomidae and Didemnidae) belonging to the class Ascidiacea and suborder Aplousobranchia. Five species new to science, two Polyclinum, two Pseudodistoma and one Polysyncraton species are described. New additional information on the distribution of five species previously known to science, including one recorded for the first time along the South African coast, is presented. A literature review and comparison of the taxonomic important characteristics is made of all species known globally for the six genera. These six genera comprise twelve Euherdmania, fifteen Aplidiopsis, forty Polyclinum thirty-one Pseudodistoma, six Atriolum and sixty-eight Polysyncraton species.
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Davis, Rohan Andrew, and davis_rohan@hotmail com. "Chemical Investigations of Great Barrier Reef Ascidians - Natural Product and Synthetic Studies." Griffith University. School of Science, 2000. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20030102.104858.
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This thesis describes the chemical investigations of several ascidian species collected from the Great Barrier Reef, Queensland, Australia. The thesis is divided into two separate components, Part A focuses on the isolation and structure elucidation of 11 previously undescribed ascidian metabolites. All structures were assigned using a combination of spectroscopic and/or chemical methods. Part B relates to the isolation and chemical conversion of a natural product to a combinatorial template. The natural product template was subsequently used in the generation of a solution-phase combinatorial chemistry library. A further two combinatorial libraries were generated from a synthesised model compound that was related to the natural product template. Part A. Investigation of Aplidium longithorax collected from the Swains Reefs resulted in the isolation of two new para-substituted cyclofarnesylated quinone derived compounds, longithorones J (30) and K (31). The former compound had its absolute stereochemistry determined by the advanced Mosher method. From an Aplidium longithorax collected from Heron Island, two new cyclofarnesylated hydroquinone compounds, longithorols C (46) and D (47) and a novel macrocyclic chromenol, longithorol E (48) were isolated. Longithorol C (46) had its absolute stereochemistry determined by the advanced Mosher method. Chemical investigation of the deep-purple colonial ascidian, Didemnum chartaceum collected from Swains Reefs led to the isolation of five new lamellarin alkaloids, which included the 20-sulfated derivatives of lamellarins B (94), C (95) and L (96), the 8-sulfated derivative of lamellarin G (97) and the non-sulfated compound, lamellarin Z (98). The known lamellarins A (63), B (80), C (64), E (65), G (67), and L (71) plus the triacetate derivatives of lamellarin D (82) and N (83) were also isolated. An aberration in the integration of signals in the 1H NMR spectra of the 20-sulfated derivatives (94-96) led to NMR relaxation studies. T1 values were calculated for all protons in the sulfated lamellarins (94-97) and their corresponding non-sulfated derivatives (80, 64, 71, 67). The protons ortho to the sulfate group in compounds (94-97) had T1 values up to five times larger than the corresponding protons in their non-sulfated derivatives (80, 64, 71, 67). A specimen of Eudistoma anaematum collected from Heron Island was shown to contain a new b-carboline alkaloid, eudistomin V (130), in addition to the two known metabolites, eudistomin H (105) and I (106). Part B. The known natural products, 1,3-diphenethylurea (29), 1,3-dimethylxanthine (30), 1,3-dimethylisoguanine (31) and the salts of tambjamine C (16), E (18) and F (19) were isolated from the ascidian, Sigillina signifera collected in Blue Lagoon, Lizard Island. Base hydrolysis on mixtures of the salts of tambjamine C (16), E (18) and F (19) resulted in the production of 4-methoxy-2,2-bipyrrole-5-carbaldehyde (26). This natural product template (26) was used in the generation of an enamine combinatorial chemistry library (98, 103-111) using solution-phase parallel synthesis. The biaryl compound, 4-(2-thienyl)-1H-pyrrole-2-carbaldehyde (59) was successfully synthesised using Suzuki-Miyaura coupling conditions and subsequently used as a template in the generation of an amine (67, 77, 80-87) and imine (78, 92-95) combinatorial library using solution-phase parallel synthesis.
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Goostrey, Anna. "Aspects of vegetative reproduction and developmental genetics in Diplosoma listerianum (Tunicata, Aplousobranchiata)." Thesis, University of Aberdeen, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367481.
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Hox and ParaHox genes are groups of key developmental transcription factors that are highly conserved throughout the Metazoa. Their order of expression along the body axis of an animal is not only highly conserved between different organisms, but is also collinear to the arrangement of individual genes along the chromosome. Studies of these developmental control genes can give valuable insights into the evolution of body plans. A total of 7 homeobox containing genes (dpl1-dpl7) were isolated form the D. listerianum genome. Four of these were members of the Hox gene family and of the ParaHox gene family. Initial fragments were isolated using the method of degenerate PCR with primers designed from the highly conserved amino acid sequence of the 1st and 3rd helix of the homeodomain. Short fragments limit gene characterisation and as such, regions flanking the degenerate PCR products were isolated, using inverse PCR, 3' and 5' RACE PCR. Phylogenetic relationships of the genes are also examined. Dpl1 exhibited high identities with the arthropod Antennapedia and the vertebrate Hox6 and Hox 7 paralogue groups. Phylogenetic analysis showed dpl1 to be more closely related to the Hox6 than to the Hox7 group genes. Dpl2 shares high identity with members of the Hox5/Scr paralogous group. Dpl3 has a high level of homology to the C. intestinalis gene CiIPF1. The Dpl3 homeodomain shared high identity with the ascidian H. roretzi and H. curvata cdx genes (Hr-cad and Hec-cdx, respectively), however differences in the hexapeptide regions, indicated high divergence of these genes in the ascidians. Dpl5 possessed features characteristic of posterior Hox genes and was most closely related to the C. intestinalis CiHbox5 gene. Dpl6 shared features common to the Hox 4 paralogous group Gsx ParaHox groups.
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Da, Silva Liberio Michelle. "Chemical and Biological Investigations of Anticancer Compounds from Australian Ascidians." Thesis, Griffith University, 2014. http://hdl.handle.net/10072/365813.
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Nature is the main source of anticancer agents with about 60% of the current anticancer drugs originating in some way from natural products. Many cytotoxic natural products have been isolated from marine invertebrates. One group of marine animals that have made significant contributions is the tunicates or ascidians. Ascidians belonging to the family Didemnidae are known to be a prolific and rich source of new chemical entities with biological activity. This study was divided into two main components. In the first part, Didemnid ascidians collected from the Great Barrier Reef (GBR) were investigated for their chemical diversity using spectroscopic and spectrometric techniques. In part two, an ascidian drug discovery screening library was generated and subsequently used to identify cytotoxic or cytostatic compounds in prostate (LNCaP) and breast (MDA-MB-231) cancer cells. The ascidian natural products isolated in part 1 were all tested in these cancer cell lines. Moreover, one of the cytotoxic compounds identified from the screening studies was subjected to mechanism of action studies.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Physical Sciences
Science, Environment, Engineering and Technology
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Stacey, Joy E. "The ecophysiology of iron and vanadium accumulation by North Atlantic ascidians /." Internet access available to MUN users only. Search for this title in:, 2009.
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Lotufo, Tito Monteiro da Cruz. ""Ascidiacea (Chordata: Tunicata) do litoral tropical brasileiro"." Universidade de São Paulo, 2002. http://www.teses.usp.br/teses/disponiveis/41/41133/tde-21052002-125049/.
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Embora tenham sido muito estudadas em diversos pontos do globo, as ascídias do litoral brasileiro são pouco conhecidas. A maior parte do litoral brasileiro está incluída na região tropical, para qual as informações são mais escassas. Com o intuito de se conhecer a fauna de ascídias do litoral tropical brasileiro foram realizadas diversas coletas em diferentes pontos desta região, abrangendo desde a zona entremarés até o infralitoral raso. Outro objetivo do presente trabalho foi o de organizar as informações já existentes a partir de revisão bibliográfica e visitas a algumas instituições que continham coleções representativas. Foram realizadas ao todo 61 coletas em pontos distribuídos entre os estados do Rio de Janeiro, Espírito Santo, Bahia, Alagoas, Pernambuco, Paraíba, Rio Grande do Norte e Ceará. Os animais foram coletados, examinados e identificados até o nível de espécie. Para cada espécie se procurou fazer um extensa revisão taxonômica, tanto a partir da literatura como do exame de tipos depositados em diferentes instituições. O presente trabalho inclui listas sinonímicas, descrições e comentários para cada espécie estudada, com fotografias para a maior parte. Foram adicionadas ainda chaves dicotômicas para todos os táxons, em todas as categorias. Até a realização deste trabalho, 90 espécies de ascídias haviam sido registradas no litoral brasileiro, das quais 54 estão listadas para o estado de São Paulo. Com a realização das campanhas de coletas foram identificadas 67 espécies que, juntamente com uma revisão criteriosa da literatura e o exame de vários tipos e outros exemplares de outras regiões do mundo, fizeram com que a lista atualizada inclua 98 espécies. Estas espécies estão distribuídas entre as 2 ordens e 3 subordens da classe, com um total de 31 gêneros incluídos em 14 dentre as 23 famílias propostas atualmente. Como resultado imediato foram registradas 9 novas ocorrências para o litoral brasileiro, com a descrição de 1 gênero e 10 espécies novas. Além disso, 8 espécies tiveram sua situação alterada por sinonimia ou separação. Juntamente com outros dados da literatura, as tabelas de ocorrências foram submetidas a uma análise de agrupamento e uma análise de endemicidade por parcimônia. As análises evidenciaram um padrão de distribuição semelhante àquele observado para outros grupos bentônicos sésseis, com a divisão da região estudada em duas províncias, a Província Brasileira e a Província Paulista.Although ascidians are well known in many regions of the globe, information about the group on Brazilian coast are very scanty. Most of the Brazilian coastline is included on the tropical region, which is the poorest known. In order to obtain an inventory of ascidians species on the Brazilian tropical coast, surveys were conducted in different points, ranging from the intertidal to the shallow subtidal depths. Another goal of the present work was to organize all available information through a revision of bibliography and visits to institutions that held representative collections. 61 visits were conducted in places along the coast of the states of Rio de Janeiro, Espírito Santo, Bahia, Alagoas, Pernambuco, Paraíba, Rio Grande do Norte e Ceará. Specimens were collected, examined and identified to the species level. An extensive taxonomic revision was made for every species, by means of literature as well as examination of types and other specimens deposited in different institutions. The present work includes synonymy lists, descriptions, pictures and remarks for each species studied. Keys for all taxa an every category were also included. Up to the present work, 90 species of ascidians had been recorded for Brazil, of which 54 are listed to the State of São Paulo. The surveys revealed a total of 67 species, expanding the list to 98 Brazilian species. Those species are distributed in 2 orders and 3 suborders of the class, with a total of 31 genera included in 14 of the 23 families currently accepted. As an immediate result, were registered 9 new records for Brazilian coast, along with the description of 1 new genus and 10 new species. Furthermore, 8 species have had its taxonomic situation altered by synonymy or separation. The present results, together with data from literature generated tables which were submitted to cluster analysis and a parsimony analysis of endemycity. These analyses revealed a distribution pattern similar to others observed for different benthic taxa. The region studied comprises two provinces, Brazilian Province and Paulista Province.
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Davis, Rohan. "Chemical Investigations of Great Barrier Reef Ascidians - Natural Product and Synthetic Studies." Thesis, Griffith University, 2000. http://hdl.handle.net/10072/366561.
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This thesis describes the chemical investigations of several ascidian species collected from the Great Barrier Reef, Queensland, Australia. The thesis is divided into two separate components, Part A focuses on the isolation and structure elucidation of 11 previously undescribed ascidian metabolites. All structures were assigned using a combination of spectroscopic and/or chemical methods. Part B relates to the isolation and chemical conversion of a natural product to a combinatorial template. The natural product template was subsequently used in the generation of a solution-phase combinatorial chemistry library. A further two combinatorial libraries were generated from a synthesised model compound that was related to the natural product template. Part A. Investigation of Aplidium longithorax collected from the Swains Reefs resulted in the isolation of two new para-substituted cyclofarnesylated quinone derived compounds, longithorones J (30) and K (31). The former compound had its absolute stereochemistry determined by the advanced Mosher method. From an Aplidium longithorax collected from Heron Island, two new cyclofarnesylated hydroquinone compounds, longithorols C (46) and D (47) and a novel macrocyclic chromenol, longithorol E (48) were isolated. Longithorol C (46) had its absolute stereochemistry determined by the advanced Mosher method. Chemical investigation of the deep-purple colonial ascidian, Didemnum chartaceum collected from Swains Reefs led to the isolation of five new lamellarin alkaloids, which included the 20-sulfated derivatives of lamellarins B (94), C (95) and L (96), the 8-sulfated derivative of lamellarin G (97) and the non-sulfated compound, lamellarin Z (98). The known lamellarins A (63), B (80), C (64), E (65), G (67), and L (71) plus the triacetate derivatives of lamellarin D (82) and N (83) were also isolated. An aberration in the integration of signals in the 1H NMR spectra of the 20-sulfated derivatives (94-96) led to NMR relaxation studies. T1 values were calculated for all protons in the sulfated lamellarins (94-97) and their corresponding non-sulfated derivatives (80, 64, 71, 67). The protons ortho to the sulfate group in compounds (94-97) had T1 values up to five times larger than the corresponding protons in their non-sulfated derivatives (80, 64, 71, 67). A specimen of Eudistoma anaematum collected from Heron Island was shown to contain a new b-carboline alkaloid, eudistomin V (130), in addition to the two known metabolites, eudistomin H (105) and I (106). Part B. The known natural products, 1,3-diphenethylurea (29), 1,3-dimethylxanthine (30), 1,3-dimethylisoguanine (31) and the salts of tambjamine C (16), E (18) and F (19) were isolated from the ascidian, Sigillina signifera collected in Blue Lagoon, Lizard Island. Base hydrolysis on mixtures of the salts of tambjamine C (16), E (18) and F (19) resulted in the production of 4-methoxy-2,2-bipyrrole-5-carbaldehyde (26). This natural product template (26) was used in the generation of an enamine combinatorial chemistry library (98, 103-111) using solution-phase parallel synthesis. The biaryl compound, 4-(2-thienyl)-1H-pyrrole-2-carbaldehyde (59) was successfully synthesised using Suzuki-Miyaura coupling conditions and subsequently used as a template in the generation of an amine (67, 77, 80-87) and imine (78, 92-95) combinatorial library using solution-phase parallel synthesis.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Science
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Salomon, Christine Elizabeth. "The localization of bioactive secondary metabolities in sponges, ascidians and their associated symbionts /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3035432.
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Tincu, John Andrew. "Acid soluble peptides from the hemocytes of the ascidians : characterization and antimicrobial activity /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2003. http://wwwlib.umi.com/cr/ucsd/fullcit?p3118434.
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Kincaid, Erin Suzanne. "Biofouling Management in the Pacific Northwest and Predation on Native versus Non-native Ascidians." PDXScholar, 2016. http://pdxscholar.library.pdx.edu/open_access_etds/3069.
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Marine non-native species threaten economic and environmental health, making it crucial to understand factors that make them successful. Research on these species, therefore, allows for greater preparedness and informed management of biological invasions and increases understanding of elements structuring biological communities. Among the marine non-native species, and particularly the fouling community, non-native ascidians are a taxon of particular concern because they can crowd out native benthic species and smother mariculture products. This thesis addresses management for ascidians and other fouling organisms and includes research on the invasiveness of this taxon in addition to the invasibility of recipient fouling communities. On the West Coast of the U.S., limited efforts have been made to coordinate biofouling management across states, despite the myriad vectors increasing propagule pressure over time along coastal states. Building on recent state and local efforts, I developed a Pacific Regional Biofouling Plan for the states of Oregon and Washington to help start a consensus-driven process by which these states could create a forum for more comprehensive coordination efforts, following California's lead. As states address authority gaps, the biofouling management framework I've written is meant to be used to guide the conversation between managers as various stages of coastal management are realized.
To better inform the scope and efficacy of management and regulatory efforts, the study of invasions ecology asks and aims to answer questions regarding recipient community interactions and characteristics of the non-native species themselves. Studies that identify characteristics that make ascidians successful (invasiveness) and determine the influence native communities have on their success (invasibility) are important for assessing overall risk of establishment and spread from non-native ascidians. Therefore, I aimed to: 1) explore the hypothesis that fouling communities on suspended, artificial structures are more invasible than benthic habitats; and 2) identify characteristics influencing predation patterns on the native Distaplia occidentalis versus non-native ascidian species using mensurative and experimental studies in Charleston Marina, Oregon. I conducted a series of feeding assays, surveys, and a caloric content analysis. Feeding assays were conducted with a suite of predators. The flatworm predator (Eurylepta leoparda) was found to be highly selective on the native ascidian Distaplia occidentalis, and only preyed on whole colony samples. Feeding assay data suggest that test (tunic) structure or thickness may be an influential factor affecting nudibranch (Hermissenda crassicornis) predation rates on native versus non-native ascidians, with greater predation on the native ascidian species. Non-native ascidians may escape predation in floating but not benthic environments on the Oregon coast due to their palatability characteristics, likely tunic structure and low caloric content. In this case, this suite of predators may indirectly facilitate the invasion of docks but provide at least partial resistance to the invasion of natural benthic areas.
The chapters herein address gaps in management and scientific knowledge regarding non-native species of the marine fouling community. Future work enhanced by my efforts could include the development of the coastal biofouling management plan, coordinated by the Western Regional Panel on Aquatic Invasive Species Coastal Committee, and broadening the geographic and taxonomic scope of my research with a more comprehensive study of predator-prey interactions involving non-native ascidians and a diverse suite of predators. These interactions may be an important factor in explaining the success of ascidians and other fouling organisms on floating structures and lack of success on nearby benthic substrata.
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Robinson, Paul A. "Studies towards the synthesis of marine polysulfide natural products." Thesis, Loughborough University, 2010. https://dspace.lboro.ac.uk/2134/6379.
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Biologically active compounds isolated from marine sources have had increasing interest in recent years with significant research going into the discovery and isolation of novel marine polysulfide natural products. Varacin, probably the most widely studied marine polysulfide to date was the subject of much debated structure elucidation attempts, and more recently several successful synthetic approaches have been published. The work published aims to increase our understanding of marine polysulfide compounds existence in nature and determine the origins of their biological activity. (+)-Aplidium trisulfide which was isolated from Aplidium Sp. D in 1989 by Munro et al has been shown to exhibit in vitro antimicrobial, antileukemic and cytotoxic properties. These intriguing biological effects have led our work towards developing a novel synthetic route toward aplidium trisulfide by both chiral and racemic routes. Aplidium trisulfide is of special significance as it is very rare to isolate enantiomeric compounds from marine sources. Two other closely related marine alkaloids fasmerianamine A and B are also of synthetic interest to us due to their close resemblance to the structure of aplidium trisulfide. The fasmerianamines were isolated by Copp et al from the marine ascidian Hypsistozoa fasmeriana in 2001.
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Ricci, Lorenzo. "A new model to study alternative developments : asexual propagation and regeneration in the basal chordate Botryllus schlosseri." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066683.
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Chez l’ascidie coloniale Botryllus schlosseri, en plus de l’embryogénèse existent deux voies de développement aboutissant à la production de la même structure : l’organisme adulte ou zooide. Ces développements alternatifs ont lieu lors de processus biologiques distincts : le bourgeonnement palléal (BP) et le bourgeonnement vasculaire (BV). Le BP est un processus de multiplication asexuée présentant une ontogénèse stéréotypée. En revanche, le BV est un phénomène régénératif, induit dans les vaisseaux sanguins de la colonie par l’ablation de tous les zooides et bourgeons palléaux. Mes travaux de recherche ont eu pour objectif de caractériser les bases moléculaires et cellulaires régissant le BP et le BV chez B. schlosseri. L’étude de gènes marqueurs des lignées méso-, endo- et ectodermiques a révélé l’existence de territoires présomptifs pour chacune de ces lignées, dès les premiers stades du BV et du BP, et suggéré l’existence d’un programme unique aux deux processus. Les lignées neurales et musculaires ont été étudiées plus en détail lors du BP, indiquant un double rôle potentiel, neuro- et myo-génétique, au tube dorsal, une structure jusqu’à présent uniquement associée au système nerveux. Une caractérisation morphologique poussée a mené à l’identification de stades précoces stéréotypés du BV lors de la régénération. Enfin, l’analyse de transcriptomes de différents stades du BP et de la régénération ont initié l’étude non biaisée des bases moléculaires du bourgeonnement chez Botryllus. L’objectif à long terme de ces travaux est de décrypter les bases moléculaires et génétiques facilitant, chez les métazoaires, l’évolution de voies de développement alternativesIn addition to embryogenesis, the colonial ascidians Botryllus schlosseri evolved two alternative developmental pathways leading to the same final structure: the adult body, or zooid. These non-embryonic ontogenesis occur during distinct biological processes: palleal budding (PB) and vascular budding (VB). PB is a process of asexual propagation, with a very stereotyped morphogenesis. Conversely, VB is a purely regenerative phenomenon, induced in the vascular system of the colony by the ablation of all zooids and palleal buds. My research work followed the objective to characterize the molecular and cellular basis of both PB and VB in B. schlosseri. The study of meso-, endo- and ectodermal lineage marker genes revealed the existence of presumptive territories of these lineages in the early palleal and vascular buds and that a single developmental program was launched in both VB and PB. Neural and muscle fates were studied in more detail for PB, indicating a potential double function, both neuro- and myo-genic for the dorsal tube, a structure so far associated with the nervous system only. A detailed morphological description of VB allowed to identify stereotyped stages during early regeneration. Eventually, a transcriptomic characterization of early VB and PB processes initiated an unbiased study of the molecular basis underlying the budding phenomenon in Botryllus. The overall goal of these research works is to unravel the molecular and genetic basis that facilitated, in Botryllus and globally in metazoan, the evolution of alternative developmental pathways
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Gineste, Mathieu. "Identification à l'échelle génomique des éléments cis-régulateurs actifs au cours du développement des ascidies." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM4095.
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Les ascidies présentent des propriétés remarquables au sein des métazoaires qui en font un modèle particulièrement intéressant pour étudier le fonctionnement et l’évolution des éléments cis-régulateurs dans un contexte développemental. Ciona intestinalis et Phallusia mammillata, deux espèces d’ascidies qui ont divergé il y a environ 300 millions d’années, combinent une grande conservation de leurs processus développementaux avec une grande divergence de leur séquence génomique. Pour comprendre comment « fabriquer » des embryons similaires avec des génomes divergents, nous avons identifié les éléments cis-régulateurs actifs au cours du développement de Ciona intestinalis et Phallusia mammillata en développant et en appliquant la méthode de ChIP-Seq sur des modifications d’histones sur des jeunes gastrulae. La définition puis la validation fonctionnelle de différentes catégories d'éléments cis-régulateurs nous a permis de révéler quelques propriétés de la cis-régulation au sein de génomes compacts et intensément remaniés. En sus, les données que nous avons produites constituent une resource fonctionnelle unique pour la caractérisation des éléments cis-régulateurs chez les ascidies et l'étude de leur évolution au sein des ChordésAscidians display remarkable features within metazoans making them particularly suited for the study of function and evolution of cis-regulatory elements in the context of embryonic development. Ciona intestinalis and Phallusia mammillata, two ascidian species that diverged about 300M years ago, combine high conservation of their developmental processes with high divergence of their genome sequence. To understand how to “make” similar embryos with divergent genomes, we identified active cis-regulatory elements during Ciona intestinalis and Phallusia mammillata development by developing and applying the ChIP-Seq method on histone modifications in early-gastrula embryos. Definition then functional validation of different categories of cis-regulatory elements led us to reveal some features of cis-regulation within compact and highly dynamic genomes. Together, our data constitute a unique functional resource for characterizing cis-regulatory elements in ascidians and questioning their evolution within the Chordates
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Barnes, Peter Brendan. "Environmental impacts and the ecology of sponges and ascidians in south-eastern Australian coastal lakes and lagoons." Department of Biological Sciences - Faculty of Science, 2009. http://ro.uow.edu.au/theses/849.
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Estuaries worldwide are under threat from urbanisation and development and will need effective management for their successful conservation. Coastal lakes and lagoons have been identified as one of the estuary types most susceptible to human impacts largely because of their isolated nature and slow flushing times. Management of estuaries will be most effective when based on a sound scientific understanding of the patterns of distribution, biology and ecology over the full range of biodiversity of these systems, however, such an understanding is lacking for many systems and many taxa. Studies of sponges and ascidians in coastal lakes and lagoons are rare compared to other taxa, particularly in the southern hemisphere. This study represents the first detailed scientific investigation of the ecology of sponges and ascidian in coastal lakes and lagoons of southeastern Australia. Consequently, a large part of this thesis was devoted to quantifying basic patterns of distribution. I started with a pilot study to develop an effective sampling design, followed by large-scale comparisons among different types of lake, comparisons among habitats within lakes and an environmental impact study. I concluded with a manipulative experiment to examine processes responsible for smallscale patterns of distribution of sponges in seagrass meadows.In the pilot study, distributions of sponges and ascidians were quantified at a hierarchy of three spatial scales in each of two coastal lakes. Nested analyses of variance were then used to identify spatial scales at which variation was significant. Most sponges and ascidians were very patchily distributed at a range of spatial scales from 10s of metres up to 100s of kilometres. Unlike other published examples of cost– benefit analyses, very few taxa were widespread over the larger spatial scales. Cost– benefit analyses done to determine the optimal sampling design revealed inclusion of patchily distributed taxa in analyses improved the overall precision of sampling for comparisons of assemblages among lakes.Large-scale comparisons of assemblages of sponges and ascidians were made among lakes of different size (big versus small), opening regime (mostly open to the ocean versus mostly closed) and level of environmental modification (extensively modified versus more pristine). Similar to other taxa studied in coastal lakes, in general there were more species in lakes mostly open to the ocean compared to the mostly closed lakes, and importantly, no sponges and only one species of ascidian was found in the small closed lakes. There also appeared to be an effect of the level of modification of a lake with relatively smaller abundances of ascidians in extensively modified lakes, and a complete absence of sponges from one of the extensively modified lakes.Habitat-associated patterns were examined at smaller spatial scales by comparing the distributions of sponges and ascidians with the species composition and percentage cover of seagrass and macroalgae within two lakes; St Georges Basin and Wallis Lake. Several patterns of association were observed, but these varied among species of sponge and ascidian. In St Georges Basin, the most common sponge, Aplysinella cf. rhax and the native ascidian Pyura stolonifera were positively correlated with the seagrass, Posidonia australis. In contrast, the introduced ascidian, Styela plicata was more abundant in areas dominated by the seagrass, Zostera capricorni. In Wallis Lake, sponges were most diverse and some species most abundant in large beds of the macroalga, Lamprothamnion sp., while other sponges were found only on the holdfasts of brown macroalgae. In both lakes, sponges were generally less common in areas dominated by dense meadows of the seagrass, Zostera capricorni.Among the many anthropogenic impacts threatening the ecology of coastal lakes, the discharge of cooling water from coal-fired power stations represents an almost ideal case study from which to develop appropriate sampling regimes for detecting impacts on sponges and ascidians. Using reference locations both within and outside Lake Macquarie which has two cooling water outlets, I found assemblages of sponges and ascidians were often more diverse, more abundant and less temporally variable near to the outlets compared to reference locations.Based on the observation that the sponge, Suberites sp. which contains photosynthetic symbionts was absent from meadows of dense Zostera capricorni, I used in situ manipulative experiments in Smiths Lake to investigate processes which maybe affecting their distribution. Individual Suberites sp. were shaded, had water flow reduced and were transplanted into areas of dense Z. capricorni. There were no measurable short-term effects of shading or reduced water flow, but transplanted sponges were quickly eaten and I concluded predation by fish was likely to be a key process determining small-scale patterns of distribution of Suberites sp. in seagrass meadows. This result was in stark contrast to the majority of previous studies of the effects of seagrass habitat complexity on predation which have found predation to decrease with increasing density or complexity.In conclusion, I have sought to provide sound scientific information to aid in the management of these systems. A simple, but nevertheless key finding was that sponges and ascidians are indeed present and widespread in coastal lakes and lagoons of southeastern Australia and should not be continually overlooked in the management and conservation of these systems. Conservation will be complex and requires an understanding of environmental impacts and the consequences of management on the full range of biodiversity. The distributions of sponges and ascidians at large ‘lakewide’ scales appear to behave similarly to other taxa. Management strategies which change the characteristics of a lake at these large spatial scales such as artificial openings of entrances could therefore be predicted to have similar effects across a range of taxa including sponges and ascidians. In contrast, at smaller spatial scales such as the complexity of seagrass meadows, some species of sponges and ascidians may behave very differently from other taxa. At present, our understanding of these naturally variable and complex systems is incomplete and will require ongoing scientific investigation to identify natural patterns of distribution, environmental impacts, important natural processes and the ecological consequences of management strategies.
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Neves, Isabela Monteiro. "Ascídias didemnidae (Tunicata, Ascidiacea) da Região de Bocas Del Toro - Panamá = Didemnidae ascidians (Tunicat, Ascidiacea) from Bocas del Toro - Panamá." reponame:Repositório Institucional da UFPR, 2015. http://hdl.handle.net/1884/37618.
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Orientadora : Profª. Drª. Rosana Moreira da RochaDissertação (mestrado) - Universidade Federal do Paraná, Setor de Ciências Biológicas, Programa de Pós-Graduação em Zoologia. Defesa: Curitiba, 06/02/2015
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Area de concentração: Zoologia
Resumo: Didemnidae é a família mais diversa e mais derivada da ordem Aplousobranchia (classe Ascidiacea). Compreende cerca de 600 espécies, representando 20% de todas as ascídias conhecidas até o momento. As águas tropicais do Caribe são conhecidas pela riqueza e abundância de invertebrados marinhos e a costa atlântica do Panamá é caracterizada pela presença de um mosaico de hábitats variados que proporcionam importantes substratos naturais para a comunidade incrustante. O presente trabalho apresenta descrições detalhadas de didemnídeos coletados entre os anos de 2003 e 2014 em 12 pontos do arquipélago de Bocas del Toro – Panamá. Foram identificadas 19 espécies, das quais cinco haviam sido registradas na região (Diplosoma listerianum, Lissoclinum verrilli, Didemnum granulatum, D. psammatodes e Trididemnum orbiculatum), sete são novos registros (Lissoclinum abdominale, Didemnum calliginosum, D. cineraceum, D. perlucidum, D. vanderhorsti, Trididemnum palmae e T. thetidis) e sete são espécies novas (Diplosoma sp. nov. 1, Diplosoma sp. nov. 2, Lissoclinum sp. nov. 1, Lissoclinum sp. nov. 2, Didemnum sp. nov., Trididemnum sp. nov. 1 e Trididemnum sp. nov. 2). Com estes resultados, o Panamá está entre as regiões do Caribe com maior número de didemnídeos registrados, mostrando a importância de se considerar a região objeto de esforço no monitoramento e na conservação dos diferentes hábitats e dos invertebrados marinhos que ali habitam. Palavras-chave: Aplousobranchia, ascídias coloniais, características morfológicas, Caribe, Diplosoma, Didemnum, Lissoclinum, taxonomia, Trididemnum, Tunicata.
Abstract: Didemnidae is the most diverse and the more derived family from Aplousobranchia order (Ascidiacea class). Comprising ca. 600 species, that represents 20% of all known ascidians. The Caribbean tropical waters are known for the richness and abundance of marine invertebrates and the Panama Atlantic coast is characterized by the presence of different habitats that provide important natural substrates for sessile communities. This paper reports detailed descriptions of didemnids collected between 2003 and 2014 in 12 points in the archipelago of Bocas del Toro - Panama. Nineteen species were identified, of which five have been previously registered in the region (Diplosoma listerianum, Lissoclinum verrilli, Didemnum granulatum, D. psammatodes and Trididemnum orbiculatum), seven are new records (Lissoclinum abdominale, Didemnum calliginosum, D. cineraceum, D. perlucidum, D. vanderhorsti, Trididemnum palmae and T. thetidis) and seven are new species (Diplosoma sp. nov. 1, Diplosoma sp. nov. 2, Lissoclinum sp. nov. 1, Lissoclinum sp. nov. 2, Didemnum sp. nov., Trididemnum sp. nov. 1 and Trididemnum sp nov. 2). With these results, Panama is among the regions of the Caribbean Sea with the highest number of didemnids, showing the importance of considering the monitoring effort and conservation of different habitats and marine invertebrates that live in this region. Keywords: Aplousobranchia, colonial ascidians, Caribbean Sea, Diplosoma, Didemnum, Lissoclinum, morphology, taxonomy, Trididemnum, Tunicata.
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Liu, Boqi. "The gene regulatory network in the anterior neural plate border of ascidian embryos." Kyoto University, 2020. http://hdl.handle.net/2433/253119.
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Takeara, Renata. "Estudo químico e avaliação da atividade citotóxica das ascídias \'Didemnum psammatodes\' (Sluiter, 1885) e \'Eudistoma vannamei\' Millar, 1977 (Tunicata: Ascidiacea)." Universidade de São Paulo, 2006. http://www.teses.usp.br/teses/disponiveis/60/60138/tde-16012007-161004/.
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Amostras de Didemnum psammatodes foram coletadas em Icapuí (CE) e Trairi (CE). O extrato metanólico de D. psammatodes, proveniente de Icapuí, foi submetido a processo de fracionamento e purificação por diversas técnicas cromatográficas, obtendo-se quatro nucleosídeos (2-deoxiuridina, 2-deoxiinosina, timidina e 2-deoxiguanosina), três esteróides em mistura (colestanol, colestanona e estigmasterol) e três derivados do glicerol éter em mistura (2,3-propanodiol, 1- heptadeciloxi; álcool batílico e 2,3-propanodiol, 1-nonadeciloxi). O extrato metanólico de D. psammatodes, proveniente de Trairi, foi inicialmente particionado, originando as fases aquosa, hexânica, clorofórmica, butanólica e hidroalcoólica. A fase hexânica inibiu o ciclo celular de ovos de ouriço do mar e exibiu toxicidade em células tumorais. Ela foi fracionada por técnicas cromatográficas e obtiveram-se três ácidos graxos metilados em mistura (miristato de metila, palmitato de metila e estearato de metila), dois esteróides em mistura (colestanol e colestanona), dois ácidos graxos em mistura (ácido palmítico e ácido esteárico) e três derivados do glicerol éter em mistura (2,3-propanodiol, 1-heptadeciloxi; álcool batílico e 2,3- propanodiol, 1-nonadeciloxi). A fase clorofórmica também inibiu o ciclo celular de ovos de ouriço do mar e exibiu toxicidade em células tumorais. Ela foi fracionada por técnicas cromatográficas e obtiveram-se seis ácidos graxos em mistura (ácido láurico, ácido mirístico, ácido pentadecanóico, ácido palmítico, ácido margárico e ácido esteárico). A fase aquosa foi submetida ao processo de fracionamento e purificação por diversas técnicas cromatográficas, obtendo-se dois nucleosídeos (uridina e timidina) e um núcleo purínico (hipoxantina). A fase butanólica resultou no isolamento e identificação de dois nucleosídeos (2-deoxiguanosina e timidina). Amostras de Eudistoma vannamei foram coletadas em São Gonçalo do Amarante (CE). O extrato metanólico de E. vannamei foi particionado, originando as fases hexânica e hidroalcoólica. A fase hexânica inibiu o ciclo celular de ovos de ouriço do xi mar e exibiu toxicidade em células de linhagem B-16. Ela foi fracionada por técnicas cromatográficas e obtiveram-se cinco ácidos graxos metilados (miristato de metila, palmitato de metila, estearato de metila, palmitoleato de metila e oleato de metila), dois esteróides (colestanona e colesterol) e cinco ácidos graxos (ácido mirístico, ácido pentadecanóico, ácido palmítico, ácido margárico e ácido esteárico). A fase hidroalcoólica resultou no isolamento e identificação de dois nucleosídeos (guanosina e adenosina). As substâncias foram identificadas por métodos espectroscópicos e cromatográficos, comparando-se os valores obtidos com aqueles da literatura e padrões. Os nucleosídeos 2-deoxiuridina e 2-deoxiguanosina inibiram o ciclo celular de ovos de ouriço do mar em ambas fases examinadas. Os ácidos graxos metilados de D. psammatodes, o ácido palmítico junto com ácido esteárico e os derivados do glicerol éter inibiram o ciclo celular de ovos de ouriço do mar durante a primeira divisão. Os ácidos graxos metilados de D. psammatodes apresentaram maior toxicidade nas linhagens tumorais analisadas, sendo que a mistura de ácidos graxos metilados de E. vannamei também mostrou toxicidade em células tumorais leucêmicas. Ambas amostras de ácidos graxos metilados mostraram efeitos antiproliferativos e citotóxicos e estas atividades envolveram a inibição da síntese de DNA e indução de apoptose e necrose.Samples of Didemnum psammatodes were collected in Icapui (Ceara State) and Trairi (Ceara State). The methanolic extract from D. psammatodes, acquired from Icapui, was submitted to fractionation and purification through several chromatographic techniques and were obtained four nucleosides (2?-deoxyuridine, 2- deoxyinosine, thyimidine, and 2?-deoxyguanosine), three steroids in mixture (cholestanol, cholestanone, and stigmasterol) and three glyceryl ethers in mixture (2,3-propanediol, 1-(heptadecyloxy), batyl alcohol, and 2,3-propanediol, 1- (nonadecyloxy)). The methanolic extract from D. psammatodes, acquired from Trairi, was initially partitionated, giving rise to aqueous, hexane, chloroform, and butanol phases. The hexane phase inhibited the sea urchin egg cell cycle and exhibited toxicity in tumor cell lines. It was fractionated by several chromatographic techniques and obtained three fatty acid methyl esters in mixture (methyl myristate, methyl palmitate, and methyl stearate), four steroids in mixture (cholestanol and cholestanone), two fatty acids in mixture (palmitic acid and stearic acid) and three glyceryl ethers in mixture (2,3-propanediol, 1-(heptadecyloxy), batyl alcohol, and 2,3- propanediol, 3-(nonadecyloxy)). The chloroform phase also inhibited the sea urchin egg cell cycle and exhibited toxicity in tumor cell lines. It was fractionated through several chromatographic techniques and obtained six fatty acids in mixture (lauric acid, myristic acid, pentadecanoic acid, palmitic acid, margaric acid, and stearic acid). The aqueous phase was submitted to fractionation and purification by several chromatographic techniques and obtained two nucleosides (uridine and thymidine) and one purinic nucleus (hypoxanthine). The butanol phase resulted in the isolation and identification of two nucleosides (2?-deoxyguanosine and thymidine). Samples of Eudistoma vannamei were collected in São Gonçalo do Amarante (Ceara State). The methanolic extract from E. vannamei was partitionated, giving rise to hexane and hydroalcoholic phases. The hexane phase inhibited the sea urchin egg cell cycle and xiii exhibited toxicity in cell line B-16. It was fractionated by chromatographic techniques and obtained five fatty acid methyl esters in mixture (methyl myristate, methyl palmitate, methyl stearate, methyl palmitoleate, and methyl oleate), two steroids (cholestanol and cholesterol), and five fatty acids (myristic acid, pentadecanoic acid, palmitic acid, margaric acid, and stearic acid). The hydroalcoholic phase resulted in the isolation and identification of two nucleosides (guanosine and adenosine). The substances were identified by spectroscopic and chromatographic methods comparing the obtained values with those of the literature and standards. The nucleosides 2?-deoxyuridine and 2?-deoxyguanosine inhibited the sea urchin egg cell cycle in both stages. The fatty acid methyl esters from D. psammatodes, the palmitic acid plus stearic acid and the glyceryl ethers inhibited the sea urchin egg cell during first cleavage. The fatty acid methyl esters from D. psammatodes presented the highest toxicity in the cell lines tested and the mixture of fatty acid methyl esters from E. vannamei showed toxicity to leukemia cell lines too. Both samples of fatty acid methyl esters showed antiproliferative and cytotoxic effects and these activities involved the inhibition of DNA synthesis and induction of both necrosis and apoptosis.
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Guignard, Léo. "Analyse quantitative de la morphogenèse animale : de l'imagerie laser haut-débit à l'embryon virtuel chez les ascidies." Thesis, Montpellier, 2015. http://www.theses.fr/2015MONTS048/document.
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Les embryons d'ascidies se développent avec un lignage cellulaire stéréotypé et évolutionairement conservé pour produire en quelques heures ou jours un têtard comportant un petit nombre de cellules. De ce fait, ils fournissent un cadre intéressant pour décrire avec une résolution cellulaire le programme de développement d’un organisme complet. Pendant mon doctorat, j’ai développé une approche quantitative pour décrire l’évolution morphologique embryonnaire pendant le développement de Phallusia mammillata. J’ai ensuite utilisé cette approche pour systématiquement caractériser en détail les logiques des événements de spécifications de destin cellulaire.Pour caractériser quantitativement les comportements cellulaires pendant l’embryogenèse, nous avons utilisé de la microscopie à feuille de lumière multi-angles pour imager des embryons entiers à haute résolution spatio-temporelle. Les membranes plasmiques étaient marquées pour permettre l’identification des cellules. Pour extraire les informations biologiques de ce jeu de donnés, j’ai développé une nouvelle méthode pour segmenter les cellules en 4D, ASTEC. Une fois appliquée aux embryons de Phallusia mammillata imagés pendant 6 heures entre le stade 64 cellules et le début des stades bourgeon caudal, cette méthode a permis de récupérer la forme et de suivre 1030 cellules pendant 640 divisions. L’embryon digital 4D résultant peut être formalisé par un graphe dynamique, dans lequel les cellules sont représentées par des sommets reliés par des arrêtes représentant au sein d’un point de temps leur voisinage spatial, et entre différents points de temps leur lignage cellulaire.Basé sur cette représentation digitale et quantitative, nous avons systématiquement identifié les événements de spécification cellulaire jusqu’au dernier stade de la gastrulation. Des simulations informatiques ont révélé que des règles remarquablement simples intégrant les aires de contacts cellulaires et les expressions spatio-temporelles booléennes de signaux moléculaires extracellulaires sont suffisantes pour expliquer les inductions cellulaires au cours du développement précoce. Ce travail suggère que pour les embryons établissant des contacts stéréotypés et précis entre cellules voisines, les contraintes génomiques sont relâchées, ce qui permet une évolution plus rapide du génomeAscidian embryos develop with stereotyped and evolutionarily conserved invariant cell lineages to produce in a few hours or days tadpole larvae with a small number of cells. They thus provide an attractive framework to describe with cellular resolution the developmental program of a whole organism. During my PhD, I developed a quantitative approach to describe the evolution of embryonic morphologies during the development of the ascidian Phallusia mammillata. I then used this approach to systematically characterize in detail the logic of cell fate induction events. To quantitatively characterize cell behaviors during embryogenesis, we used multi-angle light-sheet microscopy to image with high spatio-temporal resolution entire live embryos with fluorescently labeled plasma membranes. To extract biological information from this imaging dataset, I then developed a conceptually novel automated method for 4D cell segmentation, ASTEC. Applied to a Phallusia mammillata embryo imaged for 6 hours between the 64-cell and the initial tailbud stages, this method allows the accurate tracking and shape analysis of 1030 cells across 640 cell divisions. The resulting 4D digital embryo can be formalized as a dynamic graph, in which cells are represented by nodes, linked within a time point by edges that represent their spatial neighborhood, and between time points by temporal edges describing cell lineages.Based on this quantitative digital representation, we systematically identified cell fate specification events up to the late gastrula stage. Computational simulations revealed that remarkably simple rules integrating measured cell-cell contact areas with boolean spatio-temporal expression data for extracellular signalling molecules are sufficient to explain most early cell inductions. This work suggests that in embryos establishing precise stereotyped contacts between neighboring cells, the genomic constraints for precise gene expression levels are relaxed, thereby allowing rapid genome evolution
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Jimenez, Paula Christine. "BioprospecÃÃo de substÃncias com potencial antitumoral em ascÃdias do litoral cearense: estudos com Eudistoma vannamei Millar, 1977 (Urochordata, Ascidiacea)." Universidade Federal do CearÃ, 2004. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=2999.
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Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgicoEste trabalho avaliou, inicialmente, a citotoxicidade dos extratos hidroalcoÃlicos das 10 espÃcies de ascÃdias mais abundantes do litoral cearense atravÃs dos seguintes mÃtodos: toxicidade aguda em larvas de artemias, inibiÃÃo do desenvolvimento dos ovos de ouriÃo-do-mar, potencial hemolÃtico e inibiÃÃo da proliferaÃÃo celular de linhagens tumorais. A espÃcie Eudistoma vannamei mostrou-se a mais ativa em 3 dos 4 ensaios performados, sendo, portanto, selecionada para prosseguir com a caracterizaÃÃo quÃmica e farmacolÃgica de seus princÃpios ativos. O extrato foi particionado em diversos solventes e fracionados por cromatografia em sÃlica gel 60 e sephadex LH-20. A atividade das amostras foi monitorada pelo mÃtodo do MTT. Das 60 amostras coletadas, 15 foram ativas. A CI50 dessas 15 amostras foi verificada, novamente pelo mÃtodo do MTT, em 5 linhagens celulares tumorais: CEM, HL-60, MCF-7, HCT-8 e B-16. As fraÃÃes DCM-14 a DCM-18, derivadas da fase diclorometÃnica e quimicamente muito semelhantes entre si, como evidenciado por CCDC, foram as mais ativas, apresentando CI50 de atà 1,0 ug/mL na maioria das linhagens. A dicetopiperazina 6-etilamino-1-metil-piperazina-2,5-diona foi isolada da fase CHCl2 e detectada como o componente majoritÃrio, no entanto, foi inativa sobre a proliferaÃÃo celular. O espectro de H1RNM das fraÃÃes DCM-14 a 18 indicou, como componentes minoritÃrios, uma sÃrie de derivados desta dicetopiperazina, que nÃo foram identificados. O estudo dos efeitos das fraÃÃes sobre a viabilidade (exclusÃo por azul de tripan), proliferaÃÃo (incorporaÃÃo de BrdU e curva de crescimento) e induÃÃo de morte (morfologia celular â coloraÃÃo por H/E â anexina e coloraÃÃo por BE/AO) nas cÃlulas HL-60 demonstrou que DCM-16 e 17 sÃo as mais fortes redutoras da proliferaÃÃo celular. DCM-16 apresentou um pronunciado efeito inibitÃrio sobre a incorporaÃÃo de BrdU, o que pode indicar uma interferÃncia na duplicaÃÃo de DNA. DCM-17 inibiu satisfatoriamente a incorporaÃÃo de BrdU, mas a induÃÃo de apoptose Ã, aparentemente, seu mecanismo predominante. DCM-14 e 15 tambÃm apresentam perfis de indutoras de apoptose celular, sendo que a Ãltima demonstra alguns indÃcios de atividade necrÃtica. Os efeitos de DCM-18 foram pouco pronunciados. As atividades apresentadas por essas fraÃÃes sÃo concentraÃÃo-dependente e o aumento do tempo de contato intensifica o efeito citotÃxico.
The study, initially, evaluated the citotoxity of the hydro-alcoholic extracts of the 10 most abundant ascidian species from the coast of Cearà (Brazil), through the utilization of the following methods: brine shrimps lethality assay; development inhibition of sea urchin eggs; hemolytic potential, and inhibition of in vitro tumor cell growth. In three of the four assays performed, the Eudistoma vannamei species proved to be the most active one, and it was, therefore, selected for chemical and pharmacological characterization of its active principles. The extract was particionated by various solvents and fractionated by chromatography in silica gel 60 and sephadex LH-20 columns. The samplesâ activities were monitored through the MTT method. Of the 60 collected samples, 15 were active. The IC50 of the 15 samples was evaluated through the MTT method, in 5 tumor cell lines: CEM, HL-60, MCF-7, HCT-8 e B-16. The fractions DCM-14 to DCM-18, derived from the CHCl2 phase and chemically very similar to each other, as indicated by CCDC, were the most active ones, presenting IC50 under 1,0 ug/mL in the majority of lines. The diketopiperazine 6-ethylamino-1-methyl-piperazine-2,5-dione was isolated from CHCl2 phase and identified as the major component, however, it was inactive upon cell proliferation. The H1RNM spectra of DCM 14 to DCM 18 fractions showed a number of compounds derived from that major diketopiperazine, which were not identified, as minor components. The study about the fractions effect upon HL-60âs viability (exclusion by trypan blue), proliferation (BrdU incorporation and growth curve) and cell death induction (cell morphology - H/E staining â annexin and BE/AO) revealed DCM-16 and 17 as the most potent cell proliferation reducers. DCM-16 displayed a pronounced BrdU uptake inhibitory effect, which may indicate interference in the DNA duplication process. DCM-17 showed a satisfactorily inhibition upon BrdU uptake, however, the apoptosis induction seems to be its main mode of action. DCM-14 and 15 also displayed a cell apoptosis inductor profile, while the latter indicated some signs of necrotic activity. The activities presented by these fractions are concentration and time dependent as longer periods with cell contact intensifies its citotoxic effect.
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Vidal, Patrícia Martins. "Uso de organismos filtradores (ascidiacea) na avaliação da contaminação por mercúrio em ecossistemas costeiros do Estado do Rio de Janeiro." Niterói, 2017. https://app.uff.br/riuff/handle/1/5191.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Universidade Federal Fluminense. Instituto de Química. Programa de Pós-Graduação em Geoquímica, Niterói, RJ
necessidade no estabelecimento de prioridades para decisões de gerenciamento ambiental. O objetivo deste trabalho é o uso de organismos filtradores do grupo Ascidiacea como bioindicadores para a avaliação da contaminação em ecossistemas costeiros do Estado do Rio de Janeiro em relação a poluição/risco ecotoxicológico por mercúrio. Foram escolhidas três baías do sistema costeiro do Estado do Rio de Janeiro com diferentes graus de degradação: Baía de Guanabara (BG) amplamente poluída; Baía de Sepetiba (BS), com algumas áreas contaminadas e Baía da Ribeira (BR), com alterações antrópicas localizadas. Em cada baía, foi selecionado um ponto de coleta e capturados, durante a maré baixa, aproximadamente trinta indivíduos. As ascídias coletadas foram colocadas em sacos plásticos, lacrados, identificados e congelados. Uma vez no laboratório, os organismos foram identificados, a nível de espécie, e pesados (peso úmido). A determinação das concentrações de mercúrio total (HgT) nos organismos foi realizado no Laboratório de Especiação de Mercúrio Ambiental (LEMA) no CETEM/MCT. Para tal, foi utilizado um aparelho de absorção atômica portátil (LUMEX), específico para análises de HgT por espectrofotometria de absorção baseada no diferencial Zeeman. A determinação do metal foi feita tanto na parte interna das ascídias quanto em sua túnica de revestimento. Para a espécie Styela plicata, encontrada na BG e BS, apesar de não haver diferença significativa, foram observadas maiores [HgT], tanto na túnica quanto na parte interna, nas ascídias de BS. Tais resultados tornam-se mais evidentes ao comparamos as estações Pilar Niterói (ambiente altamente poluído) e Pilar Canal Central (ambiente menos poluído devido à intensa circulação das águas) da BG, tanto entre si, quanto em relação às amostras dessa espécie na BS. Em relação à Phallusia nigra, espécie encontrada na BR, a [HgT] foi maior na parte interna desses organismos do que os da BG e BS. As maiores [HgT] foram observadas na túnica, para as três baías, e não houve diferença significativa entre elas. Não houve correlação entre o peso (tamanho) das ascídas e a [HgT] em seus tecidos. Como a composição bioquímica da túnica de ambas as espécies é similar, a explicação da diferença de concentração do metal entre elas pode residir no fato das células morulares da P. nigra realmente acumularem maior concentração de HgT do que as células de S. plicata. A estimativa dos valores de FBC para ascídia S. plicata, é maior na BS do que na BG. O mesmo resultado foi observado quando comparado ao FBC das ascídias da BR, indicando uma maior disponibilidade do Hg em ambientes menos poluídos. Este primeiro estudo realizado no país, foi uma tentativa preliminar de avaliação das ascídias como potenciais bioindicadoras de contaminação por Hg. Portanto, como são organismos sésseis e filtradores, um maior esforço amostral para confirmar se a espécie Styela plicata pode estar presente na BR como sugerido no estudo, a fim de possibilitar uma análise comparativa mais completa em termos da gradação da contaminação por mercúrio.
The use of indicators of ecological risk due to pollution of water bodies is a need to establish priorities for environmental management decisions. The objective of this study is the use of filter feeding organisms of ascidians as bioindicators for the assessment of contamination in coastal ecosystems of the State of Rio de Janeiro in relation to pollution / ecotoxicological risk by mercury. We chose three bays of the coastal system of the State of Rio de Janeiro with different degrees of degradation: the Bay of Guanabara (BG) widely polluted; Sepetiba Bay (SB), with some contaminated areas and the Ribeira Bay (RB), with anthropogenic changes located. In each bay, was selected a collection point and captured during low tide, about thirty individuals. The ascidians collected were placed in plastic bags, sealed, identified and frozen. Once in the laboratory, organisms were identified to species level, and weighed (wet weight). The determination of concentrations of total mercury (THg) in organisms was performed at the Laboratory of Environmental Mercury Speciation (LEMA) in CETEM / MCT. To this end, we used a portable atomic absorption apparatus (LUMEX), specific analyzes of THg absorption spectrophotometry based on differential Zeeman. The determination of metal was done both on the inside of ascidians and in his coat lining. For the species Styela plicata, found in the BG and BS, although no significant differences were observed higher [THg] in both the tunica and inside, in ascidians BS. These results become more evident when comparing stations Pilar Niterói (highly polluted environment) and Pilar Central Canal (cleaner environment due to the intense movement of water) BG, both among themselves and in relation to samples of this species in the BS. Regarding Phallusia nigra species found in BR, [THg] was greater in the inner part of the bodies of BG and BS. The highest [THg] were observed in the tunica, for the three bays, and there was no significant difference between them. There was no correlation between the weight (size) of ascídas and [THg] in their tissues. As the biochemical composition of the coat of both species is similar, the explanation of the difference in concentration of the metal between them may lie in the fact that morulares cells of P. nigra actually accumulate THg higher concentration of cells of S. plicata. The estimated values for FBC ascidian S. plicata, the BS is greater than the BG. The same result was observed when compared to the FBC squirts of BR, indicating a greater availability of Hg in less polluted environments. This first study in the country, was a preliminary attempt to evaluate the ascidians as potential bioindicators of Hg contamination. Therefore, as filtrating and sessile organisms is a major effort to confirm that the sample species Styela plicata BR may be present as suggested in the study in order to facilitate a more complete comparative analysis in accordance with the gradation of mercury contamination.
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Evans, Rowan. "Reproduction of the unitary, larviparous ascidian Dendroda grossularia." Thesis, University of Liverpool, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.260360.
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Madgwick, Alicia. "Evolution des programmes transcriptionnels développementaux des ascidies Ciona robusta et Phallusia mammillata." Thesis, Montpellier, 2017. http://www.theses.fr/2017MONTT137/document.
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Comment la morphogenèse embryonnaire peut-elle être conservée malgré une divergence importante des séquences codantes et non-codantes ? Pour répondre à cette question, nous avons travaillé sur le développement précoce d’ascidies divergentes, Phallusia mammillata et Ciona intestinalis. Ces espèces partagent une morphogénèse pratiquement identique et des lignages cellulaires stéréotypés. Or, leurs génomes sont tellement divergents que leurs séquences ne peuvent pas être alignées.Nous avons choisi d’étudier les cellules précurseuses de l’endoderme au cours de deux processus développementaux conservés : spécification du destin et la gastrulation. Nous avons comparé par hybridation in situ l’expression transcriptionelle des gènes régulateurs orthologues dans Phallusia et Ciona. Nous avons trouvé que l’expression dans l’endoderme de 8 gènes régulateurs impliqués dans ces processus développementaux est qualitativement conservée entre les deux espèces.Pour étudier comment ces gènes ont conservé leur régulation malgré une divergence non-codante importante, nous avons collaboré avec l’équipe Gomez-Skarmeta pour cartographier, par ATAC-seq, la chromatine ouverte dans les deux espèces pour identifier les régions régulatrices actives à l’échelle du génome. 35 sur les 39 séquences ouvertes avoisinant les gènes de l’endoderme ont été trouvé active avant le stade larval, par éléctroporation. La plupart des séquences testées ont conservé leur activité dans les deux espèces malgré la divergence de séquence. Nous avons alors identifié des sites de fixations pour facteurs de transcription potentiels se trouvant dans les enhancers pour l’endoderme pour identifier les régulateurs dans Phallusia et Ciona.Nos résultats suggèrent des changements assez importants de l’ordre des sites de fixations sans pour autant avoir de changement dans l’architecture dans les réseaux de gènes régulateurs ; ceci explique la conservation qualitative de l’expression des gènes entre ces ascidies divergentes. En outre, nous avons trouvé que les shadow enhancers sont plus répandus qu’anticipéHow can embryonic morphogenesis be evolutionarily conserved in spite of extensive divergence in coding and non-coding genome sequences? To address this question, we worked on the early development of two very divergent ascidians, Phallusia mammillata and Ciona intestinalis. These species share an almost identical early morphogenesis and stereotyped cell lineages. Remarkably, however, their genomes are divergent to the extent that their non-coding sequences cannot be aligned and gene order has not been conserved.We focus our attention on the behaviour of endoderm precursors throughout two important evolutionarily conserved developmental processes: initial fate specification and early gastrulation. We first compared by in situ hybridisation the transcriptional expression of orthologous regulatory genes in Phallusia and in Ciona. We found that the endodermal expression of 8 regulatory genes known to be involved in these developmental processes is qualitatively conserved between the two species.To study how these genes conserved their regulation in spite of extensive non-coding sequence divergence, we collaborated with the Gomez-Skarmeta lab to map, by ATAC-seq, open chromatin regions in both species to identify active regulatory regions genomewide. Three quarters of the 39 open chromatin regions for endodermal genes behaved as active regulatory sequences by the larval stage, when tested by electroporation in embryos. Many of the tested sequences had conserved cis-regulatory activity in both species in spite of sequence divergence. We have identifed putative transcription factor binding sites in endodermal enhancers in both species to identify conserved upstream regulators shared between Phallusia and Ciona.Taken together our results suggest that extensive transcription factor binding site turn over, without radical change in GRNs architecture, may explain the qualitative conservation of gene expression patterns between highly divergent ascidian genomes. Furthermore, we found that shadow enhancers are much more prevalent than initially anticipated.Taken together our results suggest that extensive transcription factor binding site turn over, without radical change in GRNs architecture, may explain the qualitative conservation of gene expression patterns between highly divergent ascidian genomes. Furthermore, we found that shadow enhancers are much more prevalent than initially anticipated
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西川, 輝昭, Teruaki Nishikawa, D. D. Bishop John, and Dorothea Sommerfeldt A. "Occurrence of the alien ascidian Perophora japonica at Plymouth." Cambridge University Press, 2000. http://hdl.handle.net/2237/10552.
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Johnson, Sheri L. "Mating System Dynamics in a Free-Spawning Colonial Ascidian." Fogler Library, University of Maine, 2007. http://www.library.umaine.edu/theses/pdf/JohnsonSL2007.pdf.
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Bevis, Peter John. "Studies on gastrointestinal peptides in the ascidian Styela clava." Thesis, Royal Holloway, University of London, 1985. http://repository.royalholloway.ac.uk/items/2ce39101-08bf-48be-be30-1042d191f253/1/.
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Cells analogous to vertebrate endocrine cells have been described in the gut epithelium of the ascidian Styela clava. As well as some histochemical similarities, ultrastructural correlations have been demonstrated, particularly the presence of electron dense granules, clustered around and mainly below the nucleus, thinning out towards the apex. Like the endocrine cells of the vertebrate gut, the cells are often pyramidal, with a narrow apex which is occasionally observed to extend to the lumen of the gut. In addition, strong secretin immunofluorescence was observed in the endocrine-like (E-L) cells of the mucous cap of the gastric ridges. Because of these observations, acid extracts of Styela gut were assayed for secretin in the rat and in the turkey. The Styela extracts as prepared were inactive but it is possible that this reflected faults in the extraction technique. Development of a perfused Styela gut preparation, however, produced evidence to support the hypothesis that a CCK-like peptide is released into the circulation, presumably from the E-L cap cells, although CCK-like immunoreactivity is not demonstrable in these cells. The observation that in addition to CCK, bombesin and physalaemin also induce enzyme release suggests that the pre-pancreatic zymogen cells contain a rich complement of receptors, corresponding to all the classes of PI stimulating receptors which have been found on vertebrate acinar cells. There is therefore the implication that these hormones or analogues may be present in Styela. As secretin was found not to act as a secretagogue in this system, the significance of its production is unclear. By analogy with vertebrate systems it may exert some control over the secretion of mucus by the cap cells.
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Peddie, Clare M. "Lymphocyte-like functions in the solitary ascidian Ciona intestinalis." Thesis, University of St Andrews, 1995. http://hdl.handle.net/10023/13994.
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The blood cells of the solitary ascidian, Ciona intestinalis, were examined for lymphocyte-like functions with a view to clarifying the phylogenetic origin of lymphocytes in invertebrates. It was found that cells, present in the circulating blood, mediate the haemolysis of sheep red blood cells, and that a different cell type mediates cytotoxic activity against a range of mammalian tumour cell lines in vitro. The blood cells, cytotoxic to mammalian cell lines, were enriched by continuous density gradient centrifugation, and their activity was ameliorated by heat-treatment. Parameters of cytotoxic activity against the target cell line, WEHI, a mouse myelomonocytic leukemic cell (strain 3B), were ascertained by fluorochromasia and the phenomenon was found to be rapid, temperature dependent and sensitive to osmotic conditions. Cytotoxicity was also found to be dependent upon the presence of magnesium and calcium ions, effector to target cell binding, and active metabolic, cytoskeletal and secretory processes in the effector cells. The cytotoxic cells were non-adherent to glass or nylon wool and transmission electron microscope studies of the target-binding cells showed that they were undifferentiated, with a high nucleus to cytoplasm ratio, containing a few large mitochondria, some profiles of rough endoplasmic reticulum and many free ribosomes. In addition, TEM studies revealed close inter-digitation of the effector and target cell membranes and evidence of secretory activity within the effector cell, in the area of target cell binding. The effector cell population was cultured in vitro and proliferation in response to concanavalin A, phytohaemagglutinin-B, lipopolysaccharide, or allogeneic leucocytes, measured by the uptake of tritiated thymidine, showed that these cells respond to both T and B cell mitogens and exhibit a mixed leucocyte reaction. In addition, the culture of pharyngeal explants and the measurement of cytotoxic activity by cells migrating from the explants indicates that the cytotoxic cells originate in a thymus-like haemopoietic tissue. Therefore, the undifferentiated blood cells of C. intestinalis, possess functional and morphological properties consistent with phylogenetic precursors of vertebrate lymphocytes.
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Ordóñez, Sánchez Víctor. "Ecología y genética de ascidias invasoras en el Mediterráneo occidental." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/128963.
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Las invasiones biológicas son un tema de especial importancia para los biólogos marinos. Estas invasiones pueden causar daños tanto ecológicos como económicos. El Mar Mediterráneo es uno de los ecosistemas marinos con más biodiversidad de todo el globo. No obstante, es uno de los mares más castigados y contaminados por la gran actividad humana costera y por la explotación de sus recursos. En consecuencia, es una región altamente vulnerable para la introducción de especies de diferentes orígenes.
Siguiendo la introducción a una nueva área (dispersión pre-frontera), los procesos post-frontera determinan el éxito en el establecimiento de las especies no indígenas. Sin embargo, se conoce poco sobre cómo estos procesos post-frontera dan forma a la composición genética de las especies no indígenas a escalas regionales. Además, las introducciones recurrentes de especies no indígenas generan interacciones nuevas entre especies residentes que varían con las condiciones locales y la composición de la comunidad receptora. Por otro lado, el estudio de especies invasoras es a menudo confundido por cuestiones taxonómicas y por lo tanto estas especies pueden no ser reconocidas como introducidas en nuevas áreas colonizadas.
De entre los organismos marinos invasores, las ascidias se han convertido en un problema global. Puertos, marinas, instalaciones de acuacultura y otras estructuras artificiales suelen ser los hábitats donde son introducidas y proliferan. Concretamente, las ascidias no indígenas son una especial preocupación para la industria de acuacultura y, paradójicamente, el stock de bivalvos representa una importante vía para transportar estas ascidias por todo el mundo.
El objetivo principal de esta tesis doctoral es estudiar ciertos aspectos ecológicos y genéticos de la biología de cuatro ascidias invasoras en el Mediterráneo occidental.
En el primer capítulo profundizamos en los procesos post-frontera de Microcosmus squamiger estudiando su estructura genética poblacional. Esta ascidia presenta una capacidad relativamente alta de dispersión post-frontera que le permite un flujo genético entre diferentes poblaciones a pequeña escala, además, presenta dos grupos genéticos relacionados con las dos fuentes originarias (Australia) de las poblaciones introducidas mundialmente. Estos acervos genéticos están mezclados a nivel poblacional pero no a nivel de individuo.
En el segundo capítulo evaluamos los interacciones biológicas en los primeros estadios del desarrollo de Microcosmus squamiger y Styela plicata entre ellas y con mejillones, otros dominantes en las comunidades bentónicas. Parece que las dos ascidias no presentan interacciones a nivel espermático y tampoco a nivel de asentamiento larvario. En cambio, los mejillones juveniles presentan altos niveles de depredación de las larvas de estas dos ascidias, además de influenciar en su comportamiento larvario. Esto nos demuestra la importancia de la comunidad residente para el establecimiento de especies introducidas.
En el tercer capítulo estudiamos el ciclo de vida y la estructura genética poblacional del invasor Didemnum. vexillum. Esta ascidia presenta un ciclo de crecimiento y reproductor claramente estacional, afectado negativamente por las temperaturas cálidas del verano. Además, las poblaciones introducidas en el Mediterráneo muestran una diversidad baja, sugiriendo un proceso de cuello de botella en el proceso de introducción.
Finalmente, en el cuarto capítulo estudiamos el ciclo de vida de Clavelina oblonga. Veremos que esta ascidia es una especie introducida en el Mediterráneo desde hace más de 80 años pero que fue erróneamente identificada como C. phlegraea, nativa de la región. Su ciclo reproductor y de crecimiento es marcadamente estacional, favorecido por las temperaturas altas del verano, presentando hibernación en los meses más fríos.Biological invasions are of special concern to marine biologists. The Mediterranean is one of the most harmed seas by human activities. Among invasive marine organisms, ascidians have become a global problem. The main goal of this PhD thesis is to study ecological and genetic aspects of the biology of four invasive ascidians in the western Mediterranean. In the first chapter, we delve into the post-border processes of the ascidian Microcosmus squamiger studying its population genetic structure. This ascidian has a relatively high capacity of post-border dispersion, which allows gene flow between populations on a small scale. Moreover there are two genetic clusters related to the two original sources of the introduced worldwide populations. These genetic pools are mixed at the population level but not at the individual level. In the second chapter, we evaluate biological interactions in early-life history stages of Microcosmus squamiger and Styelaplicata, among themselves and with mussels. No interactions between the two ascidians were found in fertilization or larval settlement and metamorphosis processes. In contrast, larvae of both ascidians were consumed by the juvenile mussels, and the ascidians also presented shifts in larval behavior in the presence of the mussels. This highlights the importance of the resident community for the establishment of introduced species. In the third chapter, we study the life cycle and population genetic structure of the invasive Didemnum vexillum. The ascidian showed a marked seasonal growth and reproductive cycle, negatively influenced by warm summer temperatures. Additionally, introduced populations in the Mediterranean showed low diversity, suggesting a bottleneck process in the introduction. Finally, in the fourth chapter, we study the life cycle of Clavelina oblonga. This ascidian is in fact an introduced species in the Mediterranean for more than 80 years ago but was erroneously identified as C. phlegraea, native to the region. Their reproductive and growth cycle was markedly seasonal, favored by warm summer temperatures, hibernating in colder months.
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Khandelwal, Mudrika. "Structure and processing of fibrous cellulose : bacterial and ascidian material." Thesis, University of Cambridge, 2013. https://www.repository.cam.ac.uk/handle/1810/244716.
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Cleto, Cynthia. "Analysis of transcriptional elements of an ascidian troponin I gene." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=33733.
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A long-range research interest of this laboratory is the evolution of the transcriptional control mechanisms of the vertebrate troponin I (TnI) gene family. It is likely that the vertebrate TnI gene family arose from a single TnI gene present in early chordate ancestors. Analysis of transcriptional control mechanisms of the TnI gene of a primitive chordate, such as the ascidian Ciona intestinalis, may therefore provide insight into the regulatory mechanisms of the vertebrate ancestral TnI gene. As an initial step in such a study, I localized transcriptional control regions within 1.5 kb of 5'-flanking DNA of the Ciona TnI gene. I prepared a series of deletion constructs in which Ciona TnI 5'-flanking DNA segments were fused to a nuclear-targeted beta-galactosidase reporter gene. Constructs were introduced into fertilized Ciona eggs by electroporation, and following development up to the mid tailbud stage (12 h), reporter gene expression was assessed by whole-mount beta-galactosidase histochemistry. (Abstract shortened by UMI.)
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Pemberton, A. J. "Aspects of mate choice in the colonial ascidian Diplosoma listerianum." Thesis, University of Aberdeen, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.593279.
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The hermaphrodite, colonial ascidian Diplosoma listerianum (Chordata: Urochordata) mates by releasing sperm that disperse to neighbours, where they fertilise eggs that have been retained internally rather than spawned. The species is able to utilise highly dilute sperm: comparison with published information on a sea urchin, which released both eggs and sperm for external fertilisation, showed that D. listerianum maintained comparable levels of fertilisation at sperm concentrations two or three orders of magnitude lower than the echinoderm. Laboratory clones of D. listerianum displayed surprisingly high levels of sexual incompatibility. Fecundities of numerous pairwise crosses varied widely and suggested a continuous scale of computability. Although correlations of computability between reciprocal crosses appeared positive, considerable noise was present in the data and some crosses showed strongly asymmetrical compatibility. Patterns of sperm precedence with a five-day mating internal showed clear initial bias towards the first of two acting males. The proportion of second-male paternity (P2) subsequently increased with time. Estimated P2 for entire progeny arrays was consistently greater than 0.5, but varied widely. When mating interval was reduced, mate order effects appeared to be moderated. In competition with an alternative sperm source, acting males fathered more progeny if previously mated to a particular female than if no mating history existed, an advantage probably derived from fertilisations by stored sperm. When virgin acting female colonies were given mixtures of sperm at widely divergent concentrations, offspring were shared between the two sperm sources in approximately the ratio of each mixture. However, there existed a small but statistically significant deviation from the fair raffle model, in that sperm at the lower concentration consistently achieved a greater than expected share of paternity. Environmentally-determined fixed female preferences could be responsible for this negative frequency dependence ('rare male effect').
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Rocha, Rosana Moreira da. "Ascidias coloniais do canal de São Sebastião, SP : aspectos ecologicos." [s.n.], 1988. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316337.
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Orientador : A. Cecilia Z. AmaralDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Apesar dos Ascidiacea constituirem um grupo muito comum nos costões rochosos do litoral de São Paulo, foram muito pouco estudados, principalmente no que se refere aos aspectos da biologia e ecologia das espécies. No Canal de São Sebastião existe uma fauna diversificada de ascídias coloniais que recobre a face inferior de pequenos blocos de rocha, tocas e frestas. O interesse em estudar alguns aspectos da biologia das espécies, suas interações na comunidade e a influência dos mesmos na colonização e manutenção do espaço foi o que levou à execução deste trabalho. O estudo do período reprodutivo foi feito através da imersão mensal de placas de recrutamento de lajota natural. O estudo da forma e velocidade de crescimento e da sucessão de ascídias coloniais, incluindo observações sobre interações entre as espécies, foi feito através do acompanhamento de placas artificiais durante 9 meses, imersas em duas épocas diferentes (verão e inverno). As cinco espécies estudadas em maior detalhe foram: Didemnum speciosum, Diplosoma macdonaldi, Clavelina oblonga, Symplegma viride e Botrylloides nigrum, pois eram as mais frequente no substrato artificial. Estas espécies apresentaram período reprodutivo longo com interrupção nos meses mais frios, observada em C. oblonga e B. nigrum. ...Observação: O resumo, na íntegra, poderá ser visualizado no texto completo da tese digital
Abstract: Although ascidians are very abundant on rocky shores of the Southeastern Brazilian coast (Sao Paulo State), there is little information about the species biology and ecology. In the São Sebastião Channel occurs a diversified fauna of compound ascidians, which cover the underside surface of boulders, crevices and cracks. To fulfill this gap of knowledge, the study of some life-history features of the ascidian species their interrelations in the community and how these aspects influence their colonization and space maintenance ability was undertaken. The reproductive period was determined by observations of one-month submerged artificial plates throughout one year, and by dissecting colonies to look for larvae. The ascidian community succession starting on clean plates were monthly observed on 9 month submerged plates, .on which the shape and growth rate of the colonies was also analyzed. Five species were discussed: Didemnum speciosum, Diplosoma macdonaldi, Clavelina oblonga, Symplegma viride e Botrylloides nigrum. They showed a long reprodutive period with a short interruption in C. oblonga and B. nigrum during winter. ...Note: The complete abstract is available with the full electronic digital thesis or dissertations
Mestrado
Mestre em Ecologia
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Casso, Carrasco Maria. "Genomic analysis of an introduced ascidian and implications for invasiveness." Doctoral thesis, Universitat de Barcelona, 2020. http://hdl.handle.net/10803/673998.
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Invasive species constitute a major threat to global biodiversity and cause important economic losses and ecological impacts. In the marine realm, ascidians include several aggressive invasive species, some of which have worldwide colonisation ranges, such as Didemnum vexillum. In this thesis, some biological and ecological characteristics implicated in the invasiveness of the species are assessed. First, we performed a 20 month monitoring to determine settlement and growth preferences of invasive ascidian species in the Ebro Delta aquaculture facility, including D. vexillum. Our results indicated that D. vexillum has a preference for complex substrates. To minimise fouling on bivalves, spat immersion during fall and below 1 m depth is recommended. To detect new introduced species, a follow-up program based on occurrences would be sufficient. Second, a protocol for small DNA samples combining whole genome amplification (WGA) and genotyping-by-sequencing (GBS) was developed and applied to D. vexillum using a single zooid per colony to determine patterns of genomic diversity and differentiation, describe the colonisation history of the species, and study its capability to form chimeras. Our results confirmed that Japan is in the native area of the species and only one clade spread worldwide. We found that the two main mitochondrial clades are strongly differentiated at the genomic level suggesting reproductive isolation, we determined that three independent colonisation events shaped the global distribution of the species, and we found that populations are diverse and well differentiated indicating a high expansion potential of D. vexillum. Third we detected high prevalence of chimerism, and fusion was unlinked to global genetic relatedness. Finally, we analysed the microbiome of D. vexillum that showed markedly different composition than a congeneric species and water. The invasive clade had a small but abundant core and a highly diverse variable microbiome component with a strong capacity to enrich the symbionts from the environment. The microbiome structure correlated to host genetic distance, temperature and geographical distances, pointing to vertical and horizontal transmission. In conclusion, D. vexillum is an aggressive invasive species with a high adaptive capacity that may contribute to the invasiveness of this global pest.
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Yu, Deli. "Temporal control of muscle gene expression in an ascidian embryo." Kyoto University, 2019. http://hdl.handle.net/2433/242897.
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Stoner, Douglas Steven. "Life History and Populationi Biology of the Colonial Ascidian Diplosoma Similis." Thesis, University of Hawaii, Honolulu, 1989. http://hdl.handle.net/10125/18144.
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This dissertation examines two issues related to the
ecological and evolutionary consequences of sexual and
asexual reproduction in colonial marine invertebrates.
The first two chapters explore the extent to which the
planktonic larval phase limits the distribution and
abundance of a colonial ascidian, Oiplosoma similis. The
third chapter examines some of the fitness consequences
of alterations in the pattern of asexual reproduction by
colony fragmention in similis. All research was
carried out on the fringing coral reef surrounding
Coconut Island which is located in Kaneohe Bay, Oahu,
Hawaii.Typescript. Thesis (Ph. D.)--University of Hawaii at Manoa, 1989. Includes bibliographical references.
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Mortimer, Sandra 1981. "Experimental analysis of trans-splicing of an ascidian troponin I gene." Thesis, McGill University, 2007. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=101643.
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I investigated SL trans-splicing in the troponin I gene of Ciona intestinalis. Experimental mutation of the AG dinucleotide adjacent to the natural trans-splice acceptor site (-64) in CiTnI/nuclacZ constructs eliminated trans-splicing to that site in Ciona embryos but activated trans-splicing at cryptic acceptor sites at -76 and -39, adjacent to the nearest AG dinucleotides. However, not all AG dinucleotides specify cryptic acceptor sites because outron internal deletions or 3'truncation mutants were trans-spliced at a far-upstream AG-adjacent cryptic site (-346), leaving many AGs in the retained outron segments. Thus, additional sequence elements that are present only in the -346 and -76/-64/-39 regions are required for cryptic acceptor activity. All mutant constructs generated detectable beta-gal enzyme expression, although the mutant with the longest retained-outron segment appeared less active. Therefore, mRNA accumulation and translation do not require trans-splicing to the natural acceptor site, although they may be facilitated by the normal removal of the outron during trans-splicing.
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Davis, Martin Herbert. "Physical factors influencing larval behaviour in three species of solitary ascidian." Thesis, Open University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.388307.
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Milne, Bruce Forbes. "Theoretical studies of cyclic octapeptides from the marine ascidian Lissoclinum patella." Thesis, University of Aberdeen, 2002. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU168052.
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A comparative theoretical study of oxazole and thiazole was carried out in order to evaluate the performance of several theoretical methods that might be useful in studies on the much larger patellamides (1-8), a family of cyclic octapeptides from the marine ascidian Lissoclinum patella. Several density functional theory (DFT) methods were included in this study and it was found that whilst all the functionals tested performed well, HCTH and B3LYP gave results that were better than those obtained at the Hartree-Fock level and equal to or better that the MP2 method but at reduced computational cost. As a result of this preliminary work the B3LYP functional was chosen and the 6-31G(d,p) basis selected for use in the patellamide study. This level of theory was also chosen for studies of the Cu2+ binding site in the patellamides with the SBKJC effective core potential basis. (Fig. 3772) Equilibrium geometries and energies were obtained for a number of conformers/rotamers of ascidiacyclamide (1) and patellamides A (2), C (4) and D (5) at the B3LYP/6-31G(d,p) level and were used to help rationalise the empirical observations that substitutional asymmetry appears to be responsible for determining the conformational (folding) preferences in these peptides. The results showed that the energy change on folding (DeltaEfolding) was positive for all four peptides but that the various substitutions significantly reduced the magnitude of DEfolding compared with the C2 symmetric 1. Desymmetrisation of the oxazoline rings in 2 gives rise to changes in the b-turn forming portions of the macrocycle, leading to improved folding at these positions. Alternatively, the local structure around the two thiazole ring containing regions can be altered by substitution at R1 and R3, leading to improved closure of the macrocycle outwith the beta-turn and improved pi-stacking between these moieties and shorter hydrogen bonding distances in other areas of the macrocycle.
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Olguín, Uribe Guillermo. "L'ascidie mexicaine Stomozoa murayi (Kott, 1957) : chimie et écologie chimique en rapport avec son environnement bactérien." Perpignan, 1997. http://www.theses.fr/1997PERP0288.
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Cette these est consacree a l'etude de l'ascidie mexicaine stomozoa murrayi (kott, 1957) des recifs de corail des caraibes, qui n'est pas colonisee par des macro-epibiontes. Cette espece est decrite pour la premiere fois en mer des caraibes et elle donne lieu a une investigation chimique et ecologique. L'extraction chimique de cet organisme a conduit a l'isolement de l'indole-3-carbaldehyde et du 6-bromoindole-3-carbaldehyde. Ces deux composes, obtenus auparavant d'autres organismes marins, ont ete detectes en cg/sm dans la culture de la bacterie acinetobacter lwoffii, isolee de la surface de s. Murrayi. Le compose brome montre une inhibition in vitro de la fixation des larves de balane, des proprietes antibacteriennes moderees, mais ne montre pas d'activites antialgales ni phagorepulsives vis a vis de poissons. La bacterie a. Lwoffii pourrait jouer un role important en la faible colonisation sur la surface de l'ascidie s. Murrayi comme nous l'avons observe in situ.
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Callahan, Ashley G. "Harbour survey and genetic analysis of non-indigenous ascidian tunicates in Newfoundland /." Internet access available to MUN users only. Search for this title in:, 2009.
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Dias, Gustavo Muniz. "Estrutura de comunidade e variabilidade genetica de ascidias coloniais do entremares rochoso." [s.n.], 2004. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316080.
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Orientadores: Luiz Francisco Lembo Duarte, Vera Nisaka SolferiniDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Mestrado
Ecologia
Mestre em Ecologia
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Green, Kathryn Margaret. "Morphological changes during normal and pertubed metamorphosis of the ascidian herdmania curvata /." St. Lucia, Qld, 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16468.pdf.
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Khare, Parul. "CIS-regulatory elements driving muscle-specific expression of an ascidian troponin I gene." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=84044.
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My research goal was to functionally dissect the regulatory region of the gene encoding the muscle protein troponin I (TnI) in the simple chordate Ciona intestinalis. Based on evolutionary sequence conservation and computational prediction of cis-elements in the regulatory region, I designed mutants and assayed their effects in a recombinant DNA construct reporter system. I electroporated TnI DNA-linked reporter constructs into Ciona zygotes and assayed reporter activity following 12-14 hr of development. These studies showed that a conserved E-box is essential for high-level embryonic tail muscle-specific expression whereas conserved MEF-2 and overlapping CREB/TEF-1 sites were not. I carried out functional promoter identification experiments and 5' RACE studies and localized the core-promoter/transcription start-site in the Ciona TnI gene. My results point out the similarities/differences between Ciona and vertebrate Tnl gene regulation, which presumably reflect the conservation/modification of TnI gene regulatory mechanisms during chordate/vertebrate evolution.
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Prünster, Maria Mandela. "De novo myogenesis and neurogenesis during budding of the colonial ascidian, Botryllus schlosseri." Electronic Thesis or Diss., Sorbonne université, 2018. http://www.theses.fr/2018SORUS586.
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Le but de mon projet était de décrire les molécules impliquées dans le développement asexué de l'ascidie coloniale Botryllus schlosseri et d'en déduire les mécanismes associés. Les ascidies appartiennent au sous embranchement des Tuniciers, groupe frère des Vertébrés. Elles sont les organismes les plus proches de l'humain capable de se reproduire de manière asexuée par bourgeonnement. Le travail a été réalisé sur l'ascidie coloniale Botryllus qui est composée de plusieurs individus (zoïde) réunis dans une tunique commune. Lors du développement asexué de Botryllus le zoïde peut sauter les stades embryonnaires et larvaires pour directement former un nouveau corps adulte incluant toute la musculature et le système nerveux en bourgeonnant. Dans le but d'étudier l'origine cellulaire et les mécanismes sous-jacents potentiels à la myogenèse non embryonnaire, j'ai suivi l'expression de ces gènes myogéniques lors du bourgeonnement de Botryllus et j'ai reconstruit la dynamique des précurseurs des muscles. Les orthologues de ces molécules ne sont pas exprimés seulement chez les ascidies mais également lors du développement du muscle cardio-pharyngé chez les Vertébrés et l'origine commune du cœur et des muscles pharyngés dans le champ cardio-pharyngé était déjà présente chez l'ancêtre commun des Tuniciers et des Vertébrés. En étudiant l'origine cellulaire lors de la neurogenèse j'ai pu observer que des gènes larvaires qui déterminent l'axe antérieur postérieur (AP) ont été cooptés dans une structure transitoire neuronale qui donne le ganglion cérébroïde. Ils divisent la structure en trois parties, évoquant ainsi de la tripartition de système nerveux des VertébrésThe aim of this work is to describe via molecular-biological methods the asexual form of development of the colonial ascidian Botryllus schlosseri focusing on the formation of different tissues, namely muscles and nervous system, as well as exploring the potential presence of structures or cells homologous to the neural crest. Ascidians belong to the subphylum tunicates, sister group of vertebrates and are the closest relatives to man that can reproduce asexually, by budding. As colonial ascidian, the metamorphosis of Botryllus schlosseri specimen is followed by a lifelong, recurring, highly coordinated budding process, where multiple individuals (zooids) are connected and embedded in a common tunic. During asexual development, zooids can develop in a direct manner without embryonic and larval stages. To study the cellular origin and mechanisms of non-embryonic myogenesis I followed the expression pattern and dynamics of myogenic genes during asexual development and reconstructed muscle precursors. Orthologs of these genes are not only expressed during muscle formation via larval development but also during the formation of cardio-pharyngeal muscles in the vertebrate embryogenesis. I further drew a comparison of the regionalization of a transitory neurogenic structure, the dorsal tube, along the anteroposterior axis during budding with its larval counterpart, the neural tube, thus adding a RNA-expression profile of neural genes hereby proposing a scenario of cerebral ganglion formation by delamination. To better understand the nature of the dorsal tube and gangliogenesis I investigated potential involvement gene orthologs implemented in vertebrate neural crest formation
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Corbo, Joseph C. "Molecular aspects of notochord and nervous system development in the ascidian, Ciona intestinalis /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1997. http://wwwlib.umi.com/cr/ucsd/fullcit?p9735267.
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Virata, Michael J. "A novel invertebrate chordate model for Alzheimer's disease using the ascidian ciona intestinalis." Diss., [La Jolla, Calif.] : [San Diego] University of California, San Diego ; San Diego State University, 2009. http://wwwlib.umi.com/cr/ucsd/fullcit?p3372801.
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Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2009.Title from first page of PDF file (viewed October 22, 2009). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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Yagi, Kasumi. "Studies on function of Zic family transcription factor genes in early ascidian embryos." 京都大学 (Kyoto University), 2004. http://hdl.handle.net/2433/147859.
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Paiva, Amarilis Brandão de. "Estudo comparativo das assembleias de ascidias em duas regiões portuárias da costa brasileira." reponame:Repositório Institucional da UFC, 2013. http://www.repositorio.ufc.br/handle/riufc/13954.
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PAIVA, A. B. de. Estudo comparativo das assembleias de ascidias em duas regiões portuárias da costa brasileira. 2013. 86 f. Dissertação (Mestrado em Ciências Marinhas Tropicais) - Instituto de Ciências do Mar, Universidade Federal do Ceará, Fortaleza, 2013.Submitted by Nadsa Cid (nadsa@ufc.br) on 2015-11-12T20:25:50Z No. of bitstreams: 1 2013_dis_abdepaiva.pdf: 2539144 bytes, checksum: 02eaf6062ba30b8a2b146c0c8f1ad616 (MD5)
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The intensification of the maritime transport around the world is coupled with an increase in the harbors and dockings infrastructure. These structures provide hard substrata for a generally abundant and diverse encrusting fauna. It has been demonstrated that artificial substrata in ports and marinas may harbor a considerable amount of exotic species. Ascidians are among the most important groups in such environments, being transported in the hulls or ballast water of ships connecting different regions. The present study investigate the assemblage of ascidians encrusting settling plates in two different harbor areas, distant more than 20º of latitude along the Brazilian coast. The polystyrene settling plates measured 12 x 12 cm were arranged in pairs, forming a “sandwich” with a 2cm space between them, and were kept submerged for periods of three months and one year, while the experiment lasted two years. The species richness of both areas was just slightly different (33 species in Ceará and 31 in São Paulo). On the other hand, Ceará presented a larger species richness per plate than São Paulo. In São Paulo, at the limit of the tropics, a stronger influence of seasonality was detected in terms of species composition between different periods. The compositions of the assemblages from the plates submerged for three months and one year was also different. The assemblage recruiting the internal and external faces of the plates sets were also different in terms of specific composition. The yearly plates presented a lower coverage of ascidians when compared to the quarterly plates, with a corresponding increase in coverage for other groups such as sponges and bryozoans. The internal faces of yearly plates showed a greater abundance of solitary ascidians, mainly Ascidia sydneiensis. The species Rhodosoma turcicum was recorded for the first time in the northern Brazilian coast. The presence of many exotic or cryptogenic species at the studied areas highlights the importance of continuous regular monitoring of the encrusting fauna in harbors and marinas.
A intensificação do transporte marítimo ao redor do mundo vem aumentando junto com a infraestrutura de áreas portuárias. Estas estruturas proporcionam substratos rígidos que passam a abrigar uma fauna incrustante, em geral, rica e abundante. Já se demonstrou que substratos artificiais nestas áreas podem abrigar um contingente considerável de espécies exóticas. Dentre os grupos que recrutam em tais ambientes, as ascídias se destacam, podendo ser transportadas por navios entre diferentes regiões, tanto por água de lastro como por incrustações nos cascos. Neste trabalho foi realizado um levantamento das assembleias de ascídias que incrustam em placas de recrutamento artificiais, em duas regiões portuárias com mais de 20º de diferença latitudinal na costa brasileira. Os experimentos foram realizados no Porto do Pecém – CE e em uma marina no canal de São Sebastião – SP. Foram utilizados pares de placas de polietileno (12 x 12 cm), espaçadas em 2 cm formando “sanduíches”, submersas por períodos de três meses e de um ano para verificar o recrutamento da comunidade incrustante. O experimento teve duração de dois anos. A riqueza de ascídias encontrada em cada local não foi muito diferente (33 espécies no Ceará e 31 em São Paulo). No entanto, o Ceará, região de menor latitude, apresentou uma maior riqueza por placa. Em São Paulo, latitude subtropical, verificou-se uma maior influência da sazonalidade na composição das espécies dos diferentes períodos. Foram observadas diferenças nas composições das placas de três meses com as de um ano de submersão e também diferenças na composição das assembleias de ascídias nas faces internas e externas dos pares de placas. Comparando as placas trimestrais e anuais, foi detectada uma menor porcentagem de cobertura pelas ascídias nas placas anuais externas, ocorrendo aumento de outros grupos, principalmente esponjas e briozoários. Nas faces internas das placas anuais ocorre aumento da abundância de ascídias solitárias, principalmente da espécie Ascidia sydneiensis. A presença da ascídia Rhodosoma turcicum em placas do Ceará caracterizou o primeiro registro desta espécie para o nordeste setentrional brasileiro. A presença de muitas espécies exóticas e criptogênicas nas regiões de estudo alerta para a importância de monitoramentos contínuos das espécies em regiões portuárias.
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Häussler, Maximilian. "Prediction of tissue-specific cis-regulatory sequences : application to the ascidian Ciona intestinalis and the anterior neurectoderm." Paris 11, 2009. http://www.theses.fr/2009PA112078.
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Au cours de mon travail de thèse, j'ai établi une procédure pour ordonner des motifs courts selon leur distribution dans le génome de C. Intestinalis autour d'un ensemble de gènes : plus une combinaison de motifs est regroupée autour des gènes exprimés spécifiquement dans un tissu, plus le score est élevé. Dans cette approche, j'ai intégré les résultats de la dissection d'un enhancer exprimé dans le neurectoderme antérieur qui indiquait une structure dupliquée. Ma procédure montre que les sites GATTA dupliqués sont une caractéristique générale des éléments cis-régulateurs du neurectoderme antérieur. Une recherche dans le génome entier pour ces séquences suivi par un test in-vivo montre une expression dans ce territoire pour la moitié des éléments. Par la suite, j'ai essayé d'améliorer l'annotation des séquences cis-régulatrices déjà publiées, par une extraction automatique à partir de la littérature. Grâce à l'augmentation du nombre de publications en accès libre et l'amélioration des procédures expérimentales de plus en plus de ce type de données est disponible. Finalement, j'ai montré que malgré l'absence d'alignements non-codants entre les génomes des vertébrés et C. Intestinalis, on peut cependant trouver quelques loci avec une conservation extrême de l'arrangement des gènes. Pour ces cas, la recherche des éléments cis-régulateurs peut être limitée aux introns du gène voisin, ce qui était confirmé dans la littérature pour certains. Ces trois approches montrent l'utilité de la bioinformatique pour une meilleure caractérisation des séquences cis-régulatrices et ouvrent la voie aux validations expérimentales supplémentairesIn this thesis, a procedure is presented to rank combinations of short sequence motifs by their distribution around a set of genes. The better a combination matches around genes expressed in a certain tissue, the higher is its score. I applied this to an already characterized enhancer of C. Intestinalis expressed in the anterior neurectoderm which had been found by systematic mutations to be composed of a duplicated structure. The results of my procedure indicated that duplicated GA TTA-sites are an essential feature of cis-regulatory elements active in the anterior neurectoderm. Searching the genome for matches to this signature resulted in putative enhancers that drive a reporter gene in 50% of the cases in the anterior neurectoderm. In addition, I tried to improve the curation of already published cis-regulatory elements by extracting them automatically from the full text of the biological research articles. Thanks to the thriving open access publishing model and the improvement in experimental assays, more and more of this data is becoming available. Finally, I showed that in the absence of non-coding sequence alignments between the genomes of vertebrate and C. Intestinalis, one can nevertheless find a handful of loci with a very unusually conserved gene order. In these cases, the cis-regulatory search space is reduced to a set of introns, some of which were recently shown to harbor enhancers. Many of these loci have not been analyzed yet. Together, these computational approaches should lead to a better characterization of cis-regulatory sequences and pave the way for further experimental validations
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Haupaix, Nicolas. "Régulation de la voie MEK/ERK par la signalisation éphrine lors du développement neural chez l'ascidie Ciona intestinalis." Phd thesis, Université Nice Sophia Antipolis, 2014. http://tel.archives-ouvertes.fr/tel-01059798.
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Durant ma thèse, j'ai participé à une étude fonctionnelle qui a démontré que p120-RasGAP, une protéine appartenant à la famille GAP (GTPase-activating protein), est le médiateur cytoplasmique de l'éphrine lors de l'atténuation d'ERK1/2. Pour confirmer cela, j'ai réalisé une expérience de co-immunoprécipitation et j'ai démontré que p120-RasGAP s'associe au récepteur de l'éphrine, Eph3, quand celui-ci est activé par un ligand éphrine. Ce résultat indique fortement que les signaux FGF et éphrine convergent au niveau de Ras et qu'ils contrôlent de manière antagoniste son activité. Dès lors, j'ai analysé les autres événements de spécification cellulaire impliquant l'antagonisme FGF/éphrine. Chez l'embryon d'ascidie, le signal FGF est décrit comme inducteur du destin neural dans les cellules ectodermiques qui, en absence du signal FGF, adoptent le destin épidermique. L'induction neurale des ascidies a lieu au stade 32 cellules et se traduit par la spécification de quatre précurseurs neuraux (ERK+) parmi les 16 cellules ectodermiques. J'ai démontré que le signal éphrine/Eph/RasGAP antagonise le signal FGF pour générer une activation d'ERK1/2 de type tout ou rien parmi les cellules ectodermiques. Enfin, en collaboration avec Philip Abitua, doctorant dans le laboratoire du Dr. Mike Levine (UC Berkeley), nous démontrons que l'antagonisme entre les signaux éphrine et FGF est impliqué dans la régionalisation antéro-postérieure de la plaque neurale