Organotypic Modeling Platform for Adverse Outcome Pathways of Male Reproductive and Developmental Processes

Thesis (Master's)--University of Washington, 2016-06

Neogenin: A multi-functional receptor regulating diverse developmental processes

Neogenin, a close relative of the axon guidance receptor Deleted in Colorectal Cancer (DCC), has been shown to be a receptor for members of the Netrin and Repulsive Guidance Molecule (RGM) families. While Netrin-l-Neogenin interactions result in a chernoattractive axon guidance response, the interaction between Neogenin and RGMa induces a chemorepulsive response. Evidence is now accumulating that Neogenin is a multi-functional receptor regulating many diverse developmental processes, including neural tube and mammary gland formation, myogenesis and angiogenesis. Little is known of the function of Neogenin in the adult, however, a novel role in the regulation of iron homeostasis is now emerging. While the signal transduction pathways activated by Neogenin are poorly understood, it is clear that the functional outcome of Neogenin activation, at least in the embryo, depends on both the developmental context as well as the nature of the ligand. (c) 2006 Elsevier Ltd. All rights reserved.

Signals from Eph and ephrin proteins: a developmental tool kit

Interactions between Eph receptors and their ligands the ephrin proteins are critically important in many key developmental processes. Emerging evidence also supports a role for these molecules in postembryonic tissues, particularly in pathological processes, including tissue injury and tumor metastasis. We review the signaling mechanisms that allow the 14 Eph and nine ephrin proteins to deliver intracellular signals that regulate cell shape and movement. What emerges is that the initiation of these signals is critically dependent on which Eph and ephrin proteins are expressed, the level of their expression, and, in some cases, which splice variants are expressed. Diversity at the level of initial interaction and in the downstream signaling processes regulated by Eph-ephrin signaling provides a subtle, versatile system of regulation of intercellular adhesion, cell shape, and cell motility.

A hierarchical approach to model parameter optimization for developmental systems.

In the context of Systems Biology, computer simulations of gene regulatory networks provide a powerful tool to validate hypotheses and to explore possible system behaviors. Nevertheless, modeling a system poses some challenges of its own: especially the step of model calibration is often difficult due to insufficient data. For example when considering developmental systems, mostly qualitative data describing the developmental trajectory is available while common calibration techniques rely on high-resolution quantitative data. Focusing on the calibration of differential equation models for developmental systems, this study investigates different approaches to utilize the available data to overcome these difficulties. More specifically, the fact that developmental processes are hierarchically organized is exploited to increase convergence rates of the calibration process as well as to save computation time. Using a gene regulatory network model for stem cell homeostasis in Arabidopsis thaliana the performance of the different investigated approaches is evaluated, documenting considerable gains provided by the proposed hierarchical approach.

Multiple roles of mouse Numb in tuning developmental cell fates.

BACKGROUND: Notch signaling regulates multiple differentiation processes and cell fate decisions during both invertebrate and vertebrate development. Numb encodes an intracellular protein that was shown in Drosophila to antagonize Notch signaling at binary cell fate decisions of certain cell lineages. Although overexpression experiments suggested that Numb might also antagonize some Notch activity in vertebrates, the developmental processes in which Numb is involved remained elusive. RESULTS: We generated mice with a homozygous inactivation of Numb. These mice died before embryonic day E11.5, probably because of defects in angiogenic remodeling and placental dysfunction. Mutant embryos had an open anterior neural tube and impaired neuronal differentiation within the developing cranial central nervous system (CNS). In the developing spinal cord, the number of differentiated motoneurons was reduced. Within the peripheral nervous system (PNS), ganglia of cranial sensory neurons were formed. Trunk neural crest cells migrated and differentiated into sympathetic neurons. In contrast, a selective differentiation anomaly was observed in dorsal root ganglia, where neural crest--derived progenitor cells had migrated normally to form ganglionic structures, but failed to differentiate into sensory neurons. CONCLUSIONS: Mouse Numb is involved in multiple developmental processes and required for cell fate tuning in a variety of lineages. In the nervous system, Numb is required for the generation of a large subset of neuronal lineages. The restricted requirement of Numb during neural development in the mouse suggests that in some neuronal lineages, Notch signaling may be regulated independently of Numb.

The construction of national identity as a developmental process from childhood to adolescence in Catalonia

La idea que per entendre alguna cosa hem d'entendre el procés pel qual s'ha produït va ser assumida des de l'origen de l'estudi "La construcció de la identitat nacional com a procés de desenvolupament des de la infància a l'adolescència a Catalunya". Per tal d'estudiar el procés de desenvolupament relacionat amb la construcció de la identitat nacional, no és suficient considerar-lo en el seu context social, sinó que és necessari considerar la seva construcció social. Tres objectius principals van orientar el nostre estudi . Primer, indagar si els processos de categorització, identificació, coneixement, imatge, avaluació i afecte són també elements implicats en la construcció de la identitat nacional des de la infància a l'adolescència. Segon investigar el procés de desenvolupament d'aquests elements des dels 6 anys fins als 15 anys per contribuir amb dades a I'explicació sobre com es desenvolupa del coneixement social. Tres són les explicacions principals; la primera que es basa en processos cognitius d'inclusió-decentració; la segona, si aquest desenvolupament es dóna en cercles concèntrics des de I'interior (contextos quotidians) fins a l'exterior (amb intercanvis més amples i una educació formal envers la vida social); i la tercera, si el desenvolupament del coneixement social d'allò més immediat i directe es reorganitzat i adquireix nous significats per la integració dels elements més generals i abstractes. Tercer, donat el fet que el 50% de les famílies tenen el català com a llengua materna, hem estudiat la influència de la llengua o llengües utilitzades en el context familiar en el procés de construcció de la identitat nacional. Es va dissenyar una entrevista individual seguint una estructura amb les parts següents: identificació subjectiva i identificació nacional; coneixement dels països; estereotips, avaluació i sentiments, i entorn social. La mostra del present estudi va estar formada per 495 nens i adolescents de 6, 9, 12 i 15 anys d'edat. Es va utilitzar per cada grup un número similar de nens i nenes. La mostra es va dividir en tres grups segons la o les llengües utilitzades pel nen o nena en el seu context familiar. Tres van ser les categones lingüístiques utilitzades: castellà, nens que només utilitzin el castellà a casa; català, nens que només usen el català en el context familiar; i bilingües, nens que utilitzin tots dos idiomes a casa. Aquestes categories lingüístiques s'han utilitzat com a indicador dels contextos familiars. Dues conclusions principals es poden extreure d'aquest estudi. Primer, I'ús de categories nacionals no és una conseqüència del procés cognitiu d'inclusió-decentració ni en cercles concentrics (concret/abstracte). La idea d'un procés del món en paral·lel, d'un coneixement que integra simultàniament creences i sentiments de l'ambient concret o proper i de l'abstracte o llunyà pot explicar millor els nostres resultats. Els nens aprenen i pensen sobre la vida quotidara, les característiques de l'ambient, la informació circulant en el seu entom social i la importància o els diferents nivells de coneixement depenent del context. Els nens integren la informació que està circulant en el seu ambient i construeixen un món que necessàriament no ha de coincidir amb el món deis adults, però que els ajuda a comunicar-se i a entendre les situacions en les quals estan immersos. Els nens més joves són capaços d'utilitzar categories nacionals de manera similar als adolescents. Segon, la identitat nacional a Catalunya es construeix al voltant del nucli de la llengua parlada a casa. A través de tot I'estudi es pot veure un resultat consistent i reiterat. Els infants d'un entom familiar en què s'usa només el castellà s'identifiquen com a pertanyents a tots dos grups nacionals, Espanyol i Català. Els infants d'un entom familiar que utilitzen només el català s'identifiquen com a pertanyents només al grup Català. Aquestes identificacions guien com aquests nens avaluen i senten envers el propi grup nacional i els altres. A més, sembla que el context sòcio-polític és un vehicle important en la transmissió de les estructures de semblances i que I'estructura d'afecte es transmet principalment a través de I'entom familiar.

IDENTIFICATION OF GENES CONTROLLING BIOLOGICAL PROCESSES AND PATHWAYS THROUGH STATISTICAL ANALYSIS AND NETWORK RECONSTRUCTION

The developmental processes and functions of an organism are controlled by the genes and the proteins that are derived from these genes. The identification of key genes and the reconstruction of gene networks can provide a model to help us understand the regulatory mechanisms for the initiation and progression of biological processes or functional abnormalities (e.g. diseases) in living organisms. In this dissertation, I have developed statistical methods to identify the genes and transcription factors (TFs) involved in biological processes, constructed their regulatory networks, and also evaluated some existing association methods to find robust methods for coexpression analyses. Two kinds of data sets were used for this work: genotype data and gene expression microarray data. On the basis of these data sets, this dissertation has two major parts, together forming six chapters. The first part deals with developing association methods for rare variants using genotype data (chapter 4 and 5). The second part deals with developing and/or evaluating statistical methods to identify genes and TFs involved in biological processes, and construction of their regulatory networks using gene expression data (chapter 2, 3, and 6). For the first part, I have developed two methods to find the groupwise association of rare variants with given diseases or traits. The first method is based on kernel machine learning and can be applied to both quantitative as well as qualitative traits. Simulation results showed that the proposed method has improved power over the existing weighted sum method (WS) in most settings. The second method uses multiple phenotypes to select a few top significant genes. It then finds the association of each gene with each phenotype while controlling the population stratification by adjusting the data for ancestry using principal components. This method was applied to GAW 17 data and was able to find several disease risk genes. For the second part, I have worked on three problems. First problem involved evaluation of eight gene association methods. A very comprehensive comparison of these methods with further analysis clearly demonstrates the distinct and common performance of these eight gene association methods. For the second problem, an algorithm named the bottom-up graphical Gaussian model was developed to identify the TFs that regulate pathway genes and reconstruct their hierarchical regulatory networks. This algorithm has produced very significant results and it is the first report to produce such hierarchical networks for these pathways. The third problem dealt with developing another algorithm called the top-down graphical Gaussian model that identifies the network governed by a specific TF. The network produced by the algorithm is proven to be of very high accuracy.

A homeobox gene with potential developmental control function in the meristem of the conifer Picea abies

Many homeobox genes control essential developmental processes in animals and plants. In this report, we describe the first cDNA corresponding to a homeobox gene isolated from a gymnosperm, the HBK1 gene from the conifer Picea abies (L.) Karst (Norway spruce). The sequence shows distinct similarities specifically to the KNOX (knotted-like homeobox) class of homeobox genes known from different angiosperm plants. The deduced amino acid sequence of HBK1 is strikingly similar within the homeodomain (84% identical) to the maize gene Knotted1 (Kn1), which acts to regulate cell differentiation in the shoot meristem. This similarity suggested that the phylogenetic association of HBK1 with the KNOX genes might be coupled to a conservation of gene function. In support of this suggestion, we have found HBK1 to be expressed in the apical meristem in the central population of nondifferentiated stem cells, but not in organ primordia developing at the flanks of the meristem. This pattern of expression is similar to that of Kn1 in the maize meristem. We show further that HBK1, when expressed ectopically in transgenic Arabidopsis plants, causes aberrations in leaf development that are similar to the effects of ectopic expression of angiosperm KNOX genes on Arabidopsis development. Taken together, these data suggest that HBK1 has a role, similar to the KNOX genes in angiosperms, in the control of cellular differentiation in the apical meristem of spruce. The data also indicate that KNOX-gene regulation of vegetative development is an ancient feature of seed plants that was present in the last common ancestor of conifers and angiosperms.

Small molecule developmental screens reveal the logic and timing of vertebrate development

Much has been learned about vertebrate development by random mutagenesis followed by phenotypic screening and by targeted gene disruption followed by phenotypic analysis in model organisms. Because the timing of many developmental events is critical, it would be useful to have temporal control over modulation of gene function, a luxury frequently not possible with genetic mutants. Here, we demonstrate that small molecules capable of conditional gene product modulation can be identified through developmental screens in zebrafish. We have identified several small molecules that specifically modulate various aspects of vertebrate ontogeny, including development of the central nervous system, the cardiovascular system, the neural crest, and the ear. Several of the small molecules identified allowed us to dissect the logic of melanocyte and otolith development and to identify critical periods for these events. Small molecules identified in this way offer potential to dissect further these and other developmental processes and to identify novel genes involved in vertebrate development.

Investigating ontogenetic space with developmental cell lineages

Development plays a significant role in biological evolution, and is likely to prove an effective route to overcoming the limitations of direct genotype-phenotype mappings in artificial evolution. Nonetheless, the relationship between development and evolution is complex and still poorly understood. One question of current interest concerns the possible role that developmental processes may play in orienting evolution. A first step towards exploring this issue from a theoretical perspective is understanding the structure of ontogenetic space: the space of possible genotype-phenotype mappings. Using a quantitative model of development that enables ontogenetic space to be characterised in terms of complexity, we show that ontogenetic landscapes have a characteristic structure that varies with genotypic properties.

An investigation of multiple pathways of developmental intervention change

Convergence among treatment, prevention, and developmental intervention approaches has led to the recognition of the need for evaluation models and research designs that employ a full range of evaluation information to provide an empirical basis for enhancing the efficiency, efficacy, and effectiveness of prevention and positive development interventions. This study reports an investigation of a positive youth development program using an Outcome Mediation Cascade (OMC) evaluation model, an integrated model for evaluating the empirical intersection between intervention and developmental processes. The Changing Lives Program (CLP) is a community supported positive youth development intervention implemented in a practice setting as a selective/indicated program for multi-ethnic, multi-problem at risk youth in urban alternative high schools. This study used a Relational Data Analysis integration of quantitative and qualitative data analysis strategies, including the use of both fixed and free response measures and a structural equation modeling approach, to construct and evaluate the hypothesized OMC model. Findings indicated that the hypothesized model fit the data (χ2 (7) = 6.991, p = .43; RMSEA = .00; CFI = 1.00; WRMR = .459). Findings also provided preliminary evidence consistent with the hypothesis that in addition to having effects on targeted positive outcomes, PYD interventions are likely to have progressive cascading effects on untargeted problem outcomes that operate through effects on positive outcomes. Furthermore, the general pattern of findings suggested the need to use methods capable of capturing both quantitative and qualitative change in order to increase the likelihood of identifying more complete theory informed empirically supported models of developmental intervention change processes.

On the developmental continuity /discontinuity of early adolescent patterns of racial identity salience: Relations with later identities and psychosocial adjustment

Given the significant amount of attention placed upon race within our society, racial identity long has been nominated as a meaningful influence upon human development (Cross, 1971; Sellers et al., 1998). Scholars investigating aspects of racial identity have largely pursued one of two lines of research: (a) describing factors and processes that contribute to the development of racial identities, or (b) empirically documenting associations between particular racial identities and key adjustment outcomes. However, few studies have integrated these two approaches to simultaneously evaluate developmental and related adjustment aspects of racial identity among minority youth. Consequently, relations between early racial identity developmental processes and correlated adjustment outcomes remain ambiguous. Even less is known regarding the direction and function of these relationships during adolescence. To address this gap, the present study examined key multivariate associations between (a) distinct profiles of racial identity salience and (b) adjustment outcomes within a community sample of African-American youth. Specifically, a person-centered analytic approach (i.e., cluster analysis) was employed to conduct a secondary analysis of two archived databases containing longitudinal data measuring levels of racial identity salience and indices of psychosocial adjustment among youth at four different measurement occasions.^ Four separate groups of analyses were conducted to investigate (a) the existence of within-group differences in levels of racial identity salience, (b) shifts among distinct racial identity types between contiguous times of measurement, (c) adjustment correlates of racial identity types at each time of measurement, and (d) predictive relations between racial identity clusters and adjustment outcomes, respectively. Results indicated significant heterogeneity in patterns of racial identity salience among these African-American youth as well as significant discontinuity in the patterns of shifts among identity profiles between contiguous measurement occasions. In addition, within developmental stages, levels of racial identity salience were associated with several adjustment outcomes, suggesting the protective value of high levels of endorsement or internalization of racial identity among the sampled youth. Collectively, these results illustrated the significance of racial identity salience as a meaningful developmental construct in the lives of African-American adolescents, the implications of which are discussed for racial identity and practice-related research literatures. ^

Leaf-, Panel- And Latex-expressed Sequenced Tags From The Rubber Tree (hevea Brasiliensis) Under Cold-stressed And Suboptimal Growing Conditions: The Development Of Gene-targeted Functional Markers For Stress Response.

Hevea brasiliensis is a native species of the Amazon Basin of South America and the primary source of natural rubber worldwide. Due to the occurrence of South American Leaf Blight disease in this area, rubber plantations have been extended to suboptimal regions. Rubber tree breeding is time-consuming and expensive, but molecular markers can serve as a tool for early evaluation, thus reducing time and costs. In this work, we constructed six different cDNA libraries with the aim of developing gene-targeted molecular markers for the rubber tree. A total of 8,263 reads were assembled, generating 5,025 unigenes that were analyzed; 912 expressed sequence tags (ESTs) represented new transcripts, and two sequences were highly up-regulated by cold stress. These unigenes were scanned for microsatellite (SSR) regions and single nucleotide polymorphisms (SNPs). In total, 169 novel EST-SSR markers were developed; 138 loci were polymorphic in the rubber tree, and 98 % presented transferability to six other Hevea species. Locus duplication was observed in H. brasiliensis and other species. Additionally, 43 SNP markers in 13 sequences that showed similarity to proteins involved in stress response, latex biosynthesis and developmental processes were characterized. cDNA libraries are a rich source of SSR and SNP markers and enable the identification of new transcripts. The new markers developed here will be a valuable resource for linkage mapping, QTL identification and other studies in the rubber tree and can also be used to evaluate the genetic variability of other Hevea species, which are valuable assets in rubber tree breeding.

Paralisia cerebral : atividades ludicas e processos desenvolvimentais em ambiente hospitalar

Universidade Estadual de Campinas . Faculdade de Educação Física

rst Transcriptional Activity Influences kirre mRNA Concentration in the Drosophila Pupal Retina during the Final Steps of Ommatidial Patterning

Background: Drosophila retinal architecture is laid down between 24-48 hours after puparium formation, when some of the still uncommitted interommatidial cells (IOCs) are recruited to become secondary and tertiary pigment cells while the remaining ones undergo apoptosis. This choice between survival and death requires the product of the roughest (rst) gene, an immunoglobulin superfamily transmembrane glycoprotein involved in a wide range of developmental processes. Both temporal misexpression of Rst and truncation of the protein intracytoplasmic domain, lead to severe defects in which IOCs either remain mostly undifferentiated and die late and erratically or, instead, differentiate into extra pigment cells. Intriguingly, mutants not expressing wild type protein often have normal or very mild rough eyes. Methodology/Principal Findings: By using quantitative real time PCR to examine rst transcriptional dynamics in the pupal retina, both in wild type and mutant alleles we showed that tightly regulated temporal changes in rst transcriptional rate underlie its proper function during the final steps of eye patterning. Furthermore we demonstrated that the unexpected wild type eye phenotype of mutants with low or no rst expression correlates with an upregulation in the mRNA levels of the rst paralogue kin-of-irre (kirre), which seems able to substitute for rst function in this process, similarly to their role in myoblast fusion. This compensatory upregulation of kirre mRNA levels could be directly induced in wild type pupa upon RNAi-mediated silencing of rst, indicating that expression of both genes is also coordinately regulated in physiological conditions. Conclusions/Significance: These findings suggest a general mechanism by which rst and kirre expression could be fine tuned to optimize their redundant roles during development and provide a clearer picture of how the specification of survival and apoptotic fates by differential cell adhesion during the final steps of retinal morphogenesis in insects are controlled at the transcriptional level.