Constraints on Patterns of Abundance and Aggregation in Biological Systems

Understanding the mechanisms that structure biological systems is a primary goal of biology. My research shows that the biological structure is constrained in important ways by general variables such as the number of base pairs in a genome and the number of individuals and species in a community. I used a combination of macroecology, bioinformatics, statistics, mathematics, and advanced computing to pursue my research and published several peer-reviewed scientific manuscripts and open-source software as a result.I was funded through a combination of fellowships and scholarships awarded by the Utah State University School of Graduate Studies, College of Science, and Department of Biology, as well as teaching assistantships awarded through the Department of Biology at Utah State University, and research assistantships funded through a CAREER grant from the U.S. National Science Foundation (DEB-0953694) awarded to my advisor, Dr. Ethan White. With the help of my advisor, I also obtained a computing grant from Amazon Web Services in the amount of $7,500. Altogether, funding for my research and education totaled approximately$123,500. Using over 9000 communities of plants, animals, fungi, and microorganisms, I demonstrated that the forms of empirical species abundance distributions (SADs) are constrained by total abundance and species richness. Using over 300 microbial genomes, I demonstrate that nucleotide aggregation is constrained by genome length and differs between regions of coding and noncoding DNA. General state variables of genomes and ecological communities (i.e. genome length, total abundance and species richness) constrain simple structural properties of each system

Simple Structural Differences between Coding and Noncoding DNA

Background The study of large-scale genome structure has revealed patterns suggesting the influence of evolutionary constraints on genome evolution. However, the results of these studies can be difficult to interpret due to the conceptual complexity of the analyses. This makes it difficult to understand how observed statistical patterns relate to the physical distribution of genomic elements. We use a simpler and more intuitive approach to evaluate patterns of genome structure. Methodology/Principal Findings We used randomization tests based on Morisita\u27s Index of aggregation to examine average differences in the distribution of purines and pyrimidines among coding and noncoding regions of 261 chromosomes from 223 microbial genomes representing 21 phylum level groups. Purines and pyrimidines were aggregated in the noncoding DNA of 86% of genomes, but were only aggregated in the coding regions of 52% of genomes. Coding and noncoding DNA differed in aggregation in 94% of genomes. Noncoding regions were more aggregated than coding regions in 91% of these genomes. Genome length appears to limit aggregation, but chromosome length does not. Chromosomes from the same species are similarly aggregated despite substantial differences in length. Aggregation differed among taxonomic groups, revealing support for a previously reported pattern relating genome structure to environmental conditions. Conclusions/Significance Our approach revealed several patterns of genome structure among different types of DNA, different chromosomes of the same genome, and among different taxonomic groups. Similarity in aggregation among chromosomes of varying length from the same genome suggests that individual chromosome structure has not evolved independently of the general constraints on genome structure as a whole. These patterns were detected using simple and readily interpretable methods commonly used in other areas of biology

Culture perfusion schedules influence the metabolic activity and granulocyte-macrophage colony-stimulating factor production rates of human bone marrow stromal cells

The metabolic function and GM-CSF production rates of adherent human bone marrow stromal cells were investigated as functions of medium and serum feeding rates. A range of medium exchange schedules was studied, ranging from a typical Dexter culture protocol of one weekly medium exchange to a full media exchange daily, which more closely approximates what bone marrow cells experience in situ. Glucose consumption was found to be significantly higher at full daily exchange rate than at any other exchange schedule examined. However, the lactate yield on glucose was a constant, at 1.8 mol/mol, under all conditions considered. Differential serum vs. medium exchange experiment showed that both serum supply and medium nutrients were responsible for the altered behavior at high exchange rates. Glutamine consumption was found to be insignificant under all culture conditions examined. A change in exchange schedule from 50% daily medium exchange to full daily medium exchange after 14 days of culture was found to result in a transient production of GM-CSF and a change in metabolic behavior to resemble that of cultures which had full daily exchange from day one. These results suggest that both stromal cell metabolism and GM-CSF production are sensitive to medium exchange schedules. Taken together, the data presented indicate that attempts to model the function of human bone marrow in vitro may be well served by beginning with medium exchange schedules that more closely mimic the in vivo physiologic state of bone marrow.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/49880/1/1041470221_ftp.pd

Frauenliebe und Leben: Robert Schumann’s self-fulfilling prophecy

The basis of this research paper is the work of Robert Schumann, particularly his lieder cycle Frauenliebe und Leben, and how it predicted the conditions and events of Robert and Clara Schumann’s marriage. I will discuss Schumann’s composition of Frauenliebe und Leben in the context of his relationship with Clara. I will also analyze Chamisso’s poetry and Schumann’s decision to use it in this cycle. The process of Robert and Clara marrying was particularly difficult because of Clara’s father, and I will study their correspondence around the time of Frauenliebe und Leben’s composition to further my understanding of the situation as a whole. In terms of their work post-marriage I will discuss Clara’s transformation from a musician to a wife and mother; while she still composed and performed, she was forced to be mainly a wife, a mother, and an admirer of Robert’s work.. Some emphasis will be given to gender roles in nineteenth-century German marriages, which was illustrated both through the texts used in Frauenliebe und Leben and in Clara’s role in the Schumann household. I am interested in this topic because I am learning the Frauenliebe und Leben cycle for my upcoming voice recital and I want to learn more about it. I also am fascinated with the idea of two active composers marrying and having a family together. My goal with this research paper is to gain a deep understanding of the song cycle as a whole and grasp its place in Robert and Clara Schumann’s lives and compositions

Initial Results from the Variable Intensity Sonic Boom Propagation Database

An extensive sonic boom propagation database with low- to normal-intensity booms (overpressures of 0.08 lbf/sq ft to 2.20 lbf/sq ft) was collected for propagation code validation, and initial results and flight research techniques are presented. Several arrays of microphones were used, including a 10 m tall tower to measure shock wave directionality and the effect of height above ground on acoustic level. A sailplane was employed to measure sonic booms above and within the atmospheric turbulent boundary layer, and the sailplane was positioned to intercept the shock waves between the supersonic airplane and the ground sensors. Sailplane and ground-level sonic boom recordings were used to generate atmospheric turbulence filter functions showing excellent agreement with ground measurements. The sonic boom prediction software PCBoom4 was employed as a preflight planning tool using preflight weather data. The measured data of shock wave directionality, arrival time, and overpressure gave excellent agreement with the PCBoom4-calculated results using the measured aircraft and atmospheric data as inputs. C-weighted acoustic levels generally decreased with increasing height above the ground. A-weighted and perceived levels usually were at a minimum for a height where the elevated microphone pressure rise time history was the straightest, which is a result of incident and ground-reflected shock waves interacting

Learning to trust: social feedback normalizes trust behavior in first-episode psychosis and clinical high risk

Background Psychosis is characterized by problems in social functioning that exist well before illness onset, and in individuals at clinical high risk (CHR) for psychosis. Trust is an essential element for social interactions that is impaired in psychosis. In the trust game, chronic patients showed reduced baseline trust, impaired response to positive social feedback, and attenuated brain activation in reward and mentalizing areas. We investigated whether first-episode psychosis patients (FEP) and CHR show similar abnormalities in the neural and behavioral mechanisms underlying trust. Methods Twenty-two FEP, 17 CHR, and 43 healthy controls performed two trust games, with a cooperative and an unfair partner in the fMRI scanner. Region of interest analyses were performed on mentalizing and reward processing areas, during the investment and outcome phases of the games. Results Compared with healthy controls, FEP and CHR showed reduced baseline trust, but like controls, learned to trust in response to cooperative and unfair feedback. Symptom severity was not associated with baseline trust, however in FEP associated with reduced response to feedback. The only group differences in brain activation were that CHR recruited the temporo-parietal junction (TPJ) more than FEP and controls during investment in the unfair condition. This hyper-activation in CHR was associated with greater symptom severity. Conclusions Reduced baseline trust may be associated with risk for psychotic illness, or generally with poor mental health. Feedback learning is still intact in CHR and FEP, as opposed to chronic patients. CHR however show distinct neural activation patterns of hyper-activation of the TPJ

Mechanisms of impulsive choice: I. Individual differences in interval timing and reward processing

Impulsive choice behavior incorporates the psychological mechanisms involved in the processing of the anticipated magnitude and delay until reward. The goal of the present experiment was to determine whether individual differences in such processes related to individual differences in impulsive choice behavior. Two groups of rats (Delay Group and Magnitude Group) were initially exposed to an impulsive choice task with choices between smaller-sooner (SS) and larger-later (LL) rewards. The Delay Group was subsequently exposed to a temporal discrimination task followed by a progressive interval task, whereas the Magnitude Group was exposed to a reward magnitude sensitivity task followed by a progressive ratio task. Inter-task correlations revealed that the rats in the Delay Group that made more self-controlled (LL) choices also displayed lower standard deviations in the temporal bisection task and greater delay tolerance in the progressive interval task. Impulsive choice behavior in the Magnitude Group did not display any substantial correlations with the reward magnitude sensitivity and progressive ratio tasks. The results indicate the importance of core timing processes in impulsive choice behavior, and encourage further research examining the effects of changes in core timing processes on impulsive choice