Investigating the Utility of Detrital Mineral Microchemistry and Radiogenic Isotope Compositions as Provenance Discriminators

The provenance of clastic sediments remains one of the key tools for understanding the complex dynamic history of the Earth. Detritus shed from ancient orogens may be the only evidence available for determining the timing, evolution, paleogeography, and existence of tectonic events active over the 4.56 Ga of Earth history. The focus of this dissertation research is to assess the strengths and limitations of existing, as well as novel, tools for determining the provenance of siliciclastic sediments. The utility of detrital monazite crystallization ages was investigated as a provenance indicator in both modern and ancient sedimentary systems. The results from these investigations show that the ages of detrital monazite record, at a higher fidelity, the complex Appalachian Paleozoic tectonic history than does detrital zircon. In several of the analyzed samples, detrital monazite recorded multiple tectonic events that were entirely missed by the detrital zircon record, thus providing a more accurate identification and assessment of sediment donor regions. In addition, the utility of detrital garnet microchemisty was investigated as tool for quantitative sediment provenance analysis. Garnet was chemically characterized from a wide variety of lithologies that crop out within the French Broad River (western North Carolina) watershed. Mahalanobis distances measured on canonical discriminant functions successfully differentiated garnet compositions among the analyzed source rocks. These metrics successfully linked ~94% of detrital garnet compositions to the source rocks from which they were potentially derived. Finally, bootstrapping techniques were applied to detrital zircon U-Pb ages, from two modern river systems, which allowed for the determination of statistical confidence intervals that constrained the variation in the age spectra imposed by finite sampling. The technique essentially removed that portion of the sample zircon age spectra that carries little discriminating power, thus highlighting spectral components which are unique. This approach provided a framework in which detrital zircon (or other mineral) ages can be compared and interpreted in an objective and statistically constrained context

Experimental Illumination of Comprehensive Fitness Landscapes: A Dissertation

Evolution is the single cohesive logical framework in which all biological processes may exist simultaneously. Incremental changes in phenotype over imperceptibly large timescales have given rise to the enormous diversity of life we witness on earth both presently and through the natural record. The basic unit of evolution is mutation, and by perturbing biological processes, mutations may alter the fitness of an individual. However, the fitness effect of a mutation is difficult to infer from historical record, and complex to obtain experimentally in an efficient and accurate manner. We have recently developed a high throughput method to iteratively mutagenize regions of essential genes in yeast and subsequently analyze individual mutant fitness termed Exceedingly Methodical and Parallel Investigation of Randomized Individual Codons (EMPIRIC). Utilizing this technique as exemplified in Chapters II and III, it is possible to determine the fitness effects of all possible point mutations in parallel through growth competition followed by a high throughput sequencing readout. We have employed this technique to determine the distribution of fitness effects in a nine amino acid region of the Hsp90 gene of S. cerevisiae under elevated temperature, and found the bimodal distribution of fitness effects to be remarkably consistent with near-neutral theory. Comparing the measured fitness effects of mutants to the natural record, phylogenetic alignments appear to be a poor predictor of experimental fitness. In Chapter IV, to further interrogate the properties of this region, library competition under conditions of elevated temperature and salinity were performed to study the potential of protein adaptation. Strikingly, whereas both optimal and elevated temperatures produced no statistically significant beneficial mutations, under conditions of elevated salinity, adaptive mutations appear with fitness advantages up to 8% greater than wild type. Of particular interest, mutations conferring fitness benefits under conditions of elevated salinity almost always experience a fitness defect in other experimental conditions, indicating these mutations are environmentally specialized. Applying the experimental fitness measurements to long standing theoretical predictions of adaptation, our results are remarkably consistent with Fisher’s Geometric Model of protein evolution. Epistasis between mutations can have profound effects on evolutionary trajectories. Although the importance of epistasis has been realized since the early 1900s, the interdependence of mutations is difficult to study in vivo due to the stochastic and constant nature of background mutations. In Chapter V, utilizing the EMPIRIC methodology allows us to study the distribution of fitness effects in the context of mutant genetic backgrounds with minimal influence from unintended background mutations. By analyzing intragenic epistatic interactions, we uncovered a complex interplay between solvent shielded structural residues and solvent exposed hydrophobic surface in the amino acid 582-590 region of Hsp90. Additionally, negative epistasis appears to be negatively correlated with mutational promiscuity while additive interactions are positively correlated, indicating potential avenues for proteins to navigate fitness ‘valleys’. In summary, the work presented in this dissertation is focused on applying experimental context to the theory-rich field of evolutionary biology. The development and implementation of a novel methodology for the rapid and accurate assessment of organismal fitness has allowed us to address some of the most basic processes of evolution including adaptation and protein expression level. Through the work presented here and by investigators across the world, the application of experimental data to evolutionary theory has the potential to improve drug design and human health in general, as well as allow for predictive medicine in the coming era of personalized medicine

Rational Best-Value Model based on Expected Performance

The best-value procurement strategy is gaining the interest of federal and state agencies. The strategy increases the value added to a project for each dollar added. A new concept of best value, that is, a rational and flexible model based on expected performance, is presented. The model\u27s flexibility is obvious in the selection of parameters to be included in the contractor selection process and in the determination of their weights. The model\u27s rationality will be achieved through relating all awarded scores to the agency\u27s expected performance. The establishment of the best-value model relies on the past record of the contractor\u27s work for the agency as an indicator of qualification trend. This research incorporates prequalification as a first-level screening technique in selecting top contractor bids in the best-value procurement and then applies a rational scoring system in the final selection. Selection of the most appropriate contractor with the best qualifications for a given project will be based on contractor best value. Data are collected from groups of experts in the Minnesota Department of Transportation and processed through the analytic hierarchy process to establish the parameter weights. Although this research assists departments of transportation in selecting the best contractor, the results are relevant to both academics and practitioners. The paper provides practitioners with a tool for ranking contractors based on best value and provides academics with selection parameters, a model to evaluate the best value, and a methodology for quantifying the qualitative effect of subjective factors

Forging Information Literacy Skills With ANVIL: An Innovative Game-based Approach to Teaching Information Literacy

At the University of Wisconsin-Oshkosh, library staff developed a game-based tool to aid in the teaching of the concepts and skills associated with information literacy. Students watch a series of videos based on the ACRL standards for information literacy. After viewing the videos, students test their comprehension of a particular standard by playing a “bar-trivia” style game. Points are awarded for accuracy and speed, and scores are posted to a global leaderboard to promote friendly competition. This presentation will highlight the process behind game development, campus-wide implementation, and user and faculty response

A systematic survey of an intragenic epistatic landscape [preprint]

Mutations are the source of evolutionary variation. The interactions of multiple mutations can have important effects on fitness and evolutionary trajectories. We have recently described the distribution of fitness effects of all single mutations for a nine amino acid region of yeast Hsp90 (Hsp82) implicated in substrate binding. Here, we report and discuss the distribution of intragenic epistatic effects within this region in seven Hsp90 point mutant backgrounds of neutral to slightly deleterious effect, resulting in an analysis of more than 1000 double-mutants. We find negative epistasis between substitutions to be common, and positive epistasis to be rare – resulting in a pattern that indicates a drastic change in the distribution of fitness effects one step away from the wild type. This can be well explained by a concave relationship between phenotype and genotype (i.e., a concave shape of the local fitness landscape), suggesting mutational robustness intrinsic to the local sequence space. Structural analyses indicate that, in this region, epistatic effects are most pronounced when a solvent-inaccessible position is involved in the interaction. In contrast, all 18 observations of positive epistasis involved at least one mutation at a solvent-exposed position. By combining the analysis of evolutionary and biophysical properties of an epistatic landscape, these results contribute to a more detailed understanding of the complexity of protein evolution

Latent effects of Hsp90 mutants revealed at reduced expression levels

In natural systems, selection acts on both protein sequence and expression level, but it is unclear how selection integrates over these two dimensions. We recently developed the EMPIRIC approach to systematically determine the fitness effects of all possible point mutants for important regions of essential genes in yeast. Here, we systematically investigated the fitness effects of point mutations in a putative substrate binding loop of yeast Hsp90 (Hsp82) over a broad range of expression strengths. Negative epistasis between reduced expression strength and amino acid substitutions was common, and the endogenous expression strength frequently obscured mutant defects. By analyzing fitness effects at varied expression strengths, we were able to uncover all mutant effects on function. The majority of mutants caused partial functional defects, consistent with this region of Hsp90 contributing to a mutation sensitive and critical process. These results demonstrate that important functional regions of proteins can tolerate mutational defects without experimentally observable impacts on fitness

Potential Site Productivity Influences the Rate of Forest Structural Development

Development and maintenance of structurally complex forests in landscapes formerly managed for timber production is an increasingly common management objective. It has been postulated that the rate of forest structural development increases with site productivity. We tested this hypothesis for Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) forests using a network of permanent study plots established following complete timber harvest of the original old-growth forests. Forest structural development was assessed by comparing empirical measures of live tree structure to published values for Douglas-fir forests spanning a range of ages and structural conditions. The rate of forest structural development—resilience—exhibited a positive relationship with site index, a measure of potential site productivity. Density of shade-intolerant conifers declined in all study stands from an initial range of 336–4068 trees/ha to a range of 168–642 trees/ha at the most recent measurement. Angiosperm tree species declined from an initial range of 40–371 trees/ha to zero in seven of the nine plots in which they were present. Trends in shade-tolerant tree density were complex: density ranged from 0 to 575 trees/ha at the first measurement and was still highly variable (25–389 trees/ha) at the most recent measurement. Multivariate analysis identified the abundance of hardwood tree species as the strongest compositional trend apparent over the study period. However, structural variables showed a strong positive association with increasing shade-tolerant basal area and little or no association with abundance of hardwood species. Thus, while tree species succession and forest structural development occur contemporaneously, they are not equivalent processes, and their respective rates are not necessarily linearly related. The results of this study support the idea that silvicultural treatments to accelerate forest structural development should be concentrated on lower productivity sites when the management objective is reserve-wide coverage of structurally complex forests. Alternatively, high-productivity sites should be prioritized for restoration treatments when the management objective is to develop structurally complex forests on a portion of the landscape

Obesity Promotes Cooperation of Cancer Stem-Like Cells and Macrophages to Enhance Mammary Tumor Angiogenesis

Obesity is correlated with worsened prognosis and treatment resistance in breast cancer. Macrophage-targeted therapies are currently in clinical trials, however, little is known about how obesity may impact treatment efficacy. Within breast adipose tissue, obesity leads to chronic, macrophage-driven inflammation, suggesting that obese breast cancer patients may benefit from these therapies. Using a high fat diet model of obesity, we orthotopically transplanted cancer cell lines into the mammary glands of obese and lean mice. We quantified changes in tumor invasiveness, angiogenesis and metastasis, and examined the efficacy of macrophage depletion to diminish tumor progression in obese and lean mice. Mammary tumors from obese mice grew significantly faster, were enriched for cancer stem-like cells (CSCs) and were more locally invasive and metastatic. Tumor cells isolated from obese mice demonstrated enhanced expression of stem cell-related pathways including Sox2 and Notch2. Despite more rapid growth, mammary tumors from obese mice had reduced necrosis, higher blood vessel density, and greater macrophage recruitment. Depletion of macrophages in obese tumor-bearing mice resulted in increased tumor necrosis, reduced endothelial cells, and enhanced recruitment of CD8+ T cells compared to IgG-treated controls. Macrophages may be an important clinical target to improve treatment options for obese breast cancer patients

Comprehensive fitness maps of Hsp90 show widespread environmental dependence

Gene-environment interactions have long been theorized to influence molecular evolution. However, the environmental dependence of most mutations remains unknown. Using deep mutational scanning, we engineered yeast with all 44,604 single codon changes encoding 14,160 amino acid variants in Hsp90 and quantified growth effects under standard conditions and under five stress conditions. To our knowledge, these are the largest determined comprehensive fitness maps of point mutants. The growth of many variants differed between conditions, indicating that environment can have a large impact on Hsp90 evolution. Multiple variants provided growth advantages under individual conditions; however, these variants tended to exhibit growth defects in other environments. The diversity of Hsp90 sequences observed in extant eukaryotes preferentially contains variants that supported robust growth under all tested conditions. Rather than favoring substitutions in individual conditions, the long-term selective pressure on Hsp90 may have been that of fluctuating environments, leading to robustness under a variety of conditions

Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology

We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate interactions. (2) Neofunctionalization, in which a mutation leads to a new interaction with some other protein. Since many interactions are due to simple surface compatibility, we hypothesize there is an increased likelihood of interacting with other proteins in the target protein’s neighborhood. We find good agreement of the model on 10 different network properties compared to high-confidence experimental PPI networks in yeast, fruit flies, and humans. Key findings are: (1) PPI networks evolve modular structures, with no need to invoke particular selection pressures. (2) Proteins in cells have on average about 6 degrees of separation, similar to some social networks, such as human-communication and actor networks. (3) Unlike social networks, which have a shrinking diameter (degree of maximum separation) over time, PPI networks are predicted to grow in diameter. (4) The model indicates that evolutionarily old proteins should have higher connectivities and be more centrally embedded in their networks. This suggests a way in which present-day proteomics data could provide insights into biological evolution