Spatial genomic heterogeneity within localized, multifocal prostate cancer

Herein we provide a detailed molecular analysis of the spatial heterogeneity of clinically localized, multifocal prostate cancer to delineate new oncogenes or tumor suppressors. We initially determined the copy number aberration (CNA) profiles of 74 patients with index tumors of Gleason score 7. Of these, 5 patients were subjected to whole-genome sequencing using DNA quantities achievable in diagnostic biopsies, with detailed spatial sampling of 23 distinct tumor regions to assess intraprostatic heterogeneity in focal genomics. Multifocal tumors are highly heterogeneous for single-nucleotide variants (SNVs), CNAs and genomic rearrangements. We identified and validated a new recurrent amplification of MYCL, which is associated with TP53 deletion and unique profiles of DNA damage and transcriptional dysregulation. Moreover, we demonstrate divergent tumor evolution in multifocal cancer and, in some cases, tumors of independent clonal origin. These data represent the first systematic relation of intraprostatic genomic heterogeneity to predicted clinical outcome and inform the development of novel biomarkers that reflect individual prognosis.

The Effects of Density, Spatial Pattern, and Competitive Symmetry on Size Variation in Simulated Plant Populations

Patterns of size inequality in crowded plant populations are often taken to be indicative of the degree of size asymmetry of competition, but recent research suggests that some of the patterns attributed to size‐asymmetric competition could be due to spatial structure. To investigate the theoretical relationships between plant density, spatial pattern, and competitive size asymmetry in determining size variation in crowded plant populations, we developed a spatially explicit, individual‐based plant competition model based on overlapping zones of influence. The zone of influence of each plant is modeled as a circle, growing in two dimensions, and is allometrically related to plant biomass. The area of the circle represents resources potentially available to the plant, and plants compete for resources in areas in which they overlap. The size asymmetry of competition is reflected in the rules for dividing up the overlapping areas. Theoretical plant populations were grown in random and in perfectly uniform spatial patterns at four densities under size‐asymmetric and size‐symmetric competition. Both spatial pattern and size asymmetry contributed to size variation, but their relative importance varied greatly over density and over time. Early in stand development, spatial pattern was more important than the symmetry of competition in determining the degree of size variation within the population, but after plants grew and competition intensified, the size asymmetry of competition became a much more important source of size variation. Size variability was slightly higher at higher densities when competition was symmetric and plants were distributed nonuniformly in space. In a uniform spatial pattern, size variation increased with density only when competition was size asymmetric. Our results suggest that when competition is size asymmetric and intense, it will be more important in generating size variation than is local variation in density. Our results and the available data are consistent with the hypothesis that high levels of size inequality commonly observed within crowded plant populations are largely due to size‐asymmetric competition, not to variation in local density.

Analysis of Lim1 LIM domains in mouse development

Transcriptional regulation is fundamental for the precise development of all organisms. Through tight regulation, necessary genes are activated at proper spatial and temporal patterns, while unnecessary genes are repressed. A large family of regulator proteins that have been demonstrated to be involved in various developmental processes by activation and repression of target genes is the homeodomain family of proteins. To date, the function of many of these homeoproteins has been elucidated in diverse species. However, the molecular mechanism underlying the function of these proteins has not been fully understood. In this study, the molecular mechanism of the function of a LIM-homeoprotein, Lim1, was examined. In addition to the homeodomain, Lim1 contains two LIM domains that are highly conserved among species. This high conservation along with data from in vitro studies on Xenopus Lim1 suggests that the LIM domains might be important for the function of Lim1 as a transcriptional regulator. Here, the functional importance of the LIM domains of Lim1 was determined by using a novel gene-targeting strategy in mouse embryonic stem (ES) cells. A cre-loxP system was used in conjunction with the unique genomic organization of Lim1 to obtain four types of mutant ES cell lines that would allow for the in vivo analysis of the function of both the LIM domains of Lim1 together and also singularly. These four mutant Lim1 alleles either contained base-pair changes at the LIM encoding exons that alters zinc-binding amino acids of the LIM domains or contained only exogenous loxP sequences in the first intron of Lim1, which serves as the control allele. These mutations in the LIM domains would presumably abolish the zinc-finger tertiary structure of the domain and thus render the domain non-functional. Mice carrying mutations at both the LIM domains of Lim1, L1L2, die around E10 without anterior head structures anterior to rhombomere 3, identical in phenotype to the Lim1 null mutants in spite of the presence of mutant Lim1 RNA. This result demonstrates that the integrity of both the LIM domains are essential for the function of Lim1. This is further supported by the phenotype of mice carrying mutation at only the second LIM domain of Lim1, L2. The L2 mice although still carrying one intact Lim1 LIM domain, also die in utero. The L2 mice die at varying times, from around E8 to E10 with anterior defects in addition to other axial defects which have yet to be fully characterized. The results of this study so far demonstrates that the integrity of both LIM domains are required for the function of Lim1. ^

Temporal and spatial regulation of cell division by the nucleoid in Escherichia coli

Selection of division sites and coordination of cytokinesis with other cell cycle events are critical for every organism to proliferate. In E. coli, the nucleoid is proposed to exclude division from the site of the chromosome (nucleoid occlusion model). We studied the effect of the nucleoid on timing and placement of cell division. An early cell division protein, FtsZ, was used to follow development of the division septum. FtsZ forms a ring structure (Z ring) at potential division sites. The dynamics of Z ring was visualized in live cells by fusing FtsZ with a green fluorescent protein (GFP). Emanating FtsZ-GFP polymers from the constricted septum or aggregates in daughter cells were also observed, probably representing the FtsZ depolymerization and immature FtsZ nucleation processes. We next examined the nucleoid occlusion model. Mutants carrying abnormally positioned chromosomes were employed. In chromosomal partition mutants, replicated chromosomes cannot segregate. The Z ring was excluded from midcell to the edge of the nucleoid. This negative effect of nucleoids was further confirmed in replication deficient dnaA mutants, in which only a single chromosome is present in the cell center. These results suggest that the nucleoid, replicating or not, inhibits division in the area where the chromosome occupies. In addition, increasing the level of FtsZ does not overcome nucleoid inhibition. Interestingly in anucleate cells produced by both mutants, the Z ring was localized in the central part of the cell, which indicates that the nucleoid is not required for FtsZ assembly. Relaxation of chromosomes by reducing the gyrase activity or disruption of protein translation/translocation did not abolish the division inhibition capacity of the nucleoid. However, preventing transcription did compromise the nucleoid occlusion effect, leading to formation of multiple FtsZ rings above the nucleoid. In summary, we demonstrate that nucleoids negatively regulate the timing and position of division by inhibiting FtsZ assembly at unselected sites. Relief of this inhibition at midcell is coincident with the completion of DNA replication. On the other hand, FtsZ assembly does not require the nucleoid. ^

Molecular regulatory mechanisms and embryonic tissue specification in sea urchin development

To understand how a eukaryote achieves differential transcription of genes in precise spatial patterns, the molecular details of tissue specific expression of the Strongylocentrotus purpuratus Spec2a gene were investigated by functional studies of the cis-regulatory components in the upstream enhancer. Regional activation of Spec2a in the aboral ectoderm is conferred by a combination of activators and repressors. The positive regulators include previously identified SpOtx and a trans-regulatory factor binding at the CCAAT site in the Spec2a enhancer. The nuclear protein binding to the CCAAT box was determined to be the heterotrimeric CCAAT binding factor (SpCBF). SpCBF also mediates general activation in the ectoderm. The negative regulators consist of an oral ectoderm repressor (OER), an endoderm repressor (ENR), and an S. Purpuratus goosecoid homologue (SpGsc). OER functions to prevent expression in the oral ectoderm, while ENR is required to repress endoderm expression. SpGsc antagonizes the SpOtx function by competing for binding at SpOtx target genes in oral ectoderm, where it functions as an active repressor. Thus, SpOtx and SpGsc perform collectively to establish and maintain the oral-aboral axis. Finally, purification of ENR and OER proteins from sea urchin blastula stage nuclear extracts was performed using site-specific DNA-affmity chromatography. ^

Behavioral Implications of Knockout for the Dyslexia-Risk Gene Dcdc2 in Mice

Several genetic linkage and epidemiological studies have provided strong evidence that DCDC2 is a candidate gene for developmental dyslexia, a disorder that impairs a person’s reading ability despite adequate intelligence, education, and socio-economic status. Studies investigating embryonic intra-ventricular RNA interference (RNAi) of Dcdc2, a rat homolog of the DCDC2 gene in humans, indicate disruptions in neuronal migration in the rat cortex during development. Interestingly, these anatomical anomalies are consistent with post mortem histological analysis of human dyslexic patients. Other rodent models of cortical developmental disruption have shown impairment in rapid auditory processing and learning maze tasks in affected subjects. The current study investigates the rapid auditory processing abilities of mice heterozygous for Dcdc2 (one functioning Dcdc2 allele) and mice with a homozygous knockout of Dcdc2 (no functioning Dcdc2 allele). It is important to note that this genetic model for behavioral assessment is still in the pilot stage. However, preliminary results suggest that mice with a genetic mutation of Dcdc2 have impaired rapid auditory processing, as well as non-spatial maze learning and memory ability, as compared to wildtypes. By genetically knocking out Dcdc2 in mice, behavioral features associated with Dcdc2 can be characterized, along with other neurological abnormalities that may arise due to the loss of the functioning gene.

Transcriptional and translational regulators of gene expression in germ cell development

Germ cell development is a highly coordinated process driven, in part, by regulatory mechanisms that control gene expression. Not only transcription, but also translation, is under regulatory control to direct proper germ cell development. In this dissertation, I have focused on two regulators of germ cell development. One is the homeobox protein RHOX10, which has the potential to be both a transcriptional and translational regulator in mouse male germ cell development. The other is the RNA-binding protein, Hermes, which functions as a translational regulator in Xenopus laevis female germ cell development. ^ Rhox10 is a member of reproductive homeobox gene X-(linked (Rhox) gene cluster, of which expression is developmentally regulated in developing mouse testes. To identify the cell types and developmental stages in which Rhox10 might function, I characterized its temporal and spatial expression pattern in mouse embryonic, neonatal, and adult tissues. Among other things, this analysis revealed that both the level and the subcellular localization of RHOX10 are regulated during germ cell development. To understand the role of Rhox10 in germ cell development, I generated transgenic mice expressing an artificial microRNA (miRNA) targeting Rhox10. While this artificial miRNA robustly downregulated RHOX10 protein expression in vitro, it did not significantly reduce RHOX10 expression in vivo. So I next elected to knockdown RHOX10 levels in spermatogonial stem cells (SSCs), which I found highly express both Rhox10 mRNA and RHOX10 protein. Using a recently developed in vitro culture system for SSCs combined with a short-hairpin RNA (shRNA) approach, I strongly depleted RHOX10 expression in SSCs. These RHOX10-depleted cells exhibited a defect in the ability to form stem cell clusters in vitro. Expression profiling analysis revealed many genes regulated by Rhox10, including many meiotic genes, which could be downstream of Rhox10 in a molecular pathway that controls SSC differentiation. ^ RNA recognition motif (RRM) containing protein, Hermes is localized in germ plasm, where dormant mRNAs are also located, of Xenopus oocytes, which implicates its role in translational regulator. To understand the function of Hermes in oocyte meiosis, I used a morpholino oligonucleotide (MO) based knockdown approach. Microinjection of Hermes MO into fully grown oocytes, which are arrested in meiotic prophase, caused acceleration of oocytes reentry into meiosis (i.e., maturation) upon progesterone induction. Using a candidate approach, I identified at least three targets of Hermes: Ringo/Spy, Xcat2, and Mos. Ringo/Spy and Mos are known to have functions in oocyte maturation, while Ringo/Spy, Xcat2 mRNA are localized in the germ plasm of oocytes, which drives germ cell specification after fertilization. This led me to propose that Hermes functions in both oocyte maturation and germ cell development through its ability to regulate 3 crucial target mRNAs. ^

Epidemiology of allergic gastroenteritis in socio-culture perspective of rural Egypt

Diarrhea is a major public health problem in developing countries among infants and young children. Not all episodes of diarrhea are confirmed as infectious, suggesting alternate mechanisms. One such is immunoglobulin E (IgE) mediated or allergic diarrhea that can be seen in food allergy. In order to determine the relation between allergic gastroenteritis and feeding practice, a cohort of 152 infants were followed from birth to one year age in a rural community of Egypt between October, 1987 to April, 1988 were analyzed. In multivariate analysis of the data, statistically conclusive higher risk had been observed with presence of factors, like consumption of milk pudding (RR = 7.4, CI = 1.5-36.2 and p = 0.01), infant's age 3-6 months (RR = 7.7, CI = 1.3-45.9 and p = 0.02), infants whose mothers were vaccinated antenatally (RR = 3.1, CI = 1.3-7.0 and p = 1.3-7.0, p = 0.0) and wet-nursed infants (RR = 2.7, CI = 1.1-6.5 and p = 0.02). In contrast, infants who were completely breast-fed (RR = 0.13, CI = 0.02-0.6 and p = 0.01), and infants family owning a television set (RR = 0.29, CI = 0.1-0.6 and p = 0.0) were less likely to develop allergic gastroenteritis. The role of IgE on development of persistent diarrhea was also examined in a nested case-control design. Multivariate analysis revealed a significant association between detection of fecal IgE and development of persistent diarrhea compared to acute diarrhea (OR = 3.32, CI = 1.0-10.9 and p = 0.04) and health or non diarrhea (OR = 4.8, CI = 1.07-21.7 and p = 0.03) controls. ^

THE POTENTIAL EFFECTS OF A COMMUNITY DEVELOPMENT PROGRAM ON DEMOGRAPHIC VARIABLES IN HIMALAYAN INDIAN VILLAGES

A community development program operating in the mountains of North India was studied to assess its potential effects on mortality, fertility and migration patterns in the community which it served. The development program operated in Jaunpur Block, Tehri-Garhwal District, Uttar Pradesh State. Two comparable villages in the district were studied. The development program had been working in one for two years, and the other was completely untouched by the program.^ Since not enough time had elapsed since the beginning of the development program's work for any effects on demographic patterns to be visable in Jaunpur Block, this study looked to attitudes of village residents as indicators of future demographic trends. Existing demographic patterns and their interrelationship with socio-religious customs were examined in the test village. A questionnaire was then administered to ascertain attitudinal differences between the residents of the test village and the control village.^ The primary work of the community development program was to train women as village health workers. The results of the attitudinal comparison of the residents of the two villages showed a marked difference in attitudes relating to the position of women in society. The data showed a higher esteem for women in the test village than in the control village, and it is argued that this difference may be attributable to the work of the development program.^ Predicting future demographic trends in Jaunpur Block on the basis of the observed difference in villagers' attitudes toward the status of women is speculatory. Jaunpur Block appears to be in the demographic stage of pre-transition, maintaining relatively high rates of both mortality and fertility. Based on demographic transition theory the next significant change in demographic patterns in Jaunpur is predicted to be a decline in mortality, and an increase in the status of women is unrelated to this prediction.^ The community development program which was studied terminated unexpectedly during the time of this study. A case study of the program's final months is presented, and speculation on the future course of demographic trends in Jaunpur Block is related to the possible alternatives for future development in the area. ^

Territorial approaches for rural development in Latin America : a case study in Chile

Una reciente transición en el campo del desarrollo rural es el movimiento desde un enfoque reducido del sector agrícola hasta uno que adopta una visión territorial más amplia. Este pasaje intenta interpretar las interacciones entre los mundos urbano y rural de una manera más comprensiva. Esta perspectiva teórica relativamente nueva interesa particularmente a los académicos y los políticos en los países latinoamericanos donde, a partir de la mitad de los años noventa, el concepto de una nueva ruralidad se ha visto como la fuente de un nuevo enfoque para el desarrollo rural. Por lo tanto, el propósito teórico de esta investigación es explicitar los indicadores analíticos del nuevo enfoque de la ruralidad en América Latina e identificar las diferencias entre los acercamientos sectoriales y territoriales, considerando los aspectos socio-económicos, institucionales y medioambientales involucrados. La transición del enfoque sectorial a uno territorial significa también, desde un punto de vista operativo, el reconocimiento de la existencia de áreas homogéneas a partir de las cuales pueden proponerse estrategias de desarrollo rural. El propósito operativo de esta investigación consiste en proponer una metodología para identificar estas áreas con una aplicación a la Región del Maule en Chile. La conclusión subraya algunos elementos críticos que se deben considerar en la definición de estrategias del desarrollo rural territorial.

Intervención judicial y contexto socio cultural : la puesta en marcha de un trabajo interdisciplinario "in situ"

Partiendo de una noción de acceso a la justicia, que no se restringe únicamente al acceso formal de los ciudadanos al sistema judicial y al adecuado ejercicio de derechos ante los Tribunales de Justicia, sino que también abarca la Prevención y Promoción de Derechos, la Solución Colaborativa de Conflictos, la Revisión y Propuesta de las Actuaciones Públicas mediante Acciones de Interés Público y Propuestas Legislativas; se implementaron, desde la Institución Judicial (Juzgado de Familia de Tupungato), acciones en el marco de buenas prácticas que se sustentas en tres ejes: Construcción de Ciudadanía, Desarrollo Humano Sustentable y Redes Sociales. Las mismas tienden a fortalecer las conexiones entre estructuras formales e informales de la comunidad, a fin de proveer efectivamente el Acceso a la Justicia a grupos que de otra manera podrían estar excluidos de ella y a la vez favorecer el empoderamiento de los grupos vulnerables en la búsqueda de soluciones a situaciones injustas en el ámbito de los procesos tramitan por ante los Juzgados de Familia. En dicho marco, el Juzgado referido puso en marcha un Juzgado Móvil que plantea una metodología de abordaje interdisciplinario, donde la intervención del Trabajador Social resulta relevante.

Paraná y su región : Criterios básicos para proyectar políticas de gestión metropolitana

El propósito del presente trabajo es reconocer, cómo a partir de las tensiones globales y locales, de carácter socio - espacial e imbricadas en el proceso de metropolización que acusa el ámbito expandido de la ciudad de Paraná, es factible identificar y analizar los criterios básicos para proyectar una inédita gestión metropolitana dentro del espacio regional que constituyen tanto el ejido de la capital de la Provincia de Entre Ríos como el de sus tres municipios conurbados. En consecuencia y a tal fin, se intenta aquí establecer los nuevos desafíos incorporados a la gestión urbano-ambiental, tanto provincial como municipal, dentro de los que se platea articular la intervención estatal y la participación comunitaria, en el marco de un proceso de ordenamiento territorial del ámbito metropolizado en esas cuatro jurisdicciones en las que hoy habitan más de trescientos mil comprovincianos. Se trata, por tanto, de un proyecto estratégico que institucionalmente persiga la posibilidad de articular en simultáneo cuatro criterios políticos considerados aquí básicos para la gestión democrática del territorio metropolitano: la gobernabilidad, la competitividad, la sustentabilidad y la inclusión social. Criterios que, dentro de esa inteligencia, guiarán el análisis desarrollado sobre propuestas de actuación, jurídico-normativas y de gestión para abordar la compleja problemática del espacio urbano-regional. Es en tal contexto entonces, y dentro de esos principios primordiales para la intervención urbano-territorial, en el que se estima posible plantear, desde el ámbito institucional del Gobierno de la Provincia y de los gobiernos municipales, un acotado y preciso conjunto de políticas sectoriales básicas de ordenamiento que habiliten al despliegue de estrategias comunes y de consenso social posible, destinadas a transformar las críticas condiciones por las que atraviesa la conurbación en su conjunto, sin por eso vulnerar la autonomía de la jurisdicciones municipales incluidas en el espacio geográfico. Concluyendo, en el presente trabajo se analizan e identifican en forma iniciática, los criterios esenciales para el logro de los objetivos territoriales y las metas institucionales que dentro de la gestión metropolitana, puedan asumir el Estado Provincial y las jurisdicciones municipales, en tanto dispositivos gubernamentales destinados a que legal y orgánicamente, sean orientadas las políticas que tengan el propósito de afrontar tanto los procesos territoriales distorsivos como los déficit, las asimetrías y las carencias socio-ambientales que acusa la población del Gran Paraná

Estudio socio-territorial de la actividad hortícola en el partido de La Plata 1998-2002

El presente trabajo se propone identificar y caracterizar las unidades de análisis espacio-territorial (fracciones censales) de la actividad primaria intensiva, específicamente hortícola, y examinar el peso relativo de la actividad del Partido de La Plata en el contexto provincial y nacional. Se analizan las variables sobre mano de obra, superficie total, superficie cultivada a campo y bajo cubierta, régimen de tenencia de la tierra y componentes tecnológicos. Se examinan y comparan los censos hortícola de la Provincia de Buenos Aires 1998 y Nacional Agropecuario 2002 (CNA02). Los resultados son presentados en tablas, gráficos y mapas temáticos procesados en SIG ArcView.

Vocational guidance and development of competences

The present "post modern" socio-cultural modalities and the restrictions of the economic globalization lead us to reflect about the configuration of the transformations in the Vocational Guidance, committed to the concepts of "freedom", "epistemological knowledge", "competences of the subject and new roles of the school. This first exploratory incursion if the research has the purpose of retrieving the concept of freedom from the existential philosophers Heidegger and Sartre and of introducing the subject of "competences" from the social theory of Habermas. The aim is to establish new bonds between the Vocational Guidance and the above-mentioned philosophical lineaments: the freedom of the subjects and the possibility of development of those "competences" that allow to establish social, ethical and epistemological interrelations in the sphere of the Vocational Guidance, that promote a greater solidarity facing the "era of emptiness" of the post-modernity supported by Lipovestky.