Doctor of Philosophy

dissertationFollowing fertilization, mammalian embryos undergo a series of cleavage divisions during which embryonic cells are reprogrammed from a differentiated germ cell state to an undifferentiated embryonic state. Blastomeres of the 2-cell, 4-cell, and 8-cell (cleavage) embryo are ‘totipotent’, meaning they maintain the capacity to develop into all cell lineages of a developing embryo. This unique developmental potential is progressively lost in humans and other placental mammals as cells become restricted to an embryonic (inner cell mass, ICM) or extraembryonic (trophectoderm) lineage. Unlike pluripotent stem cells which can be derived from the ICM and have been extensively characterized, little is known about the totipotent cells of the cleavage stage embryo. What factors coordinate this dramatic reprogramming event and confer this unique developmental potential? Here, using RNA-sequencing, I profiled human cleavage stage embryos and identified a transcriptional program that specifically coincides with totipotency acquisition and loss. Remarkably, this totipotency transcriptional program is directly activated by DUX4 which is transiently and specifically expressed in 4-cell stage human embryos. The protein coding capacity of DUX4 has been conserved for over 100 million years; however, its evolutionary function/purpose has remained a complete mystery until now. By extending this work into mouse, I reveal a conserved functional role for DUX4-family genes in facilitating the mammalian embryonic reprogramming process through which totipotency is established

Clúster de Servicios Bancarios en el Ecuador Metodología de análisis de un Clúster o Red de Valor para el sector de Servicios Bancarios en el Ecuador

“Cluster of The Banking Services in Ecuador” is a project which studies the current situation of the Ecuadorian Financing System: how it is conformed, who its regulators are, which entities compose it, and which its support institutions are. Basically, what is intended to accomplish with this project is to understand in a better way how the national banking system works. Moreover, to make an analysis of how a business cluster could work in the country so as to reach total integration of every one of its components in order to create real competitiveness among the members of the system. The project begins with the study of the general concepts of a business cluster, a sector analysis and a supply analysis. Subsequently, a Porter five forces analysis is conducted by applying it to this industry. With this, one can understand which the factors that affect the sector are and establish the possible components of the cluster of the banking services. This study goes on to define the Porter diamond, which derives from the analysis undertaken in previous chapters. It finalizes with the definition of a possible strategy to achieve competitiveness in the sector.Este proyecto denominado “Clúster de Servicios Bancarios en el Ecuador” es el estudio de la situación actual del Sistema Financiero Ecuatoriano, ámbito en el cual se desarrolla el Sector de los Servicios Financieros en el País, cómo está conformado este último, quiénes son sus entes reguladores, las entidades que lo integran, y las instituciones de soporte. Básicamente lo que se ha querido lograr con este proyecto, es entender mejor el funcionamiento del sistema bancario nacional y realizar un análisis de cómo podría funcionar un clúster en el país de tal manera que se llegue a la integración total de todos los componentes del mismo para en lo posterior crear una real competitividad entre los miembros del sistema. El proyecto inicia con el estudio de los conceptos generales del clúster, el análisis del sector y de la oferta que existe actualmente. Posteriormente, realizamos el análisis de las cinco fuerzas de Porter aplicado a esta industria. Con este se puede entender cuáles son los factores que más afectan al sector, y luego se establecen los posibles componentes del clúster de servicios bancarios. El presente estudio continúa definiendo el diamante de Porter, el mismo que se deriva del análisis realizado en los capítulos anteriores para finalizar con la definición de una posible estrategia para poder alcanzar la competitividad en el sector

The Mexican Blindcat Project: new discoveries and future efforts

content from an oral presentation March, 2017 at the 5th Astyanax International Meeting (http://www.stowers.org/sites/all/themes/aimfc/aim2017_prog.pdf)The endangered Mexican blindcat (Prietella phreatophila, Carranza 1954) is one of only four stygobitic ictalurid catfish in North America. Members of two monotypic genera (Satan eurystomus and Trogloglanis pattersoni) are known from the Edwards Aquifer in Texas and, until recently, Prietella (represented by P. lundbergi and P. phreatophila) was only known to occur in Mexico (northern Coahuila to southern Tamaulipas). The recent discovery of P. phreatophila in a cave on the Amistad National Recreation Area in Val Verde County, Texas is the result of decades of sporadic effort on both sides of the US/Mexican border and has stimulated a renewed effort to investigate the distribution, ecology, evolutionary history, and conservation status of this species. Collaborative efforts among The San Antonio Zoo, The University of Texas at Austin, Zara Environmental and The National Park Service are currently focused on habitat surveys in Texas as well as captive husbandry and propagation. Future efforts will include collaborators from the Comisión Nacional de Áreas Naturales Protegidas, Área de Protección de Recursos Naturales Sabinas, and the Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, La Paz to conduct expanded fieldwork in Mexico, hydrogeologic studies, and surveys using environmental DNA.San Antonio Zoo; University of Texas at Austin, Biodiversity Center, College of Natural Sciences; U.S. National Park ServiceIntegrative Biolog

Conformational Behavior of Symmetrical and Unsymmetrical Mono(Alkynylpeptide)-Tungsten Complexes [post-print]

A series of N-protected amino acid alkynylesters were prepared by reaction of the amino acid carboxylate group with either propargyl alcohol (to yield the asymmetric esters 2a–c) or with 1, 4-but-2-yne diol (to yield the symmetric esters 3a–d). The alkynylesters were reacted with W(CO)3(dmtc)2 to yield monoalkyne complexes having the general formula W(CO)(dmtc)2(alkynyl ester). The monoalkyne complexes 6a–f were unstable in the presence of oxygen and had to be kept under an inert atmosphere. Analysis of the NMR spectra of the monoalkyne complexes showed that two diastereomers were formed in the synthesis, and that there was rapid rotation of the alkyne about the tungsten center at 23 °C and above with both diastereomers. At lower temperatures alkyne rotation is significantly slowed. Symmetric alkynylesters of a dipeptide (4) and tripeptide (5) were also prepared and reacted with W(CO)3(dmtc)2 to yield monoalkyne complexes. The resulting complexes (6g and 6h) also formed two diastereomers and displayed rapid rotation of the alkyne about the tungsten center at 23 °C and above, and slow rotation at lower temperatures. The amide NH protons in 6g and 6h were probed by DMSO titration to see if they were involved in intramolecular hydrogen bonds; they were not, which indicates that the peptide portions of 6g and 6h adopt an extended conformation in solution. Two peptides linked together via ester bonds to 1,4-dihydroxy-2-butyne coordinate to a tungsten center and adopt an extended conformation

Exploring Agricultural Production Systems and Their Fundamental Components with System Dynamics Modelling

Agricultural production in the United States is undergoing marked changes due to rapid shifts in consumer demands, input costs, and concerns for food safety and environmental impact. Agricultural production systems are comprised of multidimensional components and drivers that interact in complex ways to influence production sustainability. In a mixed-methods approach, we combine qualitative and quantitative data to develop and simulate a system dynamics model that explores the systemic interaction of these drivers on the economic, environmental and social sustainability of agricultural production. We then use this model to evaluate the role of each driver in determining the differences in sustainability between three distinct production systems: crops only, livestock only, and an integrated crops and livestock system. The result from these modelling efforts found that the greatest potential for sustainability existed with the crops only production system. While this study presents a stand-alone contribution to sector knowledge and practice, it encourages future research in this sector that employs similar systems-based methods to enable more sustainable practices and policies within agricultural production

The Visually Related Posterior Pretectal Nucleus in the Non-Percomorph Teleost Osteoglossum bicirrhosum Projects to the Hypothalamus

This study was done to elucidate the ancestral (plesiomorphic) condition for visual pathways to the hypothalamus in teleost fishes. Three patterns of pretectal organization can be discerned morphologically and histochemically in teleosts. Their taxonomic distribution suggests that the intermediately complex pattern (seen in most teleost groups) is ancestral to both the elaborate pattern (seen in percomorphs) and the simple pattern (seen in cyprinids). The pretectal nuclei involved can be demonstrated with acetylcholinesterase histochemistry selectively and reliably in different species of teleosts, suggesting that the same-named nuclei are homologous in representatives of the three different patterns. Whereas there are visual pathways to the hypothalamus in both the elaborate (percomorph) and the simple (cyprinid) patterns, different pretectal and hypothalamic nuclei are involved. Thus visual hypothalamic pathways in these two patterns would not appear to be homologous. In this study, circuitry within the third, i.e., the intermediately complex, pattern is investigated. It is demonstrated that visual pathways project via the pretectum to the hypothalamus in Osteoglossum bicirrhosum and that they are very similar to the visual pathways in the elaborate pattern. This suggests that the circuitry in the intermediately complex pattern, as represented by Osteoglossum, is plesiomorphic (evolutionarily primitive) and the circuitry in both the simple pattern (seen in cyprinids) and the elaborate pattern (seen in percomorphs) is apomorphic (evolutionarily derived) for teleosts

Irregular S-cone mosaics in felid retinas: spatial interaction with axonless horizontal revealed by cross-correlation

In most mammals short-wavelength-sensitive (S) cones are arranged in irregular patterns with widely variable intercell distances. Consequently, mosaics of connected interneurons either may show some type of correlation to photoreceptor placement or may establish an independent lattice with compensatory dendritic organization. Since axonless horizontal cells (A-HC’s) are supposed to direct all dendrites to overlying cones, we studied their spatial interaction with chromatic cone subclasses. In the cheetah, the bobcat, and the leopard, anti-S-opsin antibodies have consistently colabeled the A-HC’s in addition to the S cones. We investigated the interaction between the two cell mosaics, using autocorrelation and cross-correlation procedures, including a Voronoi-based density probe. Comparisons with simulations of random mosaics show significantly lower densities of S cones above the cell bodies and primary dendrites of A-HC’s. The pattern results in different long-wavelength-sensitive-L- and S-cone ratios in the central versus the peripheral zones of A-HC dendritic fields. The existence of a related pattern at the synaptic level and its potential significance for color processing may be investigated in further studies

Modeling conflict : research methods, quantitative modeling, and lessons learned.

This study investigates the factors that lead countries into conflict. Specifically, political, social and economic factors may offer insight as to how prone a country (or set of countries) may be for inter-country or intra-country conflict. Largely methodological in scope, this study examines the literature for quantitative models that address or attempt to model conflict both in the past, and for future insight. The analysis concentrates specifically on the system dynamics paradigm, not the political science mainstream approaches of econometrics and game theory. The application of this paradigm builds upon the most sophisticated attempt at modeling conflict as a result of system level interactions. This study presents the modeling efforts built on limited data and working literature paradigms, and recommendations for future attempts at modeling conflict

The advantages of information management through building information modelling

This article was published in the journal, Construction Management [© Taylor & Francis] and the definitive version is available at: http://dx.doi.org/10.1080/01446193.2013.777754As building information modelling (BIM) is positioned by governments and construction professionals as a solution to the problems in the construction industry, research is needed into the benefits BIM actually confers. The focus here is on the effectiveness of BIM as a medium for communicating information within a construction team. A case study of an offsite precast concrete fabrication facility was conducted. At the time of the study, the facility was supplying precast units for four public sector projects, and using four information management systems: e-mail, a construction project extranet tool, an Enterprise Resource Planning system and a new BIM-based system. The flow of information through the four media was measured and visualized as the projects progressed. This quantitative measurement of information flow was combined with qualitative data from interviews with facility staff. It was found that the introduction of the BIM-based system diverted information flow through the building model and away from the extranet system. The use of e-mail was largely unaffected. BIM allowed considerably more accurate, on-time and appropriate exchange of information. It is concluded it is possible to quantify some of the benefits of BIM to information management. This research paves the way for future research into the management of more construction project information linked more closely to building models

Intermittent shading can moderate coral bleaching on shallow reefs

The health of coral reefs is declining from the effects of human activity and climate change. Mass coral bleaching is often triggered by elevated water temperature and excessive solar irradiance. Shading can reduce coral bleaching risk. Shading-based management interventions, such as whole-of-reef marine fogging, have been proposed as a conservation tool for periods when coral undergoes excessive thermal stress. This study examined the effect of intermittent shade (30% for 0, 4, or 24 h) on two coral species, Duncanopsammia axifuga and Turbinaria reniformis, held at either 26.4°C or 32.4°C for 18 days. Coral fragments were assessed for bleaching (relative mean intensity of grey, chlorophyll a, and symbiont density), photochemistry (PAM fluorometry), and antioxidant biomarkers (SOD and CAT). Shading responses were species-specific, with T. reniformis more responsive to shading than D. axifuga. Thirty per cent shading delayed bleaching up to three-degree heat weeks (DHW), and 24 h shade was more protective than 4 h shade. Shading suppressed catalase activity in T. reniformis. Overall, our results suggest that intermittently shading corals for 4 h can moderate light stress and slow bleaching in some corals and could improve the efficiency of active solar radiation management in marine ecosystems