Mice with an induced mutation in collagen 8A2 develop larger eyes and are resistant to retinal ganglion cell damage in an experimental glaucoma model

PURPOSE: To study susceptibility to glaucoma injury as it may be affected by mutations in ocular connective tissue components. METHODS: Mice homozygous for an N-ethyl-N-nitrosourea induced G257D exchange (Gly to Asp) missense mutation (Aca23) in their collagen 8A2 gene were studied to measure intraocular pressure (IOP), axial length and width, number of retinal ganglion cells (RGC), and inflation responses. Three month old homozygous Aca23 mutant and wild type (WT) mice had 6 weeks exposure to elevated IOP induced by polystyrene microbead injection. Additional Aca23 and matched controls were studied at ages of 10 and 18 months. RESULTS: Aca23 mice had no significant difference from WT in IOP level, and in both strains IOP rose with age. In multivariable models, axial length and width were significantly larger in Aca23 than WT, became larger with age, and were larger after exposure to glaucoma (n=227 mice). From inflation test data, the estimates of scleral stress resultants in Aca23 mice were similar to age-matched and younger WT C57BL/6 (B6) mice, while the strain estimates for Aca23 were significantly less than those for either WT group in the mid-sclera and in some of the more anterior scleral measures (p<0.001; n=29, 22, 20 eyes in Aca23, older WT, younger WT, respectively). With chronic IOP elevation, Aca23 eyes increased 9% in length and 7% in width, compared to untreated fellow eyes (p<0.05, <0.01). With similar elevated IOP exposure, WT eyes enlarged proportionately twice as much as Aca23, increasing in length by 18% and in nasal-temporal width by 13% (both p<0.001, Mann-Whitney test). In 4 month old control optic nerves, mean RGC axon number was not different in Aca23 and WT (46,905±7,592, 43,628±11,162, respectively; p=0.43, Mann-Whitney test, n=37 and 29). With chronic glaucoma, Aca23 mice had a mean axon loss of only 0.57±17%, while WT mice lost 21±31% (median loss: 1% versus 10%, n=37, 29, respectively; p=0.001; multivariable model adjusting for positive integral IOP exposure). CONCLUSIONS: The Aca23 mutation in collagen 8α2 is the first gene defect found to alter susceptibility to experimental glaucoma, reducing RGC loss possibly due to differences in mechanical behavior of the sclera. Detailed study of the specific changes in scleral connective tissue composition and responses to chronic IOP elevation in this strain could produce new therapeutic targets for RGC neuroprotection

Susceptibilitat genètica al càncer gàstric: caracterització de les interaccions de segon ordre entre gens i variants identificades en l’estudi EPIC‐EURGAST

Curs 2012-2013En aquest Treball de Final de Grau s’exposen els resultats de l’anàlisi de les dades genètiques del projecte EurGast2 "Genetic susceptibility, environmental exposure and gastric cancer risk in an European population”, estudi cas‐control niat a la cohort europea EPIC “European Prospective lnvestigation into Cancer and Nutrition”, que té per objectiu l’estudi dels factors genètics i ambientals associats amb el risc de desenvolupar càncer gàstric (CG). A partir de les dades resultants de l’estudi EurGast2, en el què es van analitzar 1.294 SNPs en 365 casos de càncer gàstric i 1.284 controls en l’anàlisi Single SNP previ, la hipòtesi de partida del present Treball de Final de Grau és que algunes variants amb un efecte marginal molt feble, però que conjuntament amb altres variants estarien associades al risc de CG, podrien no haver‐se detectat. Així doncs, l’objectiu principal del projecte és la identificació d’interaccions de segon ordre entre variants genètiques de gens candidats implicades en la carcinogènesi de càncer gàstric. L’anàlisi de les interaccions s’ha dut a terme aplicant el mètode estadístic Model‐based Multifactor Dimensionality Reduction Method (MB‐MDR), desenvolupat per Calle et al. l’any 2008 i s’han aplicat dues metodologies de filtratge per seleccionar les interaccions que s’exploraran: 1) filtratge d’interaccions amb un SNP significatiu en el Single SNP analysis i 2) filtratge d’interaccions segons la mesura Sinèrgia. Els resultats del projecte han identificat 5 interaccions de segon ordre entre SNPs associades significativament amb un major risc de desenvolupar càncer gàstric, amb p‐valor inferior a 10‐4. Les interaccions identificades corresponen a interaccions entre els gens MPO i CDH1, XRCC1 i GAS6, ADH1B i NR5A2 i IL4R i IL1RN (que s’ha validat en les dues metodologies de filtratge). Excepte CDH1, cap altre d’aquests gens s’havia associat significativament amb el CG o prioritzat en les anàlisis prèvies, el que confirma l’interès d’analitzar les interaccions genètiques de segon ordre. Aquestes poden ser un punt de partida per altres anàlisis destinades a confirmar gens putatius i a estudiar a nivell biològic i molecular els mecanismes de carcinogènesi, i orientades a la recerca de noves dianes terapèutiques i mètodes de diagnosi i pronòstic més eficients.In this Final Degree Project the results of the genetic analysis of the nested‐case/control EurGast2 project "Genetic susceptibility, environmental exposure and gastric cancer risk in an European population” of the European EPIC cohort “European Prospective lnvestigation into Cancer and Nutrition” are exposed. Its aim is to study the genetic and environmental factors associated to the risk of developing gastric cancer (GC). In base of the EurGast2 study which analyzed 1.294 SNPs in 365 gastric cancer cases and 1.284 controls in a previous Single SNP analysis, the present hypothesis of this Final Degree Project defends that some variants with a weak marginal effect which may be associated to GC together with other variants could have not been detected. The aim of this project is to identify second order interactions between genetic variants from candidate genes implicated in gastric cancer carcinogenesis. The interaction’s analysis has been carried out applying the statistical Model‐based Multifactor Dimensionality Reduction Method MB‐MDR developed by Calle et al. in 2008 and two different methodologies have been applied in order to select the best second order interactions to explore: 1) interactions’ filtering with one significant SNP in the Single SNP analysis and 2) interactions’ filtering using the Synergy measure. The results of the project have identified that 5 second order interactions between different SNPs are statistically associated with a major risk of developing gastric cancer at a p‐value<10‐4. These interactions identified correspond to interactions between SNPs from MPO and CDH1 genes, XRCC1 and GAS6 genes, ADH1B and NR5A2 genes and IL4R and IL1RN genes (which has been validated in both independent filter methods). Except CDH1, any other of these genes have been associated statistically to gastric cancer or has been prioritized in the previous univariant analysis. This fact confirms the interest of analyzing genetic second order interactions which can represent a start point for other analysis to confirm putative genes and study at a biological and molecular level the mechanisms underpinning gastric cancer carcinogenesis which can represent a step closer to the research of new therapeutic targets and the definition of more efficient diagnosis methods

Structural analysis and multidisciplinary design of flexible fluid loaded composite canard

Mechanical performance of a composite canard subject to static aerodynamic loads was numerically studied in the present research. The canard was modeled as a symmetrically laminated curved panel, consisting of 8 plies of T300/5208 graphite/epoxy composite laminate. Modeling of this structure-fluid interaction system involves the coupling of two formulations: the solid classically treated in FEM formulation, and the fluid described by potential panel method in CFD. A structure-fluid iterative loop was implemented to simulate the relationship between the deformed aircraft wing and aerodynamic load. The outcome of the structural analysis indicated that the ply orientation have a significant effect on the mechanical performance of the composite laminates such that various design objectives can be achieved just by selecting the proper arrangement of ply orientation and thickness. Three numerical optimization techniques were applied respectively in the structural optimization design which aims at achieving the best structural performance and material efficiency while satisfying certain constraints. Gradient-based CONMIN converged quickly but only provided local optimum values. Probabilistic algorithm GA was capable of achieving the global/near-global optimums but the searching process was time-consuming. HYBRID, an automated hybridization process which combined GA and CONMIN together, has been implemented so that a single run of the algorithm gives a global optimum at reasonable computational cost. A structurally optimized design of the composite canard with lighter weight and higher stiffness has been obtained. A morphing design was performed on this structurally optimized composite panel to improve its maneuverability. An advanced design of composite canard with high structural efficiency and good maneuverability has been obtained by adjusting the ply angles. The strain energy of the host structure decreased which helps reduce the mechanical energy loss and improve the performance of the embedded or bonded actuators/sensors. The improved mechanical performance of the advanced design indicates that the adaptive laminated composite structures enhance the possibility of achieving a multi-functional structure for high performance structural applications

Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers

Background: The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses. Results: We generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes. Conclusion: The efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines

Genetic Structure of Diploid Gametes for the Production of Triploid Citrus Hybrids

Tesis por compendioThis thesis aimed to study three main aspects: (i) the mechanisms underlying unreduced pollen gamete formation in the diploid `CSO¿ tangor hybrid used as male parent in 4x x 2x triploid breeding programs, (ii) the frequencies and mechanisms involved in the unreduced 2n female gametes production for `Eureka Frost¿ and `Fino¿ lemon genotypes, and (iii) the interspecific recombination and the resulting diploid gamete structures of doubled-diploid `Mexican¿ lime to evaluate the possibility that natural interploid hybridization maybe the origin of C. latifolia (`Tahiti¿ lime type) and C. aurantifolia (`Tanepao¿ lime type) triploid varieties. The production of 54 tetraploid hybrids from 4x x 2x sexual hybridizations allowed the analysis of the mechanisms underlying unreduced pollen gamete formation. SSR and SNP molecular markers revealed that the majority of these plants were obtained from 2n pollen of the diploid tangor parent. Then, the maximum-likelihood method based on parental heterozygosity restitution (PHR) of centromeric loci revealed that both FDR (First Division Restitution ) with predominant occurrence and to a lower extend SDR (Second Division Restitution) were the mechanisms leading to unreduced male gamete formation in the tangor studied. These observations were confirmed by the analysis of PHR pattern along the linkage group (LG) 2. To our knowledge, this is the first report of tetraploid citrus progenies arising from unreduced pollen and the first description of the coexistence of two meiotic restitution mechanisms (SDR and FDR) producing unreduced pollen in citrus. In order to study the frequencies and the mechanisms involved in the unreduced 2n female gametes production in two different genotypes of lemon, we produced 43 triploid and tetraploid hybrids from 2x x 2x and 2x x 4x sexual hybridizations using `Eureka Frost¿ and `Fino¿ as female parents. The frequencies of 2n gamete production were respectively 4.9% and 8.3%. The maximum-likelihood analysis and pattern of PHR along LG1 revealed that SDR is the main mechanism of unreduced female lemon gametes (88%), followed by FDR or pre-meiotic doubling (PRD) (7%) and post-meiotic genome doubling (PMD) mechanisms (5%). This is the first report of the production of a large number of lemon progenies from 2n gametes and the first identification of a new mechanism, PMD that has never been observed in citrus and has rarely been described in other herbaceous or woody species. Across both studies, we demonstrated at the methodological level the effectiveness of using two complementary approaches, the analysis of the PHR pattern in one LG and the maximum-likelihood method based on centromeric loci for distinguishing between the different mechanisms of unreduced gamete production. We analyzed the meiotic mechanisms of a doubled diploid `Mexican¿ lime, the interspecific recombination and the resulting diploid gamete structures combining a segregation analysis of SSR and SNPs markers, a cytogenetic study and pollen viability evaluation. We concluded that the doubled-diploid `Mexican¿ lime had a predominantly disomic segregation for three LGs, intermediate inheritance with disomic tendency was found for five LGs and intermediate models for one LG. The resulting interspecific diploid gamete structures displayed high C. medica / C. micrantha heterozygosity. The revealed genetic structures of the diploid gametes produced by the doubled-diploid `Mexican¿ lime are compatible with the hypothesis that `Tahiti¿ and `Tanepao¿ triploid varieties results from interploid hybridization involving a doubled-diploid `Mexican¿ like lime. This disomic tendency limits the recombination and the diversity of the diploid gamete population; however the observed pollen viability restoration at tetraploid level could be advantageous for intensive breeding projects.Esta tesis estudia tres aspectos principales: (i) los mecanismos de la formación de gametos 2n de polen originados por un híbrido diploide (tangor `CSO¿) utilizado como parental masculino en hibridaciones sexuales 4x x 2x, (ii) las frecuencias y los mecanismos de la producción de gametos 2n femeninos en dos genotipos de limón, `Eureka Frost¿ y `Fino¿, y (iii) el análisis de la recombinación interespecífica y las estructuras de los gametos diploides originados por la lima `Mejicana¿ doble diploide para evaluar el origen de las las variedades triploides de lima C. latifolia (`Tahiti¿) y C. aurantifolia (`Tanepao¿). La obtención de 54 híbridos tetraploides a partir de hibridaciones 4x x 2x permitió analizar los mecanismos de la formación de gametos 2n de polen. El análisis molecular reveló que la mayoría de estas plantas se obtuvieron a partir de gametos 2n de polen del parental `CSO¿. A continuación, el análisis mediante el método de máxima verosimilitud indicó que FDR (Restitución de la Primera División meiótica) y SDR (Restitución de la Segunda División meiótica) son los mecanismos implicados con una mayor dominancia de FDR respecto SDR. Estos resultados se confirmaron mediante el análisis de la restitución de la heterocigosidad en el grupo de ligamiento (LG) 2. Con los datos publicados hasta la fecha, es la primera vez que se han obtenido progenies tetraploides de cítricos mediante gametos 2n de polen y es la primera descripción en cítricos de la coexistencia de dos mecanismos SDR y FDR. Para estudiar las frecuencias y los mecanismos de la producción de gametos 2n en dos genotipos de limón, se obtuvieron 43 híbridos triploides y tetraploides a partir de hibridaciones sexuales 2x x 2x y 2x x 4x utilizando los limones `Eureka Frost¿ y `Fino¿ como parentales femeninos. Las frecuencias de producción de gametos 2n fueron respectivamente 4,9% y 8,3%. El análisis de máxima verosimilitud y el patrón de PHR a lo largo del LG1 reveló que SDR es el mecanismo principal de formación de gametos 2n femeninos (88%), seguido por FDR o duplicación del genoma pre-meiosis (PRD) (7%) y se identificó un nuevo mecanismo originado a partir de la duplicación del genoma post-meiosis (PMD) (5%). En este trabajo se describe por primera vez en cítricos la producción de un elevado número de híbridos de limón a partir de gametos 2n y es la primera vez que se identifica un nuevo mecanismo PMD que nunca se ha observado en cítricos. En ambos estudios se demostró la efectividad del uso de dos métodos complementarios, el análisis del patrón de PHR a lo largo de un LG y el método de máxima verosimilitud para distinguir entre los diferentes mecanismos implicados en la formación de gametos 2n. También se ha analizado el modelo de segregación cromosómica de la lima `Mejicana¿ doble diploide (DD) así como la recombinación interespecífica y las estructuras de los gametos diploides resultantes. Se ha realizado análisis de la viabilidad del polen junto con un análisis citogenético y con marcadores SSRs y SNPs. Estos trabajos nos han permitido concluir que la lima `Mejicana¿ DD presenta una segregación predominantemente disómica para tres LGs, herencia intermedia con tendencia disómica para cinco LGs y un tipo de segregación intermedia para un LG. Las estructuras de los gametos diploides mostraron una alta heterocigosis en C. medica/C. micrantha, parentales de la lima `Mejicana¿. Las estructuras genéticas de los gametos diploides de la lima `Mejicana¿ DD son compatibles con la hipótesis de que las variedades triploides `Tahiti¿ y `Tanepao¿ se obtuvieran a partir de una hibridación interploide a partir de la lima `Mejicana¿ DD. El tipo de segregación disómico conlleva una limitación de la recombinación y la diversidad genética de la población de gametos 2n. Sin embargo la viabilidad del polen de la lima `Mejicana¿ DD en comparación con la lima `Mejicana¿ diploide permiteAquesta tesi ha tingut com a objectius l'estudi de (i) els mecanismes subjacents a la formació de pol·len de gàmetes 2n al tangor híbrid diploide `CSO', utilitzat com a progenitor masculí en els programes de millora de triploides 4x x 2x (ii) les freqüències i els mecanismes implicats en la producció gàmetes 2n en la femella als genotips de llimona `Eureka Frost¿ i Fina' (iii) la recombinació interespecífica i les estructures resultants de gàmetes diploides del doble-diploide (DD) de `llima Mèxicana' per avaluar la possibilitat que la hibridació interploid natural potser l'origen de les varietats triploides C. latifolia (llima tipus `Tahiti') i C. aurantifolia (llima tipus `Tanepao'). La producció de 54 híbrids tetraploides obtinguts d¿hibridacions sexuals 4x x 2x va permetre l'anàlisi dels mecanismes de formació de gàmetes 2n de pol·len. Els marcadors moleculars SSR i SNP van revelar que la majoria d'aquestes plantes es van obtenir de pol·len 2n del parental diploide tangor. Llavors, el mètode de màxima probabilitat va revelar que tant FDR (Restitució en la Primera Divisió), amb ocurrència predominant, com SDR (Restitució en la Segona Divisió) van ser els mecanismes que condueixen a la formació de gàmetes masculins 2n en aquest tangor. Aquestes observacions van ser confirmades per l'anàlisi de patró de RHP al llarg del cromosoma 2. Des del nostre coneixement, aquest és el primer estudi de progènies de cítrics tetraploides derivats de pol·len no reduït i la primera descripció de la coexistència de dos mecanismes de restitució meiòtiques (FDR i SDR) produint pol·len no reduït en els cítrics. Per tal d'estudiar les freqüències i els mecanismes implicats en la producció de gàmetes 2n sense reduir de la femella, en dos genotips diferents de llimona, vam obtenir 43 híbrids triploides i tetraploides d¿hibridacions sexuals 2x x 2x i 4x x 2x utilitzant `Eureka Frost ' i `Fino' com progenitors femenins. Les freqüències de la producció de gàmetes 2n van ser, respectivament, 4,9% i 8,3%. L'anàlisi de màxima probabilitat i el patró de RHP al llarg del cromosoma 1 van revelar que SDR és el principal mecanisme de gàmetes 2n en la llimona utilitzada com parent femení (88%), seguit pels mecanismes FDR o duplicació pre-meiòtica (PRD) (7%) i la duplicació del genoma post-meiòtica (PMD) (5%). Per primera volta en els cítrics s¿ha obtingut un gran nombre de progènie de llimona a partir de gàmetes 2n i s¿ha identificat un nou mecanisme, el PMD que poques vegades s'ha descrit en altres espècies herbàcies o llenyoses. A través dels dos treballs, hem demostrat, a nivell metodològic, l'eficàcia d'utilitzar dos enfocaments complementaris, és a dir, l'anàlisi del patró de RHP en un cromosoma amb el mètode de màxima probabilitat basat en loci centromèrics per distingir entre els diferents mecanismes de la producció de gàmetes 2n . Es van analitzar els mecanismes meiòtics d'un DD `llima Mèxicana', la recombinació interespecífica i les estructures resultants de gàmetes diploides combinant una anàlisi de segregació de marcadors SSR i SNP, un estudi citogenètic i l'avaluació de la viabilitat del pol·len. Hem arribat a la conclusió que el DD de `llima Mèxicana' tenia una segregació predominantment disómica en tres cromosomes, herència intermèdia amb tendència disómica en cinc cromosomes i els models intermedis per a un altre. Les estructures resultants de gàmetes diploides interespecífiques mostren alta heterozigositat C. medica / C. micrantha. Les estructures genètiques revelades dels gàmetes diploides produïts pel DD de `llima Mèxicana' són compatibles amb la hipòtesi que les varietats triploides `Tahiti¿ i `Tanepao¿ resulten de la hibridació interploide que impliquen un DD de tipus `llima Mèxicana'. Aquesta tendència disómica limita la recombinació i la diversitat de la població de gàmetes diploides, però, la restauració de la viabilitatHoussem, R. (2017). Genetic Structure of Diploid Gametes for the Production of Triploid Citrus Hybrids [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/90634Compendi

MATHEMATICAL MODELLING AND PARENTAGE ANALYSIS OF HYBRID ZONES

The theoretical framework behind the mathematical analysis of clines in nature is reviewed. Then, a simplified version of these models implemented in Mathematica is presented. Finally, parentage analysis methods are tested on simulated data in order to define a minimum number of markers needed for molecular analysis of natural populations.Palero Pastor, FE. (2009). MATHEMATICAL MODELLING AND PARENTAGE ANALYSIS OF HYBRID ZONES. http://hdl.handle.net/10251/14065Archivo delegad

Intermittent Fasting (IF) Promotes Longevity through Alterations of the Mammalian Target of Rapamycin (mTOR) and the Epigenome

Many studies with a range of subjects from Nematodes to Homo sapiens have found intermittent fasting (IF) to significantly improve the cardiometabolic health of individuals, but how IF promotes longevity through epigenetic modulations remains a sparse understanding throughout the literature. The process of aging may be characterized by a loss of cellular identity sprouted from a disrupted epigenome rich with information for a cell, while also losing the ability to recycle ineffective cellular components. The nutrient-sensing kinase Mammalian Target of Rapamycin (mTOR) is disrupted during bouts of fasting which allows for the recycling of cellular components through increased autophagy. Furthermore, the Sirtuin (SIRT) family of NAD+-dependent deacetylases is a prominent transcriptional repressor via histone deacetylation and increased DNA-methyltransferase (DNMT) activity upon deacetylation of the enzyme. Although longitudinal studies spanning many years will be needed to provide definitive evidence for the long-term effects of IF. To date, the most profound pro-longevity evidence for IF is a significant reduction in the rate of biological aging determined from global genomic DNA methylation, of which is a more accurate measure of age in comparison to chronological age. Aside from specific cases in which IF may be detrimental to health, the practice of IF may add years onto an individual’s life, and more importantly, healthy years contributing to a better quality of life