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<p>The formation of a single lumen during tubulogenesis is crucial for the development and function of many organs. Although 3D cell culture models have identified molecular mechanisms controlling lumen formation in vitro, their function during vertebrate organogenesis is poorly understood. In this work we used the zebrafish gut as a model to investigate single lumen formation during tubulogenesis. Previous work has shown that multiple small lumens enlarge through fluid accumulation and coalesce into a single lumen. However, since lumen formation occurs in the absence of apoptosis, other cellular processes are necessary to facilitate single lumen formation. </p><p>Using light sheet microscopy and genetic approaches we identified a distinct intermediate stage in lumen formation, characterized by two adjacent un-fused lumens. These lumens are separated by cell contacts that contain basolateral adhesion proteins. We observed that lumens arise independently from each other along the length of the gut and do not share a continuous apical surface. Resolution of this intermediate phenotype into a single, continuous lumen requires the remodeling of basolateral contacts between adjacent lumens and subsequent lumen fusion. </p><p>Furthermore, we provide insight into the genetic mechanisms regulating lumen formation through the analysis of the Hedgehog pathway. We show that lumen resolution, but not lumen opening, is impaired in <italic>smoothened (smo)</italic> mutants, indicating that fluid-driven lumen enlargement and resolution are two distinct processes. We also show that <italic>smo</italic> mutants exhibit perturbations in the Rab11 trafficking pathway, which led us to demonstrate that Rab11-mediated recycling, but not degradation, is necessary for single lumen formation. Taken together, this work demonstrates that lumen resolution is a distinct genetically-controlled process, requiring cellular rearrangement and lumen fusion events, to create a single, continuous lumen in the zebrafish gut.</p> / Dissertation

In higher plants oxygenic photosynthesis primarily takes place in the chloroplasts of leaves. Within the chloroplasts is an intricate membrane system, the thylakoid membrane, which is the site of light harvesting and photosynthetic electron transport. Enclosed by this membrane is the lumen space, which initially was believed to only contain a few proteins, but now is known to house a distinct set of &gt;50 proteins, many for which there is still no proposed function. The work presented in this thesis is focused on understanding the functions of the proteins in the lumen space. Using proteomic methods, we investigated first the regulation of lumenal proteins by light and secondly by dithiol-disulphide exchange, mediated by the disulphide reductase protein thioredoxin. We furthermore performed structural and functional studies of the lumenal pentapeptide repeat proteins and of the PsbP-domain protein PPD6. When studying the diurnal expression pattern of the lumen proteins, using difference gel electrophoresis, we observed an increased abundance of fifteen lumen protein in light-adapted Arabidopsis thaliana plants. Among these proteins were subunits of the oxygen evolving complex, plastocyanin and proteins of unknown function. In our analysis of putative lumenal targets of thioredoxin, we identified nineteen proteins, constituting more than 40 % of the lumen proteins observable by our methods. A subset of these putative target proteins were selected for further studies, including structure determination by x-ray crystallography. The crystal structure of the pentapeptide repeat protein TL15 was solved to 1.3 Å resolution and further biochemical characterization suggested that it may function as a novel type of redox regulated molecular chaperone in the lumen. PPD6, a member of the PsbP-family of proteins, which is unique in that it possesses a conserved disulphide bond not found in any other PsbP-family protein, was also expressed, purified and crystallized. A preliminary x-ray analysis suggests that PPD6 exists as a dimer in the crystalline state and binds zinc ions. The high representation of targets of thioredoxin among the lumen proteins, along with the characterization of the pentapeptide repeat protein family, implies that dithiol-disulphide exchange reactions play an important role in the thylakoid lumen of higher plants, regulating processes such as photoprotection, protein turnover and protein folding.

Formation of a tubular organ, such as the heart, requires cells to integrate positional and polarity signals in order to enclose a fluid or gas transporting lumen. Developing tubes must establish a site for lumen initiation, demarcate membrane domains, and modulate cell polarization and morphology. The Drosophila melanogaster embryonic heart is a mesodermal tube model displaying a unique polarity, reminiscent of vertebrate vasculature. We have characterized a role for the transmembrane adhesion receptor αPS3βPS1 integrin and its cytoplasmic adaptor Talin in heart tubulogenesis. βPS1 and Talin are early indicators of the luminal site and Talin-mediated integrin function is essential for cardioblast polarization and morphology prior to and during lumen development. Careful analysis of hearts in embryos homozygous for a null allele of rhea, the gene encoding Talin, reveals that Talin is required to correctly orient the heart cell polarity such that a continuous central open lumen is enclosed. Without proper integrin or Talin function, the luminal determinants Slit and its receptor Robo are not stabilized within the heart, a central lumen fails to form, and the midline is instead marked by continuous adhesion. Furthermore, although Talin is essential for proper βPS1 integrin localization within the heart, either of Talin’s two integrin binding sites are sufficient to stabilize βPS1 along the luminal domain and establish an open cardiac tube. Taken together, our findings reveal an instructive role for integrins and Talin in communicating polarization cues central to heart tubulogenesis. / Thesis / Doctor of Philosophy (PhD)

The pancreas is a secretory organ composed of exocrine and endocrine compartments. During development, endocrine cells delaminate from the pancreatic epithelium to associate with the local vasculature where they will secrete hormones such as insulin into the blood stream. The exocrine pancreas is composed of ductal cells which form a network of tubes to secrete and transport fluid carrying the digestive enzymes secreted from acini located at the terminal ends of ductal branches. Unlike many branched epithelia, the pancreas does not exhibit a stereotypical branching pattern. The ductal network develops from a mesh of interconnected lumens which are eventually pruned and give rise to a final tree-like structure optimized for the most economical delivery of enzymes and fluid to the digestive tract. In silico modelling suggests that fluid flow plays a role in resolving the final structure of the ductal network during development, indicating that physical forces may play a role in this self-organization Recent work in the adult human pancreas has shown that the cells of the small ducts in the most distal parts of the ductal network do not express the same transcripts as the proximal large ducts. The pancreas derives this structure and function from the differentiation and self-organization of progenitors into terminally differentiated cells which, together with mesenchymal cells and vasculature, contribute to the tissue niche of the organ. Despite the importance of this process in development and disease, little is known about how pancreatic progenitors balance differentiation with morphogenesis. The goal of this project was to uncover niche components that influence the differentiation of pancreas progenitors, and understand how identity and morphogenesis are mediated by niche-driven changes in gene expression. This remains a challenging process to understand due to limited accessibility of the embryonic pancreas. Therefore, human sphere and organoid models represent a valuable tool to address this question and were used together with expression profiling and manipulation of the extracellular environment to understand this relationship during pancreas development. Time-course bulk RNA sequencing of human pancreas progenitor spheres at different days of culture revealed the sequential processes happening as the cells form their niche, and then start proliferating and forming lumen. Notably, at the stage of lumen expansion, we observed an upregulation of genes associated with ductal epithelia, such as CFTR, MUC1, MUC6, and CA2 in tandem with increased expression of genes encoding proteins for ion and fluid secretion. This suggested hydraulics may act to integrate ductal differentiation with luminogenesis, which is consistent with in silico modelling and the secretory function of the pancreatic epithelia. Indeed, driving chloride ion secretion with the CFTR activator forskolin resulted in inflation of the sphere lumen and increased the expression of the ductal genes identified above. Induction of CFTR and MUC1 can also be achieved by inflating the lumen in a CFTR-independent manner using prostaglandin E2. This revealed the changes in gene expression were not due to a small feedback loop under the control of CFTR, and maybe due to morphological changes related to lumen inflation. Importantly, it was revealed that the induction of Cftr expression upon lumen inflation also occurred in pancreas explants isolated from embryonic mice, which suggests the relationship between lumen inflation and ductal identity is conserved between mouse and human. Datamining of single cell RNA sequencing of adult and fetal pancreas samples identified novel marker genes for progenitor, acinar, and large- and small-ducts of the human fetal pancreas. Comparison of these marker genes with gene expression patterns of pancreas progenitor spheres revealed a shift to a small-duct-like identity when the lumen is inflated. This shift seemed to be dependent on inflation of the lumen rather than cAMP signalling, as it is not observed in pancreas progenitors grown in 2D and treated with forskolin. The above experiments suggest a link between lumen inflation and small duct identity but the exact mechanism remains unclear. Lumen inflation is likely driven by an increase in hydrostatic pressure that occurs downstream of changes in osmotic pressure due to ion channel activation. Independent manipulation of osmotic pressure, hydraulic pressure, tissue stretching, and fluid shear stress will be valuable to decipher the mechanisms of ductal gene regulation. Taken together these results support the hypothesis that differential gene expression in ducts of different sizes is regulated by mechanical forces in the pancreas, and 3D sphere culture represents a powerful model to investigate these processes in finer detail.

[pt] A presente dissertação trata da questão de Maria dentro do Cristianismo, no âmbito do diálogo entre a Igreja Católica e as Igrejas protestantes. Partimos de uma abordagem sobre o ecumenismo na atualidade, com ênfase no ecumenismo espiritual, para situarmos um contexto no qual se pode aprofundar o tema de Maria. A perspectiva que adotamos foi a aproximação do ensinamento do Magistério da Igreja, conforme o Capítulo VIII da Constituição Lumen Gentium, com o qual confrontamos o livro do Grupo de Dombes Maria no desígnio de Deus e a Comunhão dos Santos, que tomamos com ponto central desta dissertação. Esse livro foi vivamente investigado e apresentamos um resumo do seu conteúdo com suas propostas de interesse ecumênico. Do mesmo livro levantamos as ideias que são tratadas nas seções finais da explanação. Nestas seções, iniciamos por enfatizar aspectos do diálogo com a Comissão Internacional Anglicano-Católica Romana (ARCIC) e a Federação Luterana Mundial. A seguir, identificamos pontos de contato do livro de Dombes e da Constituição Lumen Gentium com a Exortação Marialis Cultus, como chave para aproximações sobre uma visão da figura de Maria, tendo também em conta a ótica de alguns outros autores, em contribuições atuais. Desenvolvemos, no final, alguns aspectos teológicos e pastorais do tema, ainda em perspectiva ecumênica, e apontamos, em especial, para os elementos promotores de consenso entre as Igrejas verificados na pesquisa. Foram priorizadas metodologias e propostas que pudessem servir de base para o desenvolvimento do diálogo ecumênico sobre Maria. / [en] This dissertation deals with the question of Mary within Christianity, in the context of the dialogue between the Catholic Church and the Protestant Churches. We started with an approach to ecumenism today, with an emphasis on spiritual ecumenism, to situate a context in which the theme of Mary can be deepened. The perspective that we adopted was the approach of the teaching of the Magisterium of the Church, according to Chapter VIII of the Constitution Lumen Gentium, with which we confronted the book of the Dombes Group Mary in the design of God and the Communion of Saints, that we took as the central point for this dissertation. This book was thoroughly investigated and we presented a summary of its content with its proposals of ecumenical interest. From the same book we raised the ideas that are dealt with in the final sections of the explanation. In these sections, we started by emphasizing aspects of the dialogue with the Anglican Roman Catholic International Commission (ARCIC) and the Lutheran World Federation. Next, we identified points of contact from the book of Dombes and from the Constitution Lumen Gentium with the Exhortation Marialis Cultus, as key to approximations on a vision of the figure of Mary, also taking into account the perspective of some other authors, in current contributions. We developed, in the end, some theological and pastoral aspects of the theme, still in an ecumenical perspective, and we pointed, in particular, to the elements that promote consensus among the Churches verified in the research. Methodologies and proposals that could serve as a basis for the development of ecumenical dialogue on Mary were prioritized.

Bonaventure et la lumière : la question semble au premier abord et pour la plupart des médiévistes résolue. Pourtant, la genèse de sa définition de la lumière (II Sent., d. XIII) – notamment la manière dont les idées de Robert Grosseteste lui parviennent – reste encore à déterminer. L’idée d’un usage métaphorique et analogique de la lumière et de sa dimension épistémique permet de mieux évaluer la théorie de la connaissance comme lumière, c’est-à-dire son amplitude réelle souvent réduite à l’illumination divine de l’homme tant intellectuelle que morale. Cette connaissance de la lumière permettant de considérer la connaissance comme lumière par le truchement de la métaphore et de l’analogie donc toute une épistémologie par la lumière se vérifie dans la cosmologie et dans la théorie de la beauté du frère mineur où la lumière joue bien un rôle principiel et paradigmatique. Enfin, que toutes ces implications philosophiques et théologiques de la lumière soient récapitulées dans le Christ compris selon les Écritures, comme splendor, sol iustitiae, lux mundi, compréhension nettement inspirée de la lecture du quatrième évangile et du Livre de la Sagesse par Bonaventure, bachelier biblique, demande encore à être élucidé. C’est en cherchant tant du côté des études à la Faculté des arts de Paris de 1235-1243 que du côté des écrits de Bonaventure, bachelier biblique puis sententiaire, que la question de la lumière dans son œuvre peut être interprétée. Nous proposons donc dans cet ouvrage d’ouvrir quelques pistes de compréhension de la via lucis bonaventurienne. / Bonaventure and light: the issue seems at first and for most medievalists resolved.Yet the establishment of the genesis of his definition of light (II Sent., d. XIII) — and in particular the way in which Robert Grosseteste's ideas reach him — is still to be determined. The idea of a metaphorical and analogical use of light and its epistemic dimension makes it possible to evaluate better the theory of knowledge as light, that is, its actual amplitude, often reduced to the divine enlightenment of Man, both intellectual and moral. This knowledge of light, which makes it possible to consider knowledge as light through metaphor and analogy, and thus a whole epistemology by light, is verified in the cosmology and in the theory of beauty of the Friar Minor in which light plays indeed a principle-like and paradigmatic role. Finally, that all these philosophical and theological implications of light are recapitulated in Christ understood according to the Scriptures as splendor, sol iustitiae, lux mundi, an understanding clearly inspired by the reading of the fourth Gospel and the Book of Wisdom by Bonaventure, bachelor of the Bible, still needs to be elucidated. It is by seeking as much on the side of studies at the Faculty of Arts of Paris from 1235 to 1243 that on the writings of Bonaventure, as baccalaureus biblicus and then baccalaureus sententiarus, that the question of light in his work can be interpreted. We therefore propose in this book to open some avenues of understanding of the bonaventurian via lucis.

The functionalization of the outer lattice of in vitro reconstituted microtubules has paved the way for the development of diverse nano-device applications. The outer lattice has been metallized for the bottom-up synthesis of nanowires composed of various materials. Moreover, a wide range of biomolecules and nanoprobes have been attached to the outer surface for nano-scale transport and detection assays in conjunction with motor proteins. The functionalization of the outer lattice has certain implications: While the nanowires adopt the overall shape of the microtubules, their surface is inhomogeneous due to the absence of any morphological control. The attachment of cargo on the outer lattice creates a ‘roadblock effect’ hindering the transport activity of the motor proteins as they share a common substrate surface. In this project, the utilization of the hollow interior region of the microtubules, called the lumen (∼15 nm in diameter) is proposed to overcome these limitations. A strategy is developed to functionalize the microtubule lumen by targeting molecular cargo conjugated to lumen-binding (anti-acetyl alpha-tubulin lysine-40) antibodies. This would optimize existing motility-based applications as the outer surface would be exclusively available for the activity of the motor proteins. Furthermore, microtubules functionalized with luminal gold nanoparticle ‘seeds’ are utilized for the lumen-templated assembly of gold nanowires.

[pt] A comparação da eclesiologia de Irineu de Lião com a Lumen gentium surge no contexto do movimento de retorno às fontes cristãs nos séculos XIX e XX. O Concílio Vaticano II foi influenciado por este movimento no seu processo de aggiornamento da Igreja no mundo moderno. A nova perspectiva teológica, ainda em construção, influenciou o Concílio Vaticano II e as discussões eclesiológicas, tanto no que se referia à compreensão sobre Igreja quanto à sua atuação e presença no mundo. Tudo isso ficou mais notório com a elaboração da Constituição Dogmática Lumen gentium. De modo especial, Irineu de Lião, bispo e mártir do século II, surge como uma das fontes para este retorno na Lumem gentium que atesta duas citações diretas entre as cinco referências feitas ao texto dele em todo texto conciliar. O bispo de Lião não se incumbe de escrever um tratado teológico, na Adversus haereses e na Epideixis, mas se dedica a defender a fé cristã, que estava se emancipando das comunidades judaicas e ganhando sua autonomia de doutrina, de ensinamento e de culto. Paralelamente a este processo de emancipação crescem outras doutrinas diferentes no seio do cristianismo como foi o caso das doutrinas gnósticas. Para Irineu o conhecimento da verdade é a doutrina que a Igreja recebeu e ensina. Portanto, a agregação a Cristo necessita do conhecimento claro do que é a regula fidei, que norteará a compreensão das Sagradas Escrituras, ordenará o verdadeiro culto a Deus e conduzirá o fiel a testemunhar a presença de Cristo no mundo. A teologia sobre a Igreja em Irineu de Lião não se encontra sistematizada em seus livros, mas aparece em várias partes dos seus escritos enquanto formula suas denúncias e refutações. No entanto, para o bispo de Lião, a Igreja é obra de Deus, que criou o ser humano no seu amor de Pai, e como este se perdeu, enviou o seu Filho para recapitular toda a criação e reunir um novo povo, que ouvisse a sua voz e se voltasse para ele. O ressourcement, por mais que utilizasse de novas metodologias para a construção do pensamento teológico e o ensino de teologia, muitos dos padres conciliares ainda carregavam um modelo manualístico e indireto de abordagem teológica. Portanto, ao comparar o pensamento eclesiológico de Irineu com o desenvolvido na Lumen gentium, busca-se tanto as referências que estão no texto conciliar quanto as múltiplas concepções de Igreja que surjam por uma análise comparativa, para assim perceber como o modelo eclesiológico do início do cristianismo possibilita uma compreensão maior e mais profunda de um texto contemporâneo. / [en] The comparison of the Irenaeus of Lyon s ecclesiology with the Lumen gentium arises in the context of the return to the Christian Sources in the nineteenth and twentieth centuries. This move had a capital influence in the Second Vatican Council concerning the process of aggiornamento of the Church in the modern world. In this regard, the fresh theological perspective, that was still growing, had an impact both in the ecclesiological discussions and the comprehension about the presence and action of the Church in the world. Furthermore, this whole set has increased in importance through the devising of the Dogmatic Constitution Lumen gentium. Particularly, Irenaeus, bishop of Lyon and martyr of the second century, emerges as a central source for the Lumen gentium since the Constitution includes five references of his writings, two of which are direct quotes. Both in Adversus haereses and Epideixis, the bishop of Lyon doesn t aim to write a theological treatise. Instead of that, his target is to defend the Christian faith, which was emancipating from the Jewish communities and achieving autonomy in the doctrine, the teachings, and the way of cult. In parallel with this emancipation process, different doctrines gain ground within Christianity, as, for example, the gnostic ones. However, according to Irenaeus, the only knowledge of the truth comes from the doctrine which the Church holds and teaches. As a result, for someone to belong to Christ it is mandatory to clearly know the regula fidei, which instructs about the comprehension of the Holy Scriptures, organizes the real God s cult, and guides the devotee to testify Christ s presence in the world. There isn t a systematic Theology about the Church in Irenaeus of Lyon‘s works, but this matter is recorded in many of his complaints and denials. It can be noticed by the fact that, to him, the Church is God s work. As the human being got apart from the Father s love, God has sent his own Son to recapitulate the whole creation and gather a New People, that could hear his voice and turn back towards him. Despite the ressourcement has applied new methodologies to build up theological thinking and to teach Theology, many Council Fathers were still used to an indirect theological approach, based on the use of handbooks. Therefore, comparing the Irenaeus ecclesiology to the one developed in Lumen gentium is an assignment that requires research both in the references of the conciliar text and the multiple conceptions of Church collected through analysis. Thus, it is possible to develop a deeper knowledge of a contemporary text in light of an ecclesiological model from the beginning of Christianity.

Made available in DSpace on 2016-04-29T14:27:20Z (GMT). No. of bitstreams: 1 Jose Claudio Jordao.pdf: 523225 bytes, checksum: 838f04bbecaa3b8b2e7ddc52281207a3 (MD5) Previous issue date: 2012-02-01 / The Dogmatic Constitution Lumen Gentium on the Church, elaborated in the Ecumenical Council Vatican II, recovers the concept "People of God" to qualify the group of the baptisms believers, be them, clergyman, religious, nuns or lay. It was promulgated by Pope Paulo VI on November 21, 1964, entering for the history of the Church. as a "divisor of waters" in the theological subjects in ecclesiastical. That study intends to deepen the understanding of that concept. In the itself text of the studied document, there is the acknowledgement: "was pleased, however, to God to sanctify and to save the men, no individually, excluding all the relationship among them, but forming actually with them a people, that knew him in the truth and served him in sanctity" (LG 09). Therefore, the concept People of God, it has biblical roots that are essential in its recital, though, this study is more turn over to the subjects ecclesiastical of the Council, the before, the during and the after, particularly in the Church of Latin America. The objective was to study the concept People of God starting from Lumen Gentium cooperating so that the understanding of that concept can be enlarged among the clergyman, religious persons and nons. It had as hypothesis to be proven that the concept People of God present in the Dogmatic Constitution on the Church from Conclílio Vatican II still is not understood completely in its significanse for many baptisms believers. That study has used of the deductive method with bibliographical researches. It has had also as theoretical references the Scriptures, the key document in the discussions of the theme; a Lumen Gentum, as well as, other documents of the Teachership, besides works and periodic articles about the subject. With the development of that study it was verified that it is not still clearly understood that concept, because the hypothesis that it is not still completely understood the true meaning from the concept People of God, for many baptisms believers it was confirmed / A Constituição Dogmática Lumen Gentium sobre a Igreja, elaborada no Concílio Ecumênico Vaticano II, recupera o conceito Povo de Deus para qualificar o conjunto dos fiéis batizados, sejam eles, clérigos, religiosos (as) ou leigos (as). Foi promulgada pelo Papa Paulo VI no dia 21 de novembro de 1964, entrando para a história da Igreja, como um divisor de águas nas questões teológicas sobre eclesiologia. Esse estudo pretende aprofundar a compreensão desse conceito. No próprio texto do documento estudado, encontram-se a afirmação: Aprouve, no entanto, a Deus santificar e salvar os homens, não individualmente, excluindo toda a relação entre eles, mas formando com eles um povo, que o conhecesse na verdade e o servisse em santidade (LG 09). Portanto, o conceito Povo de Deus, tem suas raízes bíblicas que são essenciais na sua fundamentação, todavia, este estudo está mais voltado para as questões eclesiológicas do Concílio, o antes, o durante e o depois, particularmente na Igreja da América Latina. O objetivo foi estudar o conceito Povo de Deus, a partir da Lumen Gentium cooperando para que a compreensão desse conceito possa ser ampliada entre os clérigos, religiosos (as) e leigos (as). Teve como hipótese a ser comprovada a de que o conceito Povo de Deus presente na Constituição Dogmática sobre a Igreja do Concílio Vaticano II ainda não é totalmente compreendido no seu verdadeiro significado por muitos fiéis batizados. Esse estudo utilizou-se do método dedutivo com pesquisas bibliográficas. Teve também como referenciais teóricos as Sagradas Escrituras, o documento chave nas discussões do tema; a Lumen Gentium, bem como, outros documentos do Magistério, além de obras e artigos periódicos sobre o assunto. Com o desenvolvimento desse estudo verificou-se que ainda não é claramente compreendido esse conceito, pois a hipótese de que ainda não é totalmente compreendido o verdadeiro significado do conceito Povo de Deus, por muitos fiéis batizados foi confirmada