Gene Regulatory Compatibility in Bacteria: Consequences for Synthetic Biology and Evolution

Mechanistic understanding of gene regulation is crucial for rational engineering of new genetic systems through synthetic biology. Genetic engineering efforts in new organisms are often hampered by a lack of knowledge about how regulatory components function in new host contexts. This dissertation focuses on efforts to overcome these challenges through the development of generalizable experimental methods for studying the behavior of DNA regulatory sequences in diverse species at large-scale. Chapter 2 describes experimental approaches for quantitatively assessing the functions of thousands of diverse natural regulatory sequences through a combination of metagenomic mining, high-throughput DNA synthesis and deep sequencing. By employing these methods in three distinct bacterial species, we revealed striking functional differences in gene regulatory capacity. We identified regulatory sequences with activity levels with activity levels spanning several orders of magnitude, which will aid in efforts to engineer diverse bacterial species. We also demonstrate functional species-selective gene circuits with programmable host behaviors that may be useful for microbial community engineering. In Chapter 3 we provide evidence for the evolution of altered stringency in σ70-mediated transcriptional activation based on patterns of initiation and activity from promoters of diverse compositions. We show that the contrast in GC content between a regulatory element and the host genome dictates both the likelihood and the magnitude of expression. We also discuss the potential implications of this proposed mechanism on horizontal gene transfer. The next two chapters focus on efforts aimed at extending the high-throughput methods described in earlier chapters to new organisms. Chapter 4 presents an in vitro approach for multiplexed gene expression profiling. Through the development and use of cell-free expression systems made from diverse bacteria, it was possible to rapidly acquire thousands of transcriptional measurements in small volume reactions, enabling functional comparisons of regulatory sequence function across multiple species. In Chapter 5 we characterize the restriction-modification system repertoires of several commensal bacterial species. We also describe ongoing efforts to develop methods for bypassing these systems in order to increase transformation efficiencies in species that are difficult or impossible to transform using current approaches

System Engineering Applied to Fuenmayor Karst Aquifer (San Julián de Banzo, Huesca) and Collins Glacier (King George Island, Antarctica)

La ingeniería de sistemas, definida generalmente como arte y ciencia de crear soluciones integrales a problemas complejos, se aplica en el presente documento a dos sistemas naturales, a saber, un sistema acuífero kárstico y un sistema glaciar, desde una perspectiva hidrológica. Las técnicas de identificación, desarrolladas típicamente en ingeniería para representar sistemas artificiales por medio de modelos lineales y no lineales, pueden aplicarse en el estudio de los sistemas naturales donde se producen fenómenos de acoplamiento entre el clima y la hidrosfera. Los métodos evolucionan para afrontar nuevos campos de identificación donde se requieren estrategias para encontrar el modelo idóneo adaptado a las peculiaridades del sistema. En este sentido, se han considerado especialmente las herramientas basadas en la transformada wavelet utilizadas en la preparación de series temporales, suavizado de señales, análisis espectral, correlación cruzada y predicción, entre otros. Bajo este enfoque, una aplicación a mencionar entre las tratadas en esta tesis, es la determinación analítica del núcleo efectivo estacional (SEC) a través del estudio de la coherencia wavelet entre temperatura del aire y la descarga del glaciar, que establece un conjunto de períodos de muestreo aceptablemente coherentes, a partir del cual se crearán los modelos del sistema glacial. El estudio está dirigido específicamente a estimar la influencia de la precipitación sobre la descarga del acuífero kárstico de Fuenmayor, en San Julián de Banzo, Huesca, España. De la misma manera, se ocupa de las consecuencias de la temperatura del aire en la fusión del hielo glaciar, que se manifiesta en la corriente de drenaje del glaciar Collins, isla King George, Antártida. En el proceso de identificación paramétrica y no paramétrica se buscan los modelos que mejor representen la dinámica interna del sistema. Eso conduce a pruebas iterativas, donde se van creando modelos que se verifican sistemáticamente con los datos reales del muestreo, de acuerdo a un criterio de eficiencia dado. La solución mejor valorada según los resultados obtenidos en los casos tratados apuntan a estructuras de modelos en bloques. Esta tesis significa una exposición formal de la metodología de identificación de sistemas propios de la ingeniería en el contexto de los sistemas naturales, que mejoran los resultados obtenidos en muchos casos de la hidrología kárstica que comúnmente usaban métodos ad hoc ocasionales de carácter estadístico; así mismo, los enfoques propuestos en los casos de glaciología con el análisis wavelet y los modelos orientados a datos raramente considerados en la literatura, revelan información esencial ante la imposibilidad de precisar la totalidad de la física que rige el sistema. Notables resultados se derivan en la caracterización de la respuesta del manantial de Fuenmayor y su correlación con la precipitación, desde la perspectiva de un sistema lineal, que se complementa con los métodos de identificación basados en técnicas no lineales. Así mismo, la implementación del modelo para el glaciar Collins, obtenido también mediante métodos de identificación de caja negra, puede revelar una inestabilidad de los límites de los periodos activos de la descarga, y consecuentemente la variabilidad en la tendencia actual en el cambio climático global

Human factors aspects of control room design: Guidelines and annotated bibliography

A human factors analysis of the workstation design for the Earth Radiation Budget Satellite mission operation room is discussed. The relevance of anthropometry, design rules, environmental design goals, and the social-psychological environment are discussed

University of Maine Undergraduate Catalog, 2020-2021, part 2

The second part (of two) of the undergraduate catalog for the 2020-2021 academic year includes an introduction, the academic calendars, general information about the university, and sections on attending, facilities and centers, and colleges and academic programs including the Colleges of Business, Public Policy and Health, Education and Development, Engineering, Liberal Arts and Sciences, and Natural Sciences, Forestry and Agriculture

1971-1972 CATALOG ISSUE- BULLETIN

Course catalog for 1971-1972https://digitalrepository.unm.edu/course_catalogs/1079/thumbnail.jp

Optimal Sensing and Actuation Policies for Networked Mobile Agents in a Class of Cyber-Physical Systems

The main purpose of this dissertation is to define and solve problems on optimal sensing and actuating policies in Cyber-Physical Systems (CPSs). Cyber-physical system is a term that was introduced recently to define the increasing complexity of the interactions between computational hardwares and their physical environments. The problem of designing the ``cyber\u27\u27 part may not be trivial but can be solved from scratch. However, the ``physical\u27\u27 part, usually a natural physical process, is inherently given and has to be identified in order to propose an appropriate ``cyber\u27\u27 part to be adopted. Therefore, one of the first steps in designing a CPS is to identify its ``physical\u27\u27 part. The ``physical\u27\u27 part can belong to a large array of system classes. Among the possible candidates, we focus our interest on Distributed Parameter Systems (DPSs) whose dynamics can be modeled by Partial Differential Equations (PDE). DPSs are by nature very challenging to observe as their states are distributed throughout the spatial domain of interest. Therefore, systematic approaches have to be developed to obtain the optimal locations of sensors to optimally estimate the parameters of a given DPS. In this dissertation, we first review the recent methods from the literature as the foundations of our contributions. Then, we define new research problems within the above optimal parameter estimation framework. Two different yet important problems considered are the optimal mobile sensor trajectory planning and the accuracy effects and allocation of heterogeneous sensors. Under the remote sensing setting, we are able to determine the optimal trajectories of remote sensors. The problem of optimal robust estimation is then introduced and solved using an interlaced ``online\u27\u27 or ``real-time\u27\u27 scheme. Actuation policies are introduced into the framework to improve the estimation by providing the best stimulation of the DPS for optimal parameter identification, where trajectories of both sensors and actuators are optimized simultaneously. We also introduce a new methodology to solving fractional-order optimal control problems, with which we demonstrate that we can solve optimal sensing policy problems when sensors move in complex media, displaying fractional dynamics. We consider and solve the problem of optimal scale reconciliation using satellite imagery, ground measurements, and Unmanned Aerial Vehicles (UAV)-based personal remote sensing. Finally, to provide the reader with all the necessary background, the appendices contain important concepts and theorems from the literature as well as the Matlab codes used to numerically solve some of the described problems

Pathways to Water Sector Decarbonization, Carbon Capture and Utilization

The water sector is in the middle of a paradigm shift from focusing on treatment and meeting discharge permit limits to integrated operation that also enables a circular water economy via water reuse, resource recovery, and system level planning and operation. While the sector has gone through different stages of such revolution, from improving energy efficiency to recovering renewable energy and resources, when it comes to the next step of achieving carbon neutrality or negative emission, it falls behind other infrastructure sectors such as energy and transportation. The water sector carries tremendous potential to decarbonize, from technological advancements, to operational optimization, to policy and behavioural changes. This book aims to fill an important gap for different stakeholders to gain knowledge and skills in this area and equip the water community to further decarbonize the industry and build a carbon-free society and economy. The book goes beyond technology overviews, rather it aims to provide a system level blueprint for decarbonization. It can be a reference book and textbook for graduate students, researchers, practitioners, consultants and policy makers, and it will provide practical guidance for stakeholders to analyse and implement decarbonization measures in their professions