Many human genes are associated with dispersed arrays of transcriptional enhancers that regulate their expression in time and space. Studies in invertebrate model systems have suggested that these elements function as discrete and independent regulatory units, but the in vivo combinatorial properties of vertebrate enhancers remain poorly understood. To explore the modularity and regulatory autonomy of human developmental enhancers, we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules. In all of the six different combinations of elements tested, the reporter gene activity patterns were additive without signs of interference between the individual modules, indicating that regulatory specificity was maintained despite the presence of closely-positioned heterologous enhancers. Even in cases where two elements drove expression in close anatomical proximity, such as within neighboring subregions of the developing limb bud, the compound patterns did not show signs of cross-inhibition between individual elements or novel expression sites. These data indicate that human developmental enhancers are highly modular and functionally autonomous and suggest that genomic enhancer shuffling may have contributed to the evolution of complex gene expression patterns in vertebrates
My interest in the patterns of nature and culture has led me on a long journey through studies of math, sciences, and religions culminating in my current studies in art. Continuing my inquiry into processes of human perception and conception of time. My intention was to incorporate the "process" aspect of the printmaking medium into the final work by creating hybrid works that would take the "print" out of its traditional two-dimensional form. Finally, I planned to utilize the "multiple" aspect of printmaking to address ideas of patterns and evolution.
Laboratory experiments provide a wealth of information related to mechanics of fracture initiation, fracture propagation processes, factors influencing fault strength, and spatio-temporal evolution of fracture properties. Much of the existing literature reports on laboratory studies involving a coupling of thermal, hydraulic, mechanical, and/or chemical processes. As these processes operate within subsurface environments exploited for their energy resource, laboratory results provide insights into factors influencing the mechanical and hydraulic properties of geothermal systems. I report on laboratory observations of strength and fluid transport properties during deformation of simulated faults. The results show systematic trends that vary with stress state, deformation rate, thermal conditions, fluid content, and rock composition. When related to geophysical and geologic measurements obtained from engineered geothermal systems (e.g. microseismicity, wellbore studies, tracer analysis), laboratory results provide a means by which the evolving thermal reservoir can be interpreted in terms of physico-chemical processes. For example, estimates of energy release and microearthquake locations from seismic moment tensor analysis can be related to strength variations observed from friction experiments. Such correlations between laboratory and field data allow for better interpretations about the evolving mechanical and fluid transport properties in the geothermal reservoir – ultimately leading to improvements in managing the resource.
A field facility located in Bozeman, Montana provides the opportunity to test methods to detect, locate, and quantify potential CO2 leakage from geologic storage sites. From 9 July to 7 August 2008, 0.3 t CO2 d{sup -1} were injected from a 100-m long, {approx}2.5 m deep horizontal well. Repeated measurements of soil CO2 fluxes on a grid characterized the spatio-temporal evolution of the surface leakage signal and quantified the surface leakage rate. Infrared CO2 concentration sensors installed in the soil at 30 cm depth at 0 to 10 m from the well and at 4 cm above the ground at 0 and 5 m from the well recorded surface breakthrough of CO2 leakage and migration of CO2 leakage through the soil. Temporal variations in CO2 concentrations were correlated with atmospheric and soil temperature, wind speed, atmospheric pressure, rainfall, and CO2 injection rate.
We present and discuss five candidate exoplanetary systems identified with the Kepler spacecraft. These five systems show transits from multiple exoplanet candidates. Should these objects prove to be planetary in nature, then these five systems open new opportunities for the field of exoplanets and provide new insights into the formation and dynamical evolution of planetary systems. We discuss the methods used to identify multiple transiting objects from the Kepler photometry as well as the false-positive rejection methods that have been applied to these data. One system shows transits from three distinct objects while the remaining four systems show transits from two objects. Three systems have planet candidates that are near mean motion commensurabilities - two near 2:1 and one just outside 5:2. We discuss the implications that multitransiting systems have on the distribution of orbital inclinations in planetary systems, and hence their dynamical histories; as well as their likely masses and chemical compositions. A Monte Carlo study indicates that, with additional data, most of these systems should exhibit detectable transit timing variations (TTV) due to gravitational interactions - though none are apparent in these data. We also discuss new challenges that arise in TTV analyses due to the presence of more than two planets in a system.
Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~;;50 years) have resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying ?- and ?-proteobacterial populations. The resulting community is over-abundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could be a key mechanism in rapidly responding and adapting to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.
The 4th International Plant Biomechanics Conference facilitated an interdisciplinary exchange between scientists, engineers, and educators addressing the major questions encountered in the field of Plant Biomechanics. Subjects covered by the conference include: Evolution; Ecology; Mechanoreception; Cell Walls; Genetic Modification; Applied Biomechanics of Whole Plants, Plant Products, Fibers & Composites; Fluid Dynamics; Wood & Trees; Fracture Mechanics; Xylem Pressure & Water Transport; Modeling; and Introducing Plant Biomechanics in Secondary School Education.
Horizontal gene transfer enables acquisition and dissemination of novel traits including antibiotic resistance and virulence among bacteria. Frequently such traits are gained through the acquisition of clusters of functionally related genes, often referred to as genomic islands (GIs). Quantifying horizontal flow of GIs and assessing their contributions to the emergence and evolution of novel metabolic traits in bacterial organisms are central to understanding the evolution of bacteria in general and the evolution of pathogenicity and antibiotic resistance in particular, a focus of this dissertation study. Methods for GI detection have also evolved with advances in sequencing and bioinformatics, however, comprehensive assessment of these methods has been lacking. This motivated us to assess the performance of current methods for identifying islands on broad datasets of well-characterized bacterial genomes and synthetic genomes, and leverage this information to develop a novel approach that circumvents the limitations of the current state-of-the-art in GI detection. The main findings from our assessment studies were 1) the methods have complementary strengths, 2) a gene-clustering method utilizing codon usage bias as the discriminant criterion, namely, JS-CB, is most efficient in localizing genomic islands, specifically the well-studied SCCmec resistance island in methicillin resistant Staphylococcus aureus (MRSA) genomes, and 3) in general, the bottom up, gene by gene analysis methods, are inherently limited in their ability to decipher large structures such as GIs as single entities within bacterial genomes. We adapted a top-down approach based on recursive segmentation and agglomerative clustering and developed a GI prediction tool, GEMINI, which combined compositional features with segment context information to localize GIs in the Liverpool epidemic strain of Pseudomonas aeruginosa. Application of GEMINI to the genome of P. aeruginosa LESB58 demonstrated its ability to delineate experimentally verified GIs in the LESB58 genome. GEMINI identified several novel islands including pathogenicity islands and revealed the …
Genomic modifications occur slowly across generations, whereas short-term epigenetic transgenerational inheritance of adaptive phenotypes may be immediately beneficial to large numbers of individuals, acting as a bridge for survival when adverse environments occur. In this study we used dietary exposure to crude oil as an example of an environmental stressor to assess its effects from the molecular to the organismal levels in piscine and avian animal models. In addition, we assessed the role of the parental exposures on their offspring F1 generation. The research developed in this dissertation has contributed to several areas of investigation including molecular biology, animal physiology, and evolutionary biology. The quantitative information from these studies may be utilized to supplement information regarding the proximate and ultimate effects of environmental stressors on fish and bird populations. Furthermore, this information may be used as additional support for understanding the conservation of the responses from the molecular to the whole organismal levels across the vertebrate taxa, as well as their implications for population survival and maintenance. Additionally, the zebrafish (Danio rerio), the Siamese fighting fish (Betta splendens) and the king quail (Coturnix chinensis) have proven to be excellent models to start building a strong basis for understanding the effects of environmental stressors and transgenerational epigenetic phenomena using a multi-level approach. Furthermore, as more raw data and information is discovered, the concatenation of development, organismal variation, epigenetics inheritance, natural selection, speciation and evolution is being slowly decrypted.
Peregrine falcon subspecies taxonomy is widely debated due to uncertainty in their evolutionary history and unresolved phylogenetic reconstruction using both morphological and molecular data. Previous genetic work has shown limited support for subspecies taxonomy largely as a result of molecular markers used, potential contemporary gene flow, incomplete lineage sorting, and ancestral polymorphisms. With the advent of next-generation sequencing, the cost of generating large amounts of sequence data has dropped significantly, making whole genome re-sequencing (WGR) studies of non-model organisms more tangible. In this study, WGR methods have been utilized to investigate the phylogenetic relationships among all 20 currently recognized peregrine falcon subspecies. By generating whole-genome data for all 20 subspecies, subspecies specific diagnostic SNPs have been identified to aid in subspecies delimitation. Results of this study broadly support current subspecies, however, reveal that further study is needed to investigate regional relationships among subspecies in Asia, Australia, and western North America. With these results, conservation efforts can be further supported by allowing for accurate delimitation of local subspecies and subspecies boundaries.
My aim is to design a research program that emphasizes inclusivity through empiricism rather than anecdotes and benevolent sexism. To accomplish this goal, I review and build on the work assessing the influence of fertility in the female consumer experience (FCE). Fertility, especially menstruation, has been used anecdotally for too long. This research was designed to address the gap in knowledge around the way in which women perceive advertisements. More specifically, the role fertility plays in the process women go through when assessing advertisements and offerings. Does a woman's desire to seek variety become reduced when she sees a rival endorsing the offering? If this is the case, then there is a need to find a mediating variable that can overcome this effect. Internal locus of control, the level a person feels they are in control of the outcomes in their lives, was selected as a starting point. Having a high internal LOC should buffer a person's perceptions of another as a threat. A cross-sectional design from a convenience sample of university students was used to address a series of five research questions: 1) Does fertility status influence locus of control, 2) Does fertility status influence rival assessment, 3) Does locus of control mediate rival assessment, 4) Does rival assessment influence advertisement assessment and purchase intent, and 5) Does external locus of control have more than a single factor? The results from the multiple one-way ANOVAs and linear regressions were not significant, but it was promising given the limitations of the study. Namely, the rate of unusable data combined with the rate of birth control use limited the final analyses to a sample of 62 cases. Additional considerations and future research directions are outlined in chapter 5.
In a small room in Austin, Texas, a group of 15 people are single-handedly deciding what is taught to the next generation of American children. The highly politicized 15 member Texas Board of Education is currently going through the once-in-a-decade process of rewriting the teaching and textbook standards for its nearly 5 million schoolchildren. Texas is also unbelievably influential on the standards that textbook publishers use as a basis for their textbooks nationwide. Over the last 10 years, the textbooks adopted by this board found their way in upwards of 65% of American classrooms. My goal is to shed light on this important issue and the key players in this process - I explain their goals, explore the scope of their influence, and delve into the personal motivations behind their actions, which will affect public education throughout the country.
This document describes the research and training accomplishments of Dr. Kevin Atteson during the DOE fellowship period of September 1997 to September 1999. Dr. Atteson received training in molecular evolution during this period and made progress on seven research topics including: computation of DNA pattern probability, asymptotic redundancy of Bayes rules, performance of neighbor-joining evolutionary tree estimation, convex evolutionary tree estimation, identifiability of trees under mixed rates, gene expression analysis, and population genetics of unequal crossover.
Electrophoretic variation in 18 proteins encoded by 20 autosomal loci was used to compare the genetic relationships of 19 natural populations representing three species of the subgenus Neotoma. Of the 20 loci examined nine were monomorphic and fixed for the same allele in all populations. No more than seven loci were polymorphic within a single population. Genetic variability was expressed as the proportion of loci heterozygous in the average individual of a population. Heterozygosity in the three species of Neotoma studied averaged 0.078, a value within the range reported for other rodents. Although the levels of heterozygosity seen in Neotoma could not readily be explained, the variation may be attributed to ecological factors. The three species of Neotoma were compared on the basis of genetic similarity and found to form a close taxonomic unit, probably semispecies. Divergence times were obtained for the three species and found to compare well with divergence times obtained from fossil data. In general, the three species have diverged within the last 112,000 years during the Wisconsin glacial period.
Recently projected climate changes could have widespread effects on wildlife species. These effects might be positive or negative, depending on the species. Some effects might include extinction, range shifts, mismatches in phenology (timing of pollination, flowering, etc.), and population changes. If the effects of climate change are widespread, there is uncertainty on how wildlife will adapt. Some suggest that evolution and migration will enable species to adapt, whereas others contend that adaptation will be minimal because of limited habitat, and changes in climate that may occur may rapidly than adaptation can respond.
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