yes / We report a technique for the fabrication of micropockets within electrospun membranes in which to study cell behavior. Specifically, we describe a combination of microstereolithography and electrospinning for the production of PLGA (Poly(lactide-co-glycolide)) corneal biomaterial devices equipped with microfeatures.

No final do século 19, o neurônio foi descrito como a unidade funcional básica do sistema nervoso e sua formação era considerada inexistente na fase adulta, explicando a ausência de recuperação significativa em doenças neurológicas. Evidências de geração de neurônios em mamíferos adultos surgiram na década de 1960 e foram confirmadas três décadas depois. Atualmente, predomina a visão de que mamíferos adultos possuem dois nichos neurogênicos independentes: a zona subventricular (ZSV) e a zona subgranular (ZSG) do giro denteado. No entanto, a existência de nichos neurogênicos em humanos adultos é controversa. Nossa hipótese foi de que o mapeamento de nichos neurogênicos no lobo temporal humano poderia esclarecer aspectos sobre a neurogênese adulta. A detecção destes nichos foi buscada em 28 lobos temporais através de imuno-histoquímica para nestina, o marcador mais comum de células-tronco neurais, que são aquelas capazes de se autorrenovar e de gerar novas células neurais. A neurogênese foi pesquisada no hipocampo pelo uso de DCX (do inglês \"doublecortin\"), o principal marcador de neuroblastos e neurônios imaturos. Nestina foi observada em uma camada contínua formada pela ZSV, zona subpial do lobo temporal medial e ZSG, terminando no subículo. A partir do subículo, uma intensa expressão de DCX ocorreu através da principal via eferente do hipocampo até a fímbria. A visão panorâmica das marcações por nestina e DCX mostrava em conjunto uma linha que circundava as estruturas límbicas do lobo temporal. Por isto, foi denominada linha externa de células do sistema límbico (LECEL). Uma possível explicação para os resultados é que a LECEL seja um nicho neurogênico no qual a ZSV, a zona subpial do lobo temporal medial e a ZSG formam uma unidade contendo células-tronco neurais que se diferenciam em neurônios no subículo. Curiosamente, a área identificada previamente como sendo a corrente migratória rostral humana (formada por células neurais imaturas migrando a partir da ZSV do corno frontal) pode ser na verdade o fórnix, que contém axônios originados no subículo. A implicação mais intrigante dos resultados é que se as características da LECEL seguirem além do lobo temporal, então o encéfalo humano pode conter um anel neurogênico límbico, em que a neurogênese ocorreria principalmente no subículo e seria modulada pelas estruturas relacionadas à fissura coroideia. Este estudo sugere que a neurogênese ocorre de maneira orquestrada em uma área ampla do lobo temporal humano / At the end of the 19th century, the neuron was described as the basic functional unit of the nervous system. The formation of neurons was thought to be absent in adulthood, thus explaining the lack of significant recovery from neurological diseases. Evidence for the generation of neurons in adult mammals was reported in the 1960s and confirmed three decades later. Currently, the prevailing view is that adult mammals harbour two neurogenic niches: the subgranular zone (SGZ) of the dentate gyrus and the subventricular zone (SVZ). Nonetheless, the existence of these niches in adult humans is controversial. We hypothesised that mapping neurogenic niches in the human temporal lobe could clarify this issue. The presence of neurogenic niches was examined in 28 temporal lobes via immunostaining for nestin, the most common marker for neural stem cells, which are cells with the capacities of self-renewal and the generation of neural cells. The presence of neurogenesis was examined in the hippocampus with doublecortin (DCX), a prominent marker for neuroblasts and immature neurons. Nestin was observed in a continuous layer that was formed by the SVZ, the subpial zone of the medial temporal lobe and the SGZ, terminating in the subiculum. In the subiculum, remarkable DCX expression was observed through the principal efferent pathway of the hippocampus to the fimbria. A panoramic view of nestin and DCX staining collectively displayed a line that surrounded the limbic structures of the temporal lobe. Hence, we termed it the external line of cells of the limbic system (EXCEL). A possible explanation for the results is that the EXCEL is a neurogenic niche, in which the SVZ, the subpial zone of the medial temporal lobe and the SGZ form a unit containing neural stem cells that differentiate into neurons in the subiculum. Curiously, the area previously identified as the human rostral migratory stream (formed by immature neural cells that migrate from the SVZ of the frontal horn) may in truth be the fornix, which contains axons that originate in the subiculum. Perhaps most intriguingly, if the EXCEL acts as a neurogenic niche beyond the boundaries of the temporal lobe, the human brain may contain a limbic neurogenic ring, in which neurogenesis would occur in the subiculum through the modulation of choroid fissure-related structures. This study suggests that neurogenesis may occur in an orchestrated manner in a broad area of the human temporal lobe

Les homéoprotéines SIX sont codées par les gènes Sine oculis homeobox related genes Six1 à Six6 chez les vertébrés parmi lesquels Six1, Six2, Six4 et Six5 sont exprimés dans le lignage myogénique. Bien que Six1 et Six4 soient requis pour la myogenèse hypaxiale, les animaux doubles KO pour ces deux gènes (s1s4KO) forment leurs muscles épaxiaux et craniofaciaux. Nous avons caractérisé le phénotype de mutants composites des gènes Six et avons montré que l’absence de Six1 et Six2 empêchait la formation des muscles craniofaciaux et empirait les défauts de formation des muscles des membres observés chez les fœtus mutants pour Six1. Nous avons aussi observé que les fœtus dépourvus d’activité de SIX1, SIX2, SIX4 et SIX5 étaient toujours capables de former leurs muscles épaxiaux, mais que l’expression de Pax7 dans leurs progéniteurs myogéniques était fortement diminuée et mêlée à l’expression de Myogénine. Alors que les fœtus s1s4KO forment des muscles épaxiaux, leurs cellules PAX7+ ont un défaut de nichage entre la membrane plasmique des myofibres et la lame basale qui les entoure. Nos analyses transcriptomiques, nos expériences de transplantation et nos études in vitro nous ont permis de conclure que le nichage des cellules PAX7+ nécessitait un environnement adéquat combinant des propriétés des myofibres et des cellules PAX7+ ; environnement perturbé dans les muscles épaxiaux s1s4KO. Nos expériences de transplantation nous ont aussi permis de conclure que Six1 et Six4 étaient requis pour une bonne ré-innervation des myofibres après blessure et pour la mise en place du phénotype rapide de ces myofibres. De plus, les muscles transplantés avec des cellules PAX7+ fœtales s1s4KO après blessure se reforment d’un grand nombre de petites myofibres. Nous avons pu relier ce phénotype au comportement des cellules s1s4KO in vitro où elles montrent un défaut de fusion. Enfin, les homéoprotéines SIX ont besoin de co-facteurs pour induire l’expression de leurs gènes cibles, tels que les protéines EYA codées par les gènes Eya1 à Eya4 chez les vertébrés. Eya3 et Eya4 sont fortement exprimés dans les cellules satellite au cours de la régénération, cellules qui requièrent aussi Six1 pour une réparation musculaire efficace. Nous avons étudié la régénération musculaire en absence d’expression d’Eya3 et n’avons pas observé de défaut nous menant à la conclusion qu’Eya3 n’est pas requis pour la régénération musculaire adulte, mais que sa perte d’expression était peut-être compensée par un autre gène Eya chez les animaux mutants. Pour conclure, Six1 et Six2 sont indispensables à la formation des muscles craniofaciaux, et Six1 et Six4 sont requis pour la myogenèse hypaxiale, et pour l’établissement d’un environnement propice à la maturation des myofibres fœtales et au nichage des cellules PAX7+ au cours de la myogenèse épaxiale, et permettant la croissance des myofibres et leur ré-innervation après blessure. La collaboration des protéines SIX avec leurs co-facteurs EYA au cours de la myogenèse nécessite d’autres études pour mieux définir leurs fonctions. / SIX homeoproteins are encoded by the Sine oculis homeobox related genes Six1 to Six6 in vertebrates among which Six1, Six2, Six4 and Six5 are expressed in the muscle lineage. Whereas Six1 and Six4 are required for hypaxial myogenesis, double KO for those two genes (s1s4KO) still form their epaxial and craniofacial muscles. We further characterized the phenotype of compound Six mutant embryos and showed that the absence of Six1 and Six2 completely impairs craniofacial myogenesis and worsen muscle limb development observed in single Six1 mutants. We also showed that mouse fetuses devoid of SIX1, SIX2, SIX4 and SIX5 activity are still able to develop epaxial muscles, but that Pax7 expression in myogenic progenitors of these mutants is reduced and intermingled with Myogenin expression. While s1s4KO fetuses still develop epaxial muscles, their PAX7+ cells show a perturbed homing process into their niche, between the plasma membrane of a myofibre and the basal lamina surrounding it. Transcriptomic analysis, transplantation experiments and in vitro studies allowed us to conclude that the homing of PAX7+ cells into their niche during fetal myogenesis requires an adequate environment combining properties of the myofibers and the PAX7+ cells; environment disturbed in s1s4KO epaxial muscles. Transplantation experiments also led us to conclude that Six1 and Six4 are required for proper myofiber re-inervation after injury and for the establishment of the fast phenotype of myofibers. Furthermore, muscles transplanted with s1s4KO fetal PAX7+ cells after injury are formed of numerous and tiny myofibers. We could link this phenotype to the behavior of s1s4KO cells in vitro where they showed perturbed fusion. Finally, SIX homeoproteins require co-factors to induce their target genes expression, as EYA proteins encoded by Eya1 to Eya4 in vertebrates. Eya3 and Eya4 are strongly expressed in satellite cells during regeneration, cells in which Six1 is also required for proper muscle repair. We investigated muscle regeneration in absence of Eya3 expression and observed no obvious phenotype. We concluded that Eya3 is not required for muscle regeneration but that other Eya genes might compensate its function in KO mouse. To conclude, Six1 and Six2 are required for craniofacial myogenesis and Six1 and Six4 for hypaxial myogenesis and for the establishment of a proper environment allowing myofibre maturation and PAX7+ cells homing during fetal epaxial myogenesis and enabling myofibre growth and re-innervation after injury. The role of the collaboration between SIX and EYA proteins during myogenesis still needs more investigation.

The local microenvironment of hematopoietic stem cells (HSCs) in the bone marrow -referred to as stem cell niche- is thought to regulate the balance of stem cell maintenance and differentiation by a complex interplay of extrinsic signals including spatial constraints, extracellular matrix (ECM) components and cell-cell interactions. To dissect the role of niche ECM components, a set of well-defined matrix biomolecular coatings including fibronectin, laminin, collagen IV, tropocollagen I, heparin, heparan sulphate, hyaluronic acid and co-fibrils of collagen I with heparin or hyaluronic acid were prepared and analyzed with respect to adhesive interactions of human CD133+ HSCs in vitro. ECM molecule dependent adhesion areas as well as fractions of adherent HSCs were assessed by reflection interference contrast microscopy and differential interference contrast microscopy. HSCs, so far mostly classified as suspension cells, exhibited intense adhesive interactions with fibronectin, laminin, collagen IV, heparin, heparan sulphate, and collagen I based co-fibrils. An integrin mediated adhesion on fibronectin and a L-selectin mediated adhesion on heparin pointed to specific interactions based on different adhesion mechanisms. As a consequence of HSC adhesion to molecules of the vascular and the endosteal regions, both regions were confirmed as possible stem cell niches and adhesive signals were suggested as potential regulators of stem cell fate. Furthermore, the impact of a spatially organized ECM on the HSC behavior was analyzed by single cell tracking. These studies required the development of engineered three-dimensional, ECM coated microcavities with the option for single cell tracking. A semi-automated cell-tracking tool was established to accelerate data access from time-lapse image sequences. From this analysis it was possible to reveal the genealogy, localization, morphology and migration of single HSCs over a time period of 4 days. A decreased cycling frequency was observed depending on the HSC localization in the spatially constraining microcavities. Besides the revealed impact of spatial constraints on HSC fate, the newly engineered ECM-coated microcavity setup and the semi-automated cell tracking tool provide new options to study the cell fate in engineered microenvironments at single cell level for other cell types ex vivo. / Die lokale Mikroumgebung von Blutstammzellen (BSZ) im Knochenmark, bezeichnet als Stammzellnische, reguliert das Gleichgewicht von Stammzellerhaltung und -differenzierung durch ein komplexes Zusammenspiel von extrinsischen Signalen wie räumliche Beschränkungen, Komponenten der extrazellulären Matrix (EZM) und Zell-Zell Wechselwirkungen. Um die Rolle der EZM-Komponenten zu analysieren, wurden definierte Beschichtungen von Fibronektin, Laminin, Kollagen IV, monomerem Kollagen I, Heparin, Heparan Sulphat, Hyaluronsäure und Co-Fibrillen aus Kollagen I und Heparin oder Hyaluronsäure hergestellt und in vitro bezüglich der adhäsiven Wechselwirkungen von humanen CD133+ BSZ untersucht. Die Adhäsionsflächen und der Anteil adhärenter Zellen wurden in Abhängigkeit von der EZM-Beschichtung mittels Reflexions- Interferenz-Kontrast-Mikroskopie und Differentieller Interferenz Kontrast Mikroskopie bestimmt. BSZ, bisher als Suspensionszellen definiert, zeigten intensive adhäsive Wechselwirkungen mit Fibronektin, Laminin, Kollagen IV, Heparin, Heparan Sulphat und den Co-Fibrillen. Eine Integrin abhängige Adhäsion auf Fibronektin und eine L-Selektin abhängige Adhäsion auf Heparin, wiesen auf spezifische Wechselwirkungen hin, die auf unterschiedlichen Mechanismen basieren. Aufgrund der Adhäsion von BSZ sowohl zu Molekülen der vaskulären als auch der endostealen Knochenmarkregion, wurden beide Bereiche als mögliche Stammzellnische bestätigt. Adhäsive Signale sind potentielle Regulatoren der Stammzellentwicklung. Im Weiteren wurde der Einfluss einer räumlich beschränkenden EZM auf das Verhalten der BSZ durch Einzelzellverfolgung untersucht. Diese Studien erforderten die Entwicklung von dreidimensionalen EZM-beschichteten Mikrokavitäten, die das Verfolgen einzelner Zellen ermöglichten. Es wurde ein halbautomatischer Algorithmus für die Zellverfolgung etabliert, um die Datengenerierung von den Zeitreihenaufnahmen zu beschleunigen. Die Analysen ermöglichten Aussagen über die Genealogie, Lokalisierung, Morphologie und Migration einzelner BSZ während einer Analysenzeit von 4 Tagen. Eine verringerte Zellteilungsaktivität wurde in Abhängigkeit von der BSZ Lokalisierung innerhalb der räumlich einschränkenden Mikrokavitäten festgestellt. Neben diesen Erkenntnissen bieten die entwickelten Mikrokavitäten und die etablierte Einzelzellverfolgung neue Möglichkeiten auch andere Zelltypen auf Einzelzellniveau ex vivo zu untersuchen.

No final do século 19, o neurônio foi descrito como a unidade funcional básica do sistema nervoso e sua formação era considerada inexistente na fase adulta, explicando a ausência de recuperação significativa em doenças neurológicas. Evidências de geração de neurônios em mamíferos adultos surgiram na década de 1960 e foram confirmadas três décadas depois. Atualmente, predomina a visão de que mamíferos adultos possuem dois nichos neurogênicos independentes: a zona subventricular (ZSV) e a zona subgranular (ZSG) do giro denteado. No entanto, a existência de nichos neurogênicos em humanos adultos é controversa. Nossa hipótese foi de que o mapeamento de nichos neurogênicos no lobo temporal humano poderia esclarecer aspectos sobre a neurogênese adulta. A detecção destes nichos foi buscada em 28 lobos temporais através de imuno-histoquímica para nestina, o marcador mais comum de células-tronco neurais, que são aquelas capazes de se autorrenovar e de gerar novas células neurais. A neurogênese foi pesquisada no hipocampo pelo uso de DCX (do inglês \"doublecortin\"), o principal marcador de neuroblastos e neurônios imaturos. Nestina foi observada em uma camada contínua formada pela ZSV, zona subpial do lobo temporal medial e ZSG, terminando no subículo. A partir do subículo, uma intensa expressão de DCX ocorreu através da principal via eferente do hipocampo até a fímbria. A visão panorâmica das marcações por nestina e DCX mostrava em conjunto uma linha que circundava as estruturas límbicas do lobo temporal. Por isto, foi denominada linha externa de células do sistema límbico (LECEL). Uma possível explicação para os resultados é que a LECEL seja um nicho neurogênico no qual a ZSV, a zona subpial do lobo temporal medial e a ZSG formam uma unidade contendo células-tronco neurais que se diferenciam em neurônios no subículo. Curiosamente, a área identificada previamente como sendo a corrente migratória rostral humana (formada por células neurais imaturas migrando a partir da ZSV do corno frontal) pode ser na verdade o fórnix, que contém axônios originados no subículo. A implicação mais intrigante dos resultados é que se as características da LECEL seguirem além do lobo temporal, então o encéfalo humano pode conter um anel neurogênico límbico, em que a neurogênese ocorreria principalmente no subículo e seria modulada pelas estruturas relacionadas à fissura coroideia. Este estudo sugere que a neurogênese ocorre de maneira orquestrada em uma área ampla do lobo temporal humano / At the end of the 19th century, the neuron was described as the basic functional unit of the nervous system. The formation of neurons was thought to be absent in adulthood, thus explaining the lack of significant recovery from neurological diseases. Evidence for the generation of neurons in adult mammals was reported in the 1960s and confirmed three decades later. Currently, the prevailing view is that adult mammals harbour two neurogenic niches: the subgranular zone (SGZ) of the dentate gyrus and the subventricular zone (SVZ). Nonetheless, the existence of these niches in adult humans is controversial. We hypothesised that mapping neurogenic niches in the human temporal lobe could clarify this issue. The presence of neurogenic niches was examined in 28 temporal lobes via immunostaining for nestin, the most common marker for neural stem cells, which are cells with the capacities of self-renewal and the generation of neural cells. The presence of neurogenesis was examined in the hippocampus with doublecortin (DCX), a prominent marker for neuroblasts and immature neurons. Nestin was observed in a continuous layer that was formed by the SVZ, the subpial zone of the medial temporal lobe and the SGZ, terminating in the subiculum. In the subiculum, remarkable DCX expression was observed through the principal efferent pathway of the hippocampus to the fimbria. A panoramic view of nestin and DCX staining collectively displayed a line that surrounded the limbic structures of the temporal lobe. Hence, we termed it the external line of cells of the limbic system (EXCEL). A possible explanation for the results is that the EXCEL is a neurogenic niche, in which the SVZ, the subpial zone of the medial temporal lobe and the SGZ form a unit containing neural stem cells that differentiate into neurons in the subiculum. Curiously, the area previously identified as the human rostral migratory stream (formed by immature neural cells that migrate from the SVZ of the frontal horn) may in truth be the fornix, which contains axons that originate in the subiculum. Perhaps most intriguingly, if the EXCEL acts as a neurogenic niche beyond the boundaries of the temporal lobe, the human brain may contain a limbic neurogenic ring, in which neurogenesis would occur in the subiculum through the modulation of choroid fissure-related structures. This study suggests that neurogenesis may occur in an orchestrated manner in a broad area of the human temporal lobe

In order to maintain a multicellular organism cells need to interact and communicate with each other. Signalling cascades such as the Bone Morphogenic Protein (BMP) and Hedgehog (Hh) signalling pathways therefore play essential roles in development and disease. Intercellular signalling also underlies the function of stem cell niches, signalling microenvironments that regulate behaviour of associated stem cells. Range and intensity of the niche signal controls stem cell proliferation and differentation and must therefore be strictly regulated. The testis and ovary of the fruit fly Drosophila melanogaster are established models of stem cell niche biology. In the apical tip of the testis, germ line stem cell (GSCs) and somatic cyst stem cells (CySCs) are arranged around a group of postmitotic somatic cells termed hub. While it is clear which signals regulate GSC maintenance it is unclear how these signals are spatially regulated. Here I show that BMP signalling is specifically activated at the interface of niche and stem cells. This local activation is possible because the transport of signalling and adhesion molecules is coupled and directed towards contact sites between niche and stem cells. I further show that the generation of the BMP signal in the wing disc follows the same mechanism. Hh signalling controls somatic stem cell populations in the Drosophila ovary and the mammalian testis. However, it was unknown what role Hh might play in the fly testis, where the components of this signalling cascade are also expressed. Here I show that overactivation of Hh signalling leads to an increased proliferation and an expansion of the cyst stem cell compartment. Finally, while the major components of the Hh signalling pathway are known, detailed knowledge of how signal transduction is implemented at the cell biological level is still lacking. Here, I show that localisation of the key signal transducer Smo to the plasma membrane is sufficient for phosphorylation of its cytoplasmic tail and downstream pathway activation. Using advanced, microscopy based biophysical methods I further demonstrate that Smo clustering is, in contrast to the textbook model, independent of phosphorylation.

O envelhecimento é um processo gradual e intrínseco que ocorre devido a mudanças fisiológicas e fenotípicas com o avanço da idade e que acarreta na diminuição da capacidade de manter a homeostase e reparo tecidual. A perda do controle homeostático e o possível envolvimento de células-tronco e progenitores, provavelmente, é uma das causas das fisiopatologias do sistema hematopoético que acompanham o envelhecimento. O declínio na competência do sistema imune adaptativo, o aumento de doenças mielóides, leucemias e o desenvolvimento de anemias são algumas mudanças significantes e decorrentes do processo de envelhecimento. Durante a transição ontológica, a habilidade de células-tronco hematopoéticas originarem células progenitoras diminui progressivamente, sugerindo perda da capacidade de autorrenovação e diferenciação das células-tronco com o avanço da idade. O microambiente medular se divide em duas áreas distintas: nicho endosteal e nicho vascular, conhecidos por controlar a homeostase das células-tronco hematopoéticas; e é composto por uma mistura heterogênea de células, dentre elas as células-tronco mesenquimais que expressam moléculas que controlam algumas funções das células-tronco hematopoéticas. De acordo com estas observações, este trabalho investiga o papel do envelhecimento das células-tronco mesenquimais no processo de autorrenovação, multipotência e diferenciação das células-tronco hematopoéticas. Neste trabalho, avaliamos a percentagem de células-tronco hematopoéticas Lin-CD34+ e subpopulações em co-cultura com células-tronco mesenquimais derivadas de medula óssea de diferentes idades, bem como sua capacidade de autorrenovação, diferenciação, secreção da quimiocina CXCL-12 e a expressão do receptor CXCR-4. Nossos resultados mostraram diferenças significativas nos parâmetros fenotípicos e funcionais das células-tronco hematopoéticas co-cultivadas com células-tronco mesenquimais de doadores idosos. Estes dados sugerem que o envelhecimento das células-tronco mesenquimais podem influenciar na homeostase do microambiente medular / Certainly, aging is one of the best identified features of the human biology, and is also the least understood. This is largely attributed to the fact that aging is gradual and fundamentally complex, due to all modifications in the physiological and phenotypic aspects occurred during the age advancing. One of the most striking features of aging is the decreased ability to maintain homeostasis and tissue repair. Consistent with those findings, many of the pathophysiological conditions affecting aging, such as anemia, dysplasia, leukemia and anemia suggest an imbalance between cell losses and the ability to self-renew or differentiation. The decline in homeostatic maintenance and regenerative potential of tissues during aging has been associated with changes in stem cells. Increasing evidences point to the stem cells as major accountable for the aging pathophysiology in several tissues. Thus, studies in mammals comprise a careful evaluation of mechanisms connected to stem cells. The increasing age is accompanied by many pathophysiological changes in the hematopoietic system wherein the etiology suggests loss of homeostatic control and a possible involvement of stem and progenitor cells. The clinically relevant changes are related to adaptive immune system diminished competence, the increase of myeloid diseases including leukemia and the onset of anemia in the elderly. The hematopoietic stem cell microenvironment is located in the bone marrow and is divided in two domains: the endosteal niche near to the bone surface and vascular niche associated with the sinusoidal endothelium; the niche consist of several heterogeneous cells types, among them, the mesenchymal stem cells. The mesenchymal stem cells express molecules that control hematopoietic stem cells functions. Therefore, this study investigates the role of mesenchymal stem cells aging in the self-renewal, multipotency and differentiation of hematopoietic stem cells. This study evaluated the percentage of hematopoietic stem cell Lin-CD34+ and subpopulations in co-culture with mesenchymal stem cell bone marrow-derived from donors with different ages, their ability of self-renewal, differentiation, secretion of chemokine CXCL-12 and expression of the CXCR-4 receptor. Our results suggest that the mesenchymal stem cells aging can affect the bone marrow niche homeostasis

Breathing is essential for human life, yet tens of millions of people in the U.S. alone suffer from lung diseases. With each breath, lungs are exposed to the external environment. Inhaled air first passes through the trachea, bronchi, and finally the bronchioles before it reaches the alveoli where gases are exchanged. A barrier of epithelial cells protects the airways. In addition, epithelial glands also secrete protein-rich fluids onto the airway surfaces to help maintain sterility. Injury, disease, or other factors can damage these cells, and regiospecific stem cells (SCs) can divide to replace them. However, many important details about lung SCs are still unknown. For example, what processes control SC division? How do region-specific SCs differ from one another? And how does disease or injury impact SC biology? We found that some processes that regulate lung development also control adult SC division following injury. We show that SCs from airway glands give rise to surface epithelial cell types and glandular cell types. In contrast, surface SCs only generated surface cell types. Finally, we identify a type of cell in the glands that can regenerate surface cell types after severe injury. These studies provide new insights into the neighborhoods in which SCs reside in the large airways and processes that control their contribution to airway repair following injury. Overall, this research provides important new insights into adult SC biology and conditions affecting lung health.

L’organogenèse post-embryonnaire des racines latérales joue un rôle essentiel dans l’établissement de l’architecture du système racinaire des plantes, et donc dans leur croissance et leur performance. L’objectif de cette thèse est de caractériser le réseau de gènes régulant le développement des racines latérales et en particulier, l’organisation fonctionnelle du primordium de racine latérale, formant un nouveau méristème racinaire, chez la plante modèleArabidopsis thaliana en combinant des études de biologie des systèmes appliquées à la dynamique du transcriptome lors de la formation des racines latérales avec la caractérisation fonctionnelle de gènes candidats pour la régulation de ce phénomène d’organogenèse.La première partie de la thèse concerne l’identification des cibles de PUCHI, un facteur de transcription de type AP2/EREBP impliqué dans le contrôle de la prolifération et de la différentiation cellulaire dans le primordium de racine latérale. Le phénotype liés à la parte de fonction de PUCHI a été caractérisé en détail et à mis en évidence un rôle de ce facteur de transcription dans l'initiation des racines latérales et le développement et l'organisation des primordia. Par l’analyse de profils spatiaux et temporels d’expression de gènes, nous avons pu mettre en évidence que l’expression de gènes codant des protéines impliquées dans la biosynthèse des acides gras à très longues chaînes (VLCFA) est transitoirement activée durant la formation de la racine latérale et que cette dynamique est dépendante de PUCHI. De plus, le mutant kcs1-5, perturbé dans la biosynthèse de VLCFAs, présente un phénotype de développement des racines latérales similaire à celui de puchi-1. Par ailleurs, la perte de fonction puchi-1 augmente fortement la formation de cals continus dans des racines cultivées sur milieu inducteur riche en auxine, ce qui est cohérent avec le rôle récemment décrit des VLCFA racinaires dans la formation et l’organisation de cals distincts lorsque la racine est cultivé sur milieu inducteur de cals. L'ensemble de nos résultats démontre que PUCHI régule positivement l’expression de gènes de biosynthèse de VLCFAs lors de la formation de racines latérales et la callogenèse. Nos résultats confortent également l’hypothèse selon laquelle la formation des racines latérales et celle de cals racinaires partagent des mécanismes de régulation communs.La seconde partie de la thèse s’intéresse à l’identification de facteurs régulateurs clés dans l’organisation fonctionnelle du primordium de racine latérale et particulièrement, l’organisation d’un nouveau méristème racinaire. J’ai contribué à produire de nouvelles lignées de plantes permettant de suivre en temps réel par microscopie confocale la mise en place des identités cellulaires caractéristiques d’un méristème racinaire dans le primordium de racine latérale en développement. En utilisant un algorithme d’inférence de réseau de gènes, j’ai produit puis analysé les relations prédites de régulation entre gènes d’intérêt, afin d’identifier des gènes candidats potentiellement impliqués dans la formation du centre quiescent, un élément clé dans l’organisation du primordium et la mise en place du nouveau méristème racinaire. La caractérisation fonctionnelle de certains de ces gènes candidats a été initiée.Ces travaux de thèse ont donc contribué à mieux comprendre les mécanismes de régulation de la formation des racines latérales chez Arabidopsis thaliana. / Post-embryonic lateral root organogenesis plays an essential role in defining plant root system architecture, and therefore plant growth and fitness. The aim of the thesis is to elucidate the gene regulatory network regulating lateral root development and de novo root meristem formation during root branching in the model plant Arabidopsis thaliana by combining a system-biology based analysis of lateral root primordium transcritome dynamics with the functional characterization of genes possibly involved in regulating lateral root organogenesis.The first part of the thesis deals with the identification the target genes of PUCHI, an AP2/EREBP transcription factor that is involved in controlling cell proliferation and differentiation during lateral root formation. We showed that loss of PUCHI function leads to defects lateral root initiation and primordium growth and organisation. We found that several genes coding for proteins of the very long chain fatty acid (VLCFA) biosynthesis machinery are transiently induced in a PUCHI-dependent manner during lateral root development. Moreover, a mutant perturbed in VLCFA biosynthesis (kcs1-5) displays similar lateral root development defects as does puchi-1. In addition, puchi-1 loss of function mutant roots show enhanced and continuous callus formation in auxin-rich callus induction medium, consistent with the recently reported role of VLCFAs in organizing separated callus proliferation on this inductive growing medium. Thus, our results show that PUCHI positively regulates the expression of VLCFA biosynthesis genes during lateral root development, and further support the hypothesis that lateral root and callus formation share common genetic regulatory mechanisms.A second part of the thesis specifically addresses the issue of identifying key regulators of root meristem organization in the developing lateral root primordium. Material enabling the tracking of meristem cell identity establishment in developing primordia with live confocal microscopy was generated. A gene network inference was run to predict potential regulatory relationships between genes of interest during the time course of lateral root development. It identified potential regulators of quiescent center formation, a key step in functional organization of the lateral root primordia into a new root apical meristem. The characterization of some of these candidate genes was initiated.Altogether, this work participated in deciphering the genetic regulation of lateral root formation in Arabidopsis thaliana .

Adult stem cells are a small population present within several tissues of an individual, possessing two unique properties: one, the ability to differentiate to give rise to all the cell types of the tissue, and second, the ability to self-renew and make more of their own kind. Owing to these two properties, stem cells underlie the process of organogenesis during development and tissue homeostasis in adult life. In the past decade a small sub-population of cells having phenotypic and functional properties similar to normal stem cells have been identified within several tumors. Only this sub-population of cancer cells seems to have the ability to both initiate and maintain tumors. These cells have been termed as ‘cancer stem cells’ (CSCs) owing to their striking similarities with the normal stem cells of the tissue. It is therefore of fundamental importance to understand normal stem cell biology in order to understand tumorigenesis. The rarity of normal stem cells within adult tissues, the absence of specific cell surface markers to identify and isolate them, and the absence of suitable culture conditions to maintain them has marred our understanding of stem cell behaviour. Recently, growth of mammary cells in serum free suspension cultures resulted in the generation of floating spheroids termed “mammospheres” that were shown to be enriched in stem/progenitor cell population. We established the mammosphere system in our laboratory using mastectomy samples obtained from the Kidwai Memorial Institute of Oncology. In order to understand the composition of the spheres, the stem cell characteristics within them, and the long term self renewal potential of human mammary epithelial stem cells, a detailed phenotypic and functional characterization of the mammospheres was carried out. Phenotypic Characterization: Confocal microscopy of propidium iodide stained mammospheres demonstrated that these spheres are cellular and not hollow structures. Immunostaining revealed that primary mammospheres expressed the epithelial markers like E Cadherin, ESA, CK14, CK18 and CK 19, but failed to express nestin or CD34, indicating their epithelial origin, devoid of contamination from haematopoeitic or neural stem cells. The sizes of mammospheres ranged from 40 to 110 μm, while that of the cells within them ranged from 9-15 μm. Although the sizes of the largest and smallest spheres through subsequent passages remained consistent, the proportion of small spheres increased in later passages. These results indicate the difference in the sphere initiating cells. While a large sphere might be generated by a stem cell, a smaller sphere might be originating from a progenitor. Thus, heterogeneity exists within mammospheres, with respect to size and composition. Unique cell surface markers coupled with flow cytometry serves as useful tools to isolate stem cells. However, no specific marker profile has been reported for normal human breast stem cells. In several tissues, like blood, brain etc, markers of normal stem cells have been successfully used to isolate cancer stem cells within that tissue. Since breast cancer stem cells have already been identified as CD24low/-44high cells, we explored if the same marker profile would hold true to identify normal breast stem cells as well. Two-colour based flow cytometry revealed that only the CD24low/-44high subpopulation of mammospheres could re-generate mammospheres, as well as give rise to all the other cellular fractions. These data demonstrated that normal and cancerous breast stem cells share identical marker profile. Functional Characterization: In addition to cell surface markers, a Hoechst dye based strategy used to isolate stem cells, exploits their unique property to efflux certain lipophilic drugs and small molecules due to the overexpression of ABC family of cell surface transporters. Cells effluxing Hoechst appear as a low fluorescing ‘Side population’ (SP) in a bivariate FACS plot. We detected a small, but distinct SP in human breast cells, which had a CD24low44low profile, and failed to initiate new mammospheres. Thus, the SP cells in mammospheres failed to correspond to the stem cell subpopulation. The hallmark feature of a stem cell is its long term self renewal ability, given that it is the longest lived cell in the body. Long term culture of mammospheres was carried out by passaging the spheres every week. We failed to observe mammosphere formation beyond four passages though there were live, proliferating and undifferentiated cells in fourth passage spheres. These results suggested that either the mammopsheres didn’t contain stem cells to begin with, or their stemness is restricted to four in vitro passages. In order to assess if mammospheres contained stem cells to begin with, we assayed for telomerase activity, since in the adult tissue, only stem cells retain telomerase activity. Telomerase, an enzyme that maintains the length of telomeres through multiple rounds of cell division, is not active in somatic cells. We detected the expression and activity of this enzyme in primary mammospheres, suggesting that the spheres may contain stem cells withinthem Another unique property of a stem cell is its ‘quiescence’, owing to their infrequent divisions. This property is studied by chasing a label (like BrdU or H3-Thymidine), which is taken up by the cells at an earlier time point and retained within the cell after prolonged periods, like weeks or months. In long term culture of mammospheres, using BrdU as the label, 1-2 distinct cells could be detected within late passage spheres which had retained the label, indicating that stem cells may be present within the fourth passage mammospheres as well. Staining for β-Galactosidase activity revealed that almost 70% cells derived from fourth passage spheres were senescent. We speculated that this senescent environment might be one of the inhibitory reasons for further mammosphere formation. Alteration of mammosphere culture conditions for long term maintenance of stem cells. A high level of atmospheric O2 is known to be one of the reasons for inducing senescence in cells. Culturing cells in conventional tissue culture conditions exposes them to high levels of O2 (21%) as against the physiological levels of 1-3% O2. Therefore, to assess the effects of lowered, or physiologically relevant levels of O2 on mammosphere stem cell biology, the mammospheres were cultured in 3% O2. Under this altered condition, a close to 3-fold increase was observed in the number of mammospheres formed coupled with a significant increase in their survival and proliferation. In order to understand the molecular basis of this observation, a microarray based global gene expression profiling was carried out. We observed a significant upregulation of VEGF, a gene responsive to hypoxia; three growth factor related genes, namely adrenomedullin, cMET and osteopontin. Upregulation of β Catenin, the downstream effector of the Wnt signaling pathway was also observed, indicating a possible mechanism for the increase in self renewal seen in 3% O2. We also observed downregulation of the cell cycle inhibitor, Chk1, which in part might explain the observed increase in proliferation. The increase in the number of proliferating cells might be one of the reasons for an increase in the number of spheres, as observed in 3% O2. Even though a significant decrease in the number of senescent cells was detected at 3% O2, mammosphere formation was not seen beyond four passages. It is therefore possible that there are other physico-chemical parameters, comprising the niche of the mammospheres, coupled to the O2 level, which need to be improvised for long term culture of human mammary epithelial stem cells. To summarize, this work reports for the first time that human mammary epithelial stem cells have an identical marker profile as breast cancer stem cells, which is CD24low/-CD44high. It has also been demonstrated for the first time that in long term mammosphere culture, the number of self renewal divisions of human mammary stem cells is restricted to four in vitro passages, at which most of the cells undergo senescence. Altering one of the parameters of the niche, by culturing mammospheres at physiological O2 level failed to prolong the in vitro lifespan of the spheres, although cell survival, proliferation and sphere formation increased, indicating that the niche requirements of human mammary epithelial stem cells for their long term self renewal needs to be further characterized.