Abstract The study gathered information about polyamine metabolism throughout the Scots pine (Pinus sylvestris L.) zygotic embryogenesis and about physiological events occurring simultaneously in the megagametophyte tissue. Additionally, novel sequence data of the Scots pine polyamine genes were used for studying the evolution of polyamine genes in plants. Phylogenetic analyses revealed that the eukaryotic ornithine decarboxylase (ODC) might have evolved from a multifunctional bacterial progenitor. In conifers, the alternative arginine decarboxylase (ADC) pathway is preferred in putrescine biosynthesis, which may have caused the relaxed purifying selection in the ODC genes. The phylogenetic analysis of spermidine synthase (SPDS), spermine synthase (SPMS) and thermospermine synthase (ACL5) sequences supported the view that eukaryotic SPDS genes are derived from a common ancestor, whereas SPMS genes have evolved several times from SPDS genes. The identified Scots pine sequence was defined as a putative thermospermine synthase (TSPMS) encoding gene and named PsACL5. The phylogenetic analysis of polyamine oxidase (PAO) sequences supported the view that plants possess several different PAOs, which may have different catalytic properties. The consistency of the polyamine concentration profiles during Scots pine zygotic embryogenesis suggested that polyamines have an important role in the embryo development and that individual polyamines may have different roles at different developmental stages. Generally, the polyamine concentrations increased at the early stages but decreased at the late stages of embryo development. Only the free putrescine fraction remained stable throughout the embryo development. Putrescine was almost solely produced via the ADC pathway and the ADC enzyme was at least partially transcriptionally regulated. Both ADC mRNA transcripts and ADC protein localized in dividing cells of embryos, which implicated the essential role of ADC in the mitosis of plant cells. The megagametophyte was viable from the early phases of embryo development until the early germination of mature seeds. However, the megagametophyte cells in the narrow embryo surrounding region (ESR) died via morphologically necrotic cell death. In the dying cells, extensive nucleic acid fragmentation caused the unspecific hybridization of probes in an in situ mRNA hybridization assay. The occurrence of necrotic cell death in Scots pine embryogenesis indicated that developmentally and physiologically regulated necrotic cell death is evolutionarily conserved and exists also in plants. / Tiivistelmä Työssä tutkittiin polyamiiniaineenvaihduntaa ja megagametofyyttisolukossa tapahtuvia fysiologisia muutoksia metsämännyn (Pinus sylvestris L.) alkionkehityksen aikana. Polyamiineja (putreskiini, spermidiini ja spermiini) syntetisoivia ja hajottavia entsyymejä koodaavien geenien emäsjärjestys selvitettiin metsämännystä. Sekvenssejä käytettiin kasvien polyamiinigeenien evoluution tutkimiseen. Tutkimuksessa todettiin, että eukaryooteissa putreskiinin biosynteesistä vastaava entsyymi, ornitiinidekarboksylaasi (ODC), on voinut kehittyä bakteerien lysiinikarboksylaasista (LDC), joka dekarboksyloi sekä ornitiinia että lysiiniä. Kasveissa putreskiinia voidaan tuottaa myös arginiinidekarboksylaasin (ADC) kautta, mikä on johtanut ODC-geeneihin kohdistuvan puhdistavan valinnan heikentymiseen. Aminopropyyli-ryhmiä liittävien entsyymien osalta tutkimus tukee käsitystä, jonka mukaan eukaryoottiset spermidiinisyntaasit (SPDS) ovat kehittyneet yhteisestä kantamuodosta, kun taas spermiinisyntaasi (SPMS) on syntynyt useita kertoja SPDS-geenin kahdentumisen kautta. Metsämännystä tunnistettiin termospermiinisyntaasia (TSPMS) koodaava geeni, jolle annettiin nimeksi PsACL5. Fylogeneettisen analyysin perusteella kasveissa on useita erilaisia polyamiinien hajotuksesta vastaavia polyamiinioksidaaseja (PAO), joiden katalyyttiset ominaisuudet voivat poiketa toisistaan. Metsämännyllä polyamiinipitoisuudet vaihtelivat alkionkehitysvaiheen mukaan yhdenmukaisesti eri vuosina, mikä viittaa polyamiinien tärkeään rooliin alkionkehityksessä. Polyamiinipitoisuudet kasvoivat varhaisen ja pienenivät myöhäisen alkionkehityksen aikana lukuun ottamatta vapaan putreskiinin pitoisuutta, joka pysyi samana koko alkionkehityksen ajan. Putreskiinia tuotettiin alkioissa lähes pelkästään ADC-reitin kautta, ja ADC-entsyymin säätelyn todettiin tapahtuvan ainakin osittain transkription tasolla. Koska sekä ADC-geenin lähetti-RNA että ADC-entsyymi löytyivät alkion jakautuvista soluista, on ilmeistä, että ADC-entsyymillä on tärkeä tehtävä kasvisolujen mitoosissa. Megagametofyytti säilyi elossa koko alkionkehityksen ajan lukuun ottamatta alkio-onteloa reunustavia soluja, jotka olivat morfologialtaan nekroottisia. Nukleiinihappojen voimakas pilkkoutuminen aiheutti soluissa koettimien epäspesifisen sitoutumisen, kun geenien ilmenemistä paikannettiin lähetti-RNA:han in situ hybridisaatio-menetelmällä. Tutkimuksessa löydetty männyn alkiokehitykseen liittyvä nekroottinen solukuolema osoitti ensimmäistä kertaa, että fysiologista ja kehityksellistä nekroottista solukuolemaa esiintyy myös kasveissa.

O estudo do metabolismo de poliaminas (PAS), envolvendo parâmetros fisiológicos, bioquímicos e moleculares, pode gerar uma melhor compreensão do processo de maturação, e criar estratégias importantes para a otimização da embriogênese somática (ES) em cana-de-açúcar. O objetivo deste trabalho foi estudar a relação entre os conteúdos endógenos de PAs, associados à determinação da competência embriogenética e a maturação progressiva de embriões somáticos em cana-de-açúcar. Calos embriogênicos (E) e não-embriogênicos (NE) da variedade SP-803280, foram submetidos a diferentes tratamentos, utilizando agentes de maturação adicionados ao meio MS. Observou-se que as culturas NE não foram capazes de promover a diferenciação de embriões somáticos, devido principalmente, ao alto grau de oxidação das culturas. Os tratamentos suplementados com 0,75 e 1,5 g.L-1 de carvão ativado (CA), foram os que apresentaram as maiores freqüências de formação de embriões somáticos. A partir dos resultados obtidos, foi possível associar a ES em calos de cana-de-açúcar ao aumento do conteúdo endógeno de Spd (Espermidina) e Spm (Espermina), principalmente Spd, acompanhado por uma redução nos níveis de Put (Putrescina). / Somatic embryogenesis (SE) is a highly potential supplier of the material involved in the regeneration and genetic transformation of transgenic plants. The aim was to study correlations between endogenous PA contents, associated to defining embryogenetic competence and the progressive maturation of somatic embryos. Embryogenic (E) and non-embryogenic (NE) calli from the SP-803280 variety, were submitted to different maturation treatments. It was found that the NE cultures submitted to the two maturation experiments, were incapable of promoting somatic embryo differentiation, mainly due to browning. It was noted that in the first experiment, total PA endogenous content of the E callus was higher than in the NE, although, in the control, no significant differences between both callus types were encountered. We can associate the progression of sugarcane somatic embryogenesis to an increase in endogenous content of Spd e Spm, mainly Spd, accompanied for a reduction in Put levels. Thus, it was shown that somatic embryo maturation in sugarcane can be related with PA biosynthesis, thereby indicating the importance of their metabolism in the competence of sugarcane embryogenic cultures.

No description available.

Tesis por compendio / [EN] Cannabis sativa L. (Cannabaceae) is an angiosperm, allogamous and dicotyledonous species that includes short and neutral-day varieties with dioecious specimens (males and females), and monoecious plants. Among its many applications, its industrial and medicinal uses stand out. Despite the fact that cannabis has been used by humans since ancient times and the growing interest that the C. sativa therapeutic properties have aroused in researchers around the world, the psychoactivity of some of its varieties, derived from its ¿9-tetrahydrocannabinol (THC) content, has motivated the prohibition of its cultivation for almost sixty years. The strict control to which cannabis has been subjected has prevented professionals from all over the world from carrying out genetic breeding programs for this species, which has resulted in the absence of uniform varieties. In this Doctoral Thesis, different biotechnological tools for cannabis genetic improvement have been developed. In the first place, given the lack of reproducibility of some cannabis plant in vitro regeneration protocols and the great influence that the genotype exerts on their effectiveness, plant in vitro regeneration competence of different explants was evaluated. As a result, an hormone-free protocol from C. sativa hypocotyls that presents high regeneration rates (ranging from 32.26% to 71.15%) in all the genotypes evaluated, also presenting a 17.94% of spontaneous rooting rate of regenerants has been developed. At the same time, the polysomatic pattern of different cannabis explants has been studied, and it has been possible to regenerate, from them, a significant percentage of mixoploid specimens (17.65% from cotyledons and 13.33% from hypocotyls) that, as described in the existing literature, could show a greater capacity for cannabinoid synthesis. On the other hand, given the absence of scientific publications in this regard, and the potential that this technique presents to alleviate the intrinsic variability of this species, the most in-depth study to date on the male floral biology of C. sativa has been developed. Up to 476,903 microspores and pollen grains per male flower, with in vivo microspore viability rates from 53.71 to 70.88% have been found. Furthermore, all stages of development of the microgametophyte have been correlated with an easily measurable floral morphological marker such as the bud length, identifying bud length intervals containing mostly vacuolate microspores and young bi-cellular pollen grains in all the phenotypes evaluated. In this way, and although the starch presence in C. sativa microspores and pollen grains follows a similar pattern to that observed in species recalcitrant to androgenesis, it has been possible to address the induction of microspore embryogenesis in this species, obtaining for the first time microspore-derived multicellular structures after one week long cold-shock bud pretreatment. Finally, as a prerequisite for the genetic editing of C. sativa by using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas systems, and taking advantage of the in vitro plant regeneration protocol which resulted from this Doctoral Thesis, it has been possible to develop for the first time a protocol for the production of stably transformed cannabis plants, which represents a historical milestone in the genetic improvement of the species. After co-culture with A. tumefaciens and subsequent culture in antibiotic-containing selective regeneration medium, hypocotyls achieved 23.1% and 5.0% of regeneration and transformation rates respectively. As a whole, the present Doctoral Thesis provides a range of biotechnological tools that will allow the development of a new generation of high-yield cannabis varieties with uniform traits, resistant to multiple biotic and abiotic stresses, and therefore being suitable for both industrial and medicinal use. / [ES] Cannabis sativa L. (Cannabaceae) es una especie angiosperma, alógama y dicotiledónea compuesta por variedades de día corto y día neutro que presentan ejemplares dioicos (machos y hembras), y plantas monoicas. Entre sus múltiples aplicaciones destacan tanto su uso industrial como su uso medicinal. A pesar de que el cannabis ha sido empleado por el ser humano desde tiempos ancestrales, la psicoactividad que presentan algunas de sus variedades, derivada de su contenido en ¿ 9 -tetrahidrocannabinol (THC), ha motivado la prohibición de su cultivo durante casi sesenta años. La estricta fiscalización a la que ha sido sometido el cannabis, ha impedido llevar a cabo programas de mejora genética de esta especie, lo que se ha traducido en la ausencia de variedades uniformes. En esta Tesis Doctoral se han desarrollado diferentes herramientas biotecnológicas para la mejora genética del cannabis. En primer lugar, dada la falta de reproducibilidad de algunos protocolos de cultivo in vitro de cannabis y la gran influencia que el genotipo ejerce en la efectividad de los mismos, se evaluó la capacidad de regeneración in vitro de diferentes explantes. Como resultado, se ha desarrollado un protocolo libre de hormonas a partir de hipocótilos de C. sativa que presenta altas tasas de regeneración (las cuales oscilan del 32,26% al 71,15%) en todos los genotipos evaluados, presentando además un 17,94% de tasa de enraizado espontáneo de los regenerantes. A su vez, se ha estudiado el patrón polisomático de diferentes explantes de cannabis y se ha conseguido regenerar, a partir de los mismos, un porcentaje significativo de ejemplares mixoploides (17,65% procedentes de cotiledones y 13,33% de hipocotilos) que, tal y como describe la bibliografía existente, podrían mostrar una mayor capacidad de síntesis de cannabinoides. Por otro lado, dada la ausencia de publicaciones científicas al respecto y el potencial que esta técnica presenta para paliar la variabilidad intrínseca de esta especie, se ha desarrollado el estudio más profundo hasta la fecha relativo a la biología floral masculina de C. sativa. Se han descrito hasta 476.903 microsporas y granos de polen por flor masculina, con tasas de viabilidad in vivo de las microsporas del 53,71 al 70,88%. Además, se han correlacionado todas las etapas de desarrollo del microgametofito con la longitud de la yema, identificando intervalos de longitud de yema que contienen mayoritariamente microsporas vacuoladas y granos de polen joven bicelular en todos los fenotipos evaluados. De este modo, y aunque la presencia de almidón en las microsporas y granos de polen de C. sativa sigue un patrón similar al observado en especies recalcitrantes a la androgénesis, ha sido posible abordar la inducción de la embriogénesis de microsporas en esta especie, consiguiendo producir por primera vez estructuras multicelulares derivadas de las microsporas tras aplicar sobre las yemas un pretratamiento de frío de una semana de duración. Finalmente, como requisito previo para la edición genética de C. sativa mediante los sistemas CRISPR/Cas, y haciendo uso del protocolo de regeneración in vitro de plantas surgido de la presente Tesis Doctoral, se ha conseguido desarrollar por primera vez un protocolo para producir plantas de cannabis transformadas genéticamente de forma estable, lo que supone un hito histórico en la mejora genética de la especie. Después del cocultivo con A. tumefaciens y el posterior cultivo en medio de regeneración selectiva con antibióticos, los hipocótilos lograron respectivamente un 23,1% y un 5,0% de tasas de regeneración y transformación. En su conjunto, la presente Tesis Doctoral proporciona un abanico de herramientas biotecnológicas que permitirán el desarrollo de una nueva generación de variedades de cannabis de alto rendimiento, que presenten caracteres homogéneos, resistentes a múltiples estreses tanto bióticos como abióticos, y siendo así aptas tanto para un uso industrial como medicinal. / [CAT] Cannabis sativa L. (Cannabaceae) és una espècie angiosperma, alógama i dicotiledònia composta per varietats de dia curt i dia neutre que presenten exemplars dioics (mascles i femelles), i plantes monoiques. Entre les seues múltiples aplicacions destaquen tant el seu ús industrial com el seu ús medicinal. Tot i que el cànnabis ha sigut emprat per l'ésser humà des de temps ancestrals, la psicoactivitat que presenten algunes de les seues varietats, derivada del seu contingut en ¿9-tetrahidrocannabinol (THC), ha motivat la prohibició del seu cultiu durant gairebé seixanta anys. L'estricta fiscalització a la qual ha sigut sotmés el cànnabis, ha impedit que professionals de tot el món puguen dur a terme programes de millora genètica d'aquesta espècie, la qual cosa s'ha traduït en l'absència de varietats uniformes. En aquesta Tesi Doctoral s'han desenvolupat diferents eines biotecnològiques per a la millora genètica del cànnabis. En primer lloc, donada la falta de reproducibilitat d'alguns protocols de cultiu in vitro de cànnabis i la gran influència que el genotip exerceix en l'efectivitat d'aquests, es va avaluar la capacitat de regeneració in vitro de diferents explants. Com a resultat, s'ha desenvolupat un protocol lliure d'hormones a partir de hipocòtils de C. sativa que presenta altes taxes de regeneració (les quals oscil·len del 32,26% al 71,15%) en tots els genotips avaluats, presentant a més un 17,94% de taxa d'arrelat espontani dels regenerants. Al mateix temps, s'ha estudiat el patró polisomàtic de diferents explants de cànnabis i s'ha aconseguit regenerar, a partir d'aquests, un percentatge significatiu d'exemplars mixoploids (17,65% procedents de cotilèdons i 13,33% de hipocòtils) que, tal com descriu la bibliografia existent, podrien mostrar una major capacitat de síntesi de cannabinoids. D'altra banda, donada l'absència de publicacions científiques sobre aquest tema i el potencial que aquesta tècnica presenta per a pal·liar la variabilitat intrínseca d'aquesta espècie, s'ha desenvolupat l'estudi més profund fins hui relatiu a la biologia floral masculina de C. sativa. S'han descrit fins a 476.903 microspores i grans de pol·len per flor masculina, amb taxes de viabilitat in vivo de les microspores del 53,71 al 70,88%. A més, s'han correlacionat totes les etapes de desenvolupament del microgametòfit amb la longitud de la gemma, identificant intervals de longitud de gemma que contenen majoritàriament microspores vacuolades i grans de pol·len jove bi-cel·lular en tots els fenotips avaluats. D'aquesta manera, i encara que la presència de midó en les microspores i grans de pol·len de C. sativa segueix un patró similar a l'observat en espècies recalcitrants a la androgènesi, ha sigut possible abordar la inducció de la embriogènesi de microspores en aquesta espècie, aconseguint produir per primera vegada estructures multicel·lulars derivades de les microspores després d'aplicar sobre les gemmes un pretractament de fred d'una setmana de duració. Finalment, com a requisit previ per a l'edició genètica de C. sativa mitjançant els sistemes CRISPR/Cas, i fent ús del protocol de regeneració in vitro de plantes sorgit de la present Tesi Doctoral, s'ha aconseguit desenvolupar per primera vegada un protocol per a produir plantes de cànnabis transformades genèticament de manera estable, la qual cosa suposa una fita històrica en la millora genètica de l'espècie. Després del cocultiu amb A. tumefaciens i el posterior cultiu en medi de regeneració selectiva amb antibiòtics, els hipocòtils van aconseguir respectivament un 23,1% i un 5,0% de taxes de regeneració i transformació. En el seu conjunt, la present Tesi Doctoral proporciona un ventall d'eines biotecnològiques que permetran el desenvolupament d'una nova generació de varietats de cànnabis d'alt rendiment, que presenten caràcters homogenis, resistents a múltiples estressos tant biòtics com abiòtics, i sent així aptes tant per a un ús industrial com medicinal. / Galán Ávila, A. (2021). Development of biotechnological tools for the genetic improvement of Cannabis sativa L [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/176013 / Compendio

Fibronectin is an extracellular multidomain glycoprotein that directs and regulates a variety of cell processes such as proliferation, development, haemostasis, embryogenesis, and wound healing. As a major component of blood, fibronectin exists as a soluble disulphide linked dimer, but it can also be incorporated into an insoluble cross-linked fibrillar network to form a major component of the extracellular matrix. Fibronectin is composed of an extended chain of module repeats termed Fn1, Fn2, and Fn3 that bind to a wide range of transmembrane receptors and extracellular matrix components, including collagen. The gelatin binding domain of fibronectin was first isolated as a 45kDa proteolytic fragment and has since been found to be composed of six modules: 6Fn1-1Fn2-2Fn2-7Fn1-8Fn1-9Fn1 (in this notation nFX represents the nth type X module in the native protein). This domain has been reported to bind to both collagen and denatured collagen (gelatin), but with 10-100 times higher affinity to the latter; it can be purified to homogeneity on a gelatin affinity column. In the work presented here, fragments of the gelatin binding domain are expressed in P. pastoris, purified to homogeneity, and investigated at the molecular level. Through a dissection approach, surface plasmon resonance (SPR) is used to characterise the recombinantly produced protein, to accumulate more information about the function of the full domain. NMR is used to assess the folding of the protein fragments at atomic resolution. In particular, the secondary structure of 8Fn1-9Fn1 is mapped using inter-strand NOEs, which suggests that the construct takes the fold of a pair of typical Fn1 modules. Gelatin affinity chromatography is used to confirm that both Fn1 and Fn2 modules contribute to gelatin binding, possibly in two clusters (1Fn2-2Fn2 and 8Fn1-9Fn1). The 7Fn1 module may perform a structural role in linking together these two interaction sites, in the same way as suggested for 6Fn1, which is thought to act in a structural manner to enhance the binding of 1Fn2-2Fn2 to gelatin. Three carbohydrate moieties are found on this domain, one on 2Fn2 and two on 8Fn1. Here, by means of expressing different protein length fragments, and by site directed mutagenesis, the role of each sugar chain is investigated independently. The sugar chain on 2Fn2 does not appear to promote binding to collagen, nor does the first sugar chain on 8Fn1 (N-linked to N497), implying another role for these sugars such as protection from proteolysis. However, the presence of at least a single GlcNAc sugar residue on the second sugar chain site on 8Fn1 (N- linked to N511) is essential for full affinity binding to collagen. Direct binding of the 8Fn1-9Fn1 module pair to collagen is assessed with a short collagen peptide and the binding is monitored by NMR. The peptide appears to bind, predominantly to the final strand of 8Fn1, the first β- strand of 9Fn1, and the linker between the two modules, with μM affinity. A model for bound peptide is proposed. The highly conserved amino acid motif Ile-Gly-Asp (IGD) is found on four of the nine N-terminal Fn1 modules of fibronectin. Tetrapeptides containing the IGD were demonstrated to promote the migration of fibroblast cells into a native collagen matrix. Two of these “bioactive” IGD motifs are found within the gelatin binding domain, one on 7Fn1 and one on 9Fn1. In this study, the motif in the 8Fn1-9Fn1 module pair is shown to be located in a tightly constrained loop within 9Fn1. By site directed mutagenesis, the IGD motifs of 7Fn1 and 9Fn1 are subjected to single amino acid substitutions, and their ability to stimulate cell migration assessed in our assay. By NMR, the fold of the IGD mutant proteins is found to be unaffected by the mutation with respect to the wild type, with the exception of small perturbations around the substitution site. While the wild type module is able to stimulate fibroblast migration, the mutant proteins show reduced or negligible bioactivity. The larger fragments show far more potency in stimulating fibroblast migration, with 8Fn1-9Fn1 (one IGD motif) 104 times more potent than the IGD peptide, and the full gelatin binding domain (two IGD motifs) 106 times more potent than the 8Fn1-9Fn1. Potential mechanisms for this enormous enhancement of the IGD potency in different contexts are discussed.

Infertility affects 15% of reproductive-aged couples. The milieu surrounding the growing embryo is of outmost importance, and should be optimised during in vitro fertilisation (IVF). Many biological processes, such as angiogenesis, coagulation, and immune processes need to be well regulated for a pregnancy to occur and progress normally. Histidine-rich glycoprotein (HRG) is a plasma protein that regulates components of these systems by building complexes with various ligands. A single nucleotide polymorphism (SNP) in HRG, denoted HRG C633T, seem to be of importance for IVF treatment outcomes. The aim of this thesis was to further investigate the proposed human fertility effects of the HRG C633T SNP. According to the findings of this thesis, the HRG C633T genotype is associated with primary recurrent miscarriage. Male HRG C633T genotype is associated with semen characteristics in infertile men, and pregnancy rates following IVF. However, the distribution of the HRG C633T SNP does not differ between infertile and fertile couples. We further examined the role of the region surrounding the HRG C633T SNP for regulation of endometrial angiogenesis and human embryo development. The region affects primary endometrial endothelial cell migration, proliferation and tube-formation in vitro but does not appear to affect human embryo development. No effect of the HRG peptide was noted on the secretome of human embryos. However, early embryos secrete proteins into the surrounding culture media and the level of secretion of VEGF-A, IL-6, EMMPRIN and PlGF is greater in embryos of higher developmental stages. In conclusion, the HRG C633T genotype appears to play a role only if infertility is established. The region surrounding HRG C633T SNP is of relevance in vitro for regulation of human endometrial endothelial cell angiogenesis. To predict which embryos to transfer in IVF, we have highlighted a number of proteins of interest for further investigation.

Nous proposons dans cette thèse de caractériser quantitativement la variabilité à différentes échelles au cours de l'embryogenèse. Pour ce faire, nous utilisons une combinaison de modèles mathématiques et de résultats expérimentaux. Dans la première partie, nous utilisons une petite cohorte d'oursins digitaux pour construire une représentation prototypique du lignage cellulaire, reliant les caractéristiques des cellules individuelles avec les dynamiques à l'échelle de l'embryon tout entier. Ce modèle probabiliste multi-niveau et empirique repose sur les symétries des embryons et sur les identités cellulaires; cela permet d'identifier un niveau de granularité générique pour observer les distributions de caractéristiques cellulaires individuelles. Le prototype est défini comme le barycentre de la cohorte dans la variété statistique correspondante. Parmi plusieurs résultats, nous montrons que la variabilité intra-individuelle est impliquée dans la reproductibilité du développement embryonnaire. Dans la seconde partie, nous considérons les mécanismes sources de variabilité au cours du développement et leurs relations à l'évolution. En nous appuyant sur des résultats expérimentaux montrant une pénétrance incomplète et une expressivité variable de phénotype dans une lignée mutante du poisson zèbre, nous proposons une clarification des différents niveaux de variabilité biologique reposant sur une analogie formelle avec le cadre mathématique de la mécanique quantique. Nous trouvons notamment une analogie formelle entre l'intrication quantique et le schéma Mendélien de transmission héréditaire. Dans la troisième partie, nous étudions l'organisation biologique et ses relations aux trajectoires développementales. En adaptant les outils de la topologie algébrique, nous caractérisons des invariants du réseaux de contacts cellulaires extrait d'images de microscopie confocale d'épithéliums de différentes espèces et de différents fonds génétiques. En particulier, nous montrons l'influence des histoires individuelles sur la distribution spatiales des cellules dans un tissu épithélial. / We propose in this thesis to characterize variability quantitatively at various scales during embryogenesis. We use a combination of mathematical models and experimental results. In the first part, we use a small cohort of digital sea urchin embryos to construct a prototypical representation of the cell lineage, which relates individual cell features with embryo-level dynamics. This multi-level data-driven probabilistic model relies on symmetries of the embryo and known cell types, which provide a generic coarse-grained level of observation for distributions of individual cell features. The prototype is defined as the centroid of the cohort in the corresponding statistical manifold. Among several results, we show that intra-individual variability is involved in the reproducibility of the developmental process. In the second part, we consider the mechanisms sources of variability during development and their relations to evolution. Building on experimental results showing variable phenotypic expression and incomplete penetrance in a zebrafish mutant line, we propose a clarification of the various levels of biological variability using a formal analogy with quantum mechanics mathematical framework. Surprisingly, we find a formal analogy between quantum entanglement and Mendel’s idealized scheme of inheritance. In the third part, we study biological organization and its relations to developmental paths. By adapting the tools of algebraic topology, we compute invariants of the network of cellular contacts extracted from confocal microscopy images of epithelia from different species and genetic backgrounds. In particular, we show the influence of individual histories on the spatial distribution of cells in epithelial tissues.

Nous proposons dans cette thèse de caractériser quantitativement la variabilité à différentes échelles au cours de l'embryogenèse. Pour ce faire, nous utilisons une combinaison de modèles mathématiques et de résultats expérimentaux. Dans la première partie, nous utilisons une petite cohorte d'oursins digitaux pour construire une représentation prototypique du lignage cellulaire, reliant les caractéristiques des cellules individuelles avec les dynamiques à l'échelle de l'embryon tout entier. Ce modèle probabiliste multi-niveau et empirique repose sur les symétries des embryons et sur les identités cellulaires; cela permet d'identifier un niveau de granularité générique pour observer les distributions de caractéristiques cellulaires individuelles. Le prototype est défini comme le barycentre de la cohorte dans la variété statistique correspondante. Parmi plusieurs résultats, nous montrons que la variabilité intra-individuelle est impliquée dans la reproductibilité du développement embryonnaire. Dans la seconde partie, nous considérons les mécanismes sources de variabilité au cours du développement et leurs relations à l'évolution. En nous appuyant sur des résultats expérimentaux montrant une pénétrance incomplète et une expressivité variable de phénotype dans une lignée mutante du poisson zèbre, nous proposons une clarification des différents niveaux de variabilité biologique reposant sur une analogie formelle avec le cadre mathématique de la mécanique quantique. Nous trouvons notamment une analogie formelle entre l'intrication quantique et le schéma Mendélien de transmission héréditaire. Dans la troisième partie, nous étudions l'organisation biologique et ses relations aux trajectoires développementales. En adaptant les outils de la topologie algébrique, nous caractérisons des invariants du réseaux de contacts cellulaires extrait d'images de microscopie confocale d'épithéliums de différentes espèces et de différents fonds génétiques. En particulier, nous montrons l'influence des histoires individuelles sur la distribution spatiales des cellules dans un tissu épithélial. / We propose in this thesis to characterize variability quantitatively at various scales during embryogenesis. We use a combination of mathematical models and experimental results. In the first part, we use a small cohort of digital sea urchin embryos to construct a prototypical representation of the cell lineage, which relates individual cell features with embryo-level dynamics. This multi-level data-driven probabilistic model relies on symmetries of the embryo and known cell types, which provide a generic coarse-grained level of observation for distributions of individual cell features. The prototype is defined as the centroid of the cohort in the corresponding statistical manifold. Among several results, we show that intra-individual variability is involved in the reproducibility of the developmental process. In the second part, we consider the mechanisms sources of variability during development and their relations to evolution. Building on experimental results showing variable phenotypic expression and incomplete penetrance in a zebrafish mutant line, we propose a clarification of the various levels of biological variability using a formal analogy with quantum mechanics mathematical framework. Surprisingly, we find a formal analogy between quantum entanglement and Mendel’s idealized scheme of inheritance. In the third part, we study biological organization and its relations to developmental paths. By adapting the tools of algebraic topology, we compute invariants of the network of cellular contacts extracted from confocal microscopy images of epithelia from different species and genetic backgrounds. In particular, we show the influence of individual histories on the spatial distribution of cells in epithelial tissues.

Introduction : La Vitamine A (rétinol, ROL) et son métabolite l’acide rétinoïque (AR) sont essentielles pour l’embryogénèse. L’excès comme l’insuffisance d’AR sont nocives. L’AR est régularisé dans l’embryon par des gènes spécifiques (ALDH, CRABP, CYP). Hypothèse : Les grandes variations d’AR dans le plasma des adultes normaux, nous ont orienté à mesurer les rétinoïdes (ROL et RA) dans le sang de cordon ombilical, pour évaluer des corrélations avec des polymorphismes des gènes impliquées dans le métabolisme de l’AR et le développement rénal-(RALDH2, CRABP2, CYP26A1; B1). Vérifier pour des corrélations entre ces rétinoïdes et/ou avec la taille de reins à la naissance. Méthodes : Extraction du ROL et RA du sang de cordon ombilical de 145 enfants et analyse par HPLC. Le volume des reins a été mesuré par ultrasonographie et l’ADN génomique leucocytaire extrait (FlexiGene DNA-Kit). 10 échantillons d’ADN ont été exclus (qualité). Les htSNP : ALDH1A2, CRABP2, CYP26A1;B1 du génome humain (HapMap) ont été séquencés et génotypés (Sequenom iPlex PCR).Des testes bio-statistiques des fréquences génotypiques et alléliques ont été effectués (Single-Locus, χ2, Kruskal-Wallis, Allelic-Exact).Des corrélations (ROL, RA, SNPs, V-reins) ont été analysés (Kendall-tau /Oakes). Résultats : La Δ RA (0.07-550.27 nmol/l) non corrélé avec la Δ ROL (51.39-3892.70 nmol/l). Il n’y a pas d’association ROL ou RA avec les volumes des reins ou avec les SNPs/ CYP21A1;B1. Corrélations trouvées : 1. (p=0.035), polymorphisme génétique ALDH1A2-SNP (rs12591551:A/C) hétérozygote/CA, (25enfants, 19%) avec moyennes d’AR (62.21nmol/l). 2. (p=0.013), polymorphisme CRABP2-SNP (rs12724719:A/G) homozygote/AA (4 enfants, 3%) avec hautes valeurs moyennes d’AR (141,3 nmol/l). Discussion-Conclusion : Les grandes ΔRA suggèrent une variabilité génique individuelle du métabolisme de ROL. Les génotypes (CA)-ALDH1A2/ SNP (rs12591551:A/C) et (AA) -CRABP2/SNP (rs12724719:A/G) sont associés à des valeurs moyennes hautes d’AR, pouvant protéger l’embryogénèse lors d’une hypovitaminose A maternelle. / Introduction: Vitamin A (retinol, ROL) modulate the embryogenesis thorough RA, its metabolite. Excess or deficiency being pathologic, the RA is tight regulated in the embryo thorough specific genes (ALDH, CRABP, CYP, etc.) important for Vitamin A metabolism. Hypothesis: High RA variations in healthy adults plasma, oriented to ROL, RA evaluation in human cord blood, in regard of possible correlations with polymorphisms of genes involved in RA metabolism and kidney development (RALDH2, CRABP2, CYP26A1,B1). Correlations between ROL and RA and/or with birth kidney size might also occur. Methods: Cord blood ROL and RA were extracted and HPLC analysed, from 145 Montreal healthy newborns. Kidney volumes already measured by ultrasonography. Genomic leucocytary DNA extraction was performed with FlexiGene DNA-Kit. 10 samples excluded (DNA quality). htSNP choices: ALDH1A2, CRABP2, CYP26A1;B1 were made on HapMap human genome. Sequencing, genotyping (Sequenom iPlex PCR) was made for these genes eventual SNPs. Biostatistics tests for genotype and allelic frequencies (Single-Locus, χ2, Kruskal-Wallis, Allelic-Exact) and Kendall-tau /Oakes analysis for eventual ROL, RA, SNPs, V-reins correlations, were performed. Results: No correlation found between Δ RA (0.07-550.27 nmol/L) and Δ ROL (51.39-3892.70 nmol/L). No association ROL or RA with kidney volumes nor with SNPs/ CYP21A1;B1. Found correlations: 1. (p=0.035), polymorphism ALDH1A2-SNP (rs12591551:A/C) heterozygous/CA, (25babies, 19%) with RA (mean ~62.21nmol/L). 2. (p=0.013), polymorphism CRABP2-SNP (rs12724719: A/G) homozygous/AA (4babies, 3%) with RA (mean~141, 3 nmol/L). Discussion/Conclusion: Big Δ RA not correlated with Δ ROL suggests individual genetic variance on RA metabolism. Genotypes (CA)-ALDH1A2/SNP (rs12591551:A/C) and (AA)-CRABP2/SNP (rs12724719: A/G) are associated with high cord blood RA mean and may be embryogenesis protective in a maternal hypovitaminosis-A, environment.

Le gène par-4 code pour une kinase à sérine/thréonine très conservée qui régule la polarisation précoce et la division cellulaire asymétrique de l’embryon de C. elegans. Une mutation de par-4 entraîne la létalité embryonnaire en perturbant trois processus: la ségrégation asymétrique des déterminants cellulaires, la régulation asynchrone de la progression du cycle cellulaire et la contractilité du réseau d’actomyosine. Pour identifier des régulateurs des voies de signalisation de PAR-4, nous avons procédé à un criblage pour des suppresseurs de la létalité embryonnaire associée à une mutation de par-4. Nous avons identifié 6 gènes qui codent pour des homologues conservés avec des activités définies telles que la phosphorylation, l’ubiquitination, la protéolyse et l’échafaudage. En employant l’imagerie quantitative pour suivre des événements cellulaires dépendants de PAR-4, nous avons déterminé quels processus sont contrôlés par chaque suppresseur durant le développement embryonnaire de C. elegans. Des analyses moléculaires de ces suppresseurs ont révélé des détails sur le mécanisme par lequel PAR-4 régule la polarisation cellulaire et promeut la division cellulaire asymétrique. / The gene lkb1 codes for a highly conserved serine/threonine kinase. The orthologue of lkb1 in the nematode Caeonorhabditis elegans, termed par-4, regulates early polarization and asymmetric cell division in the embryo. A mutation in par-4 causes embryonic lethality by perturbing three main cellular processes: asymmetric segregation of cell fate determinants, asynchronic regulation of cell cycle progression and contractility of the actomyosin network. To identify regulators of the PAR-4/LKB1-dependent pathways, we performed a screen for suppressors of the embryonic lethality associated with a mutation in par-4. We identified 6 genes that have conserved homologs with defined activities including protein phosphorylation, ubiquitination, proteolysis and scaffolding. We used quantitative imaging of specific PAR-4-dependent cellular events to determine which of these are controlled by each suppressor during early C. elegans embryonic development. Molecular analysis of these suppressors revealed details on the mechanism through which PAR-4 regulates cell polarization and promotes asymmetric cell division.