Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 110-114).

Thesis (Ph. D.) -- University of Tennessee, Knoxville, 2005. / Vita. Includes bibliographical references. Also available online via the University of Tennessee ETD website (http://web.utk.edu/~thesis/etd.shtml).

A protocol was developed to measure ammonia emission concentrations from dairies using an isolation flux chamber. A hybrid dairy in Comanche county, Texas, was measured for one week each during August 2002 and January 2003. Sixty total ammonia samples were taken from the free stall barn, open lot, mixing tank, separated solids, compost, and two lagoons using the developed protocol. The ammonia concentration measurements were made using a chemiluminescence analyzer located inside a mobile laboratory. From the emission concentrations recorded, it was estimated that 9.68 metric tons of ammonia were produced from this dairy per year. An emission factor of 13.34 ± 28.80 kilograms per day per thousand head of cattle (kg/day/1000 head) was estimated for this dairy (±95% confidence intervals) during summer conditions. For winter conditions the emission factor was 12.05 ± 12.89 kg/day/1000 head. The 11% difference of the emission factors from summer to winter conditions was predominantly from the change in ambient and control volume temperatures (a mean difference of approximately 25 degrees Celsius), differences in source temperatures, and seasonal variability in husbandry. The adsorption of ammonia onto different polymer tubing used in pollutant stream conveyance was researched for possible systematic losses. Teflon and low density polyethylene (LDPE) were tested for ammonia losses with treatments of: temperature, length, and inlet concentration. Inlet concentration and temperature were significant factors used to describe ammonia adsorption for Teflon, whereas LDPE was also affected by tubing length. These factors were used to create a model to correct the summer dairy measurements for ammonia losses, resulting in an emission factor increase of 8.3% over the original value obtained from the flux chamber. A nitrogen mass balance was performed to estimate the amount of nitrogen available for ammonia formation as excreted - 177.5 kilograms per year per animal (wet basis). The amount of ammonia excreted per year was also estimated to be 26.63 kilograms per year. The measured ammonia emitted from the dairy was five times less than the ammonia excreted and thirty-six times less than the total nitrogen excreted.

The fluffy gene of Neurospora crassa is required for asexual sporulation. It encodes an 88 kDa polypeptide containing a typical fungal Zn2Cys6 DNA binding motif. To identify the target genes on which FL may act, I sought to identify target sequences to which the FL protein binds. Several strategies were attempted to obtain purified FL protein. Purification was achieved by expressing the DNA binding domain of FL in Escherichia coli as a fusion with glutathione S-transferase followed by affinity purification using glutathione sepharose chromatography. DNA binding sites were selected by in vitro binding assays. Comparison of the sequences of selected clones suggested that FL binds to the motif 5??-CGG(N)9CCG-3??. A potential binding site was found in the promoter region of the eas (ccg-2) gene, which encodes a fungal hydrophobin. In vitro competitive binding assays revealed a preferred binding site for FL in the eas promoter, 5??-CGGAAGTTTCCTCCG-3??, which is located 1498 bp upstream of the eas translation initiation codon. In vivo experiments using a foreign DNA sequence tag confirmed that this sequence is a target site for FL regulation. Using Saccharomyces cerevisiae as an experimental system, I demonstrated that the C-terminal portion of FL functions in transcriptional activation. Microarray analysis was performed to study the role of fl in gene regulation on a large scale. mRNA levels in a fl mutant were compared to those in a strain overexpressing the fl gene. Experiments with cDNA microarray containing 13% of the total number of predicted N. crassa genes revealed 122 genes differentially expressed in response to overexpression of fl. Among these, eas displayed the greatest level of response. The cDNA microarray approach also revealed a number of genes that may be indirectly regulated by fl but may be involved in development. This information provides a foundation for further analysis of the role of fl in conidial development.

Linear factor models have attracted considerable interest over recent years especially in the econometrics literature. The intuitively appealing idea to explain a panel of economic variables by a few common factors is one of the reasons for their popularity. From a statistical viewpoint, the need to reduce the cross-section dimension to a much smaller factor space dimension is obvious considering the large data sets available in economics and finance. One of the characteristics of the traditional factor model is that the process is stationary in the time dimension. This appears restrictive, given the fact that over long time periods it is unlikely that e.g. factor loadings remain constant. For example, in the capital asset pricing model (CAPM) of Sharpe (1964) and Lintner (1965), typical empirical results show that factor loadings are time-varying, which in the CAPM is caused by time-varying second moments. In this thesis we generalize the tools of factor analysis for the study of stochastic processes whose behavior evolves over time. In particular, we introduce a new class of factor models with loadings that are allowed to be smooth functions of time. To estimate the resulting nonstationary factor model we generalize the properties of the principal components technique to the time-varying framework. We mainly consider separately two classes of Evolutionary Factor Models: Evolutionary Static Factor Models (Chapter 2) and Evolutionary Dynamic Factor Models (Chapter 3). In Chapter 2 we propose a new approximate factor model where the common components are static but nonstationary. The nonstationarity is introduced by the time-varying factor loadings, that are estimated by the eigenvectors of a nonparametrically estimated covariance matrix. Under simultaneous asymptotics (cross-section and time dimension go to infinity simultaneously), we give conditions for consistency of our estimators of the time varying covariance matrix, the loadings and the factors. This paper generalizes to the locally stationary case the results given by Bai (2003) in the stationary framework. A simulation study illustrates the performance of these estimators. The estimators proposed in Chapter 2 are based on a nonparametric estimator of the covariance matrix whose entries are computed with the same moothing parameter. This approach has the advantage of guaranteeing a positive definite estimator but it does not adapt to the different degree of smoothness of the different entries of the covariance matrix. In Chapter 5 we give an additional theoretical result which explains how to construct a positive definite estimate of the covariance matrix while while permitting different smoothing parameters. This estimator is based on the Cholesky decomposition of a pre-estimator of the covariance matrix. In Chapter 3 we introduce the dynamics in our modeling. This model generalizes the dynamic (but stationary) factor model of Forni et al. (2000), as well as the nonstationary (but static) factor model of Chapter 2. In the stationary (dynamic) case, Forni et al. (2000) show that the common components are estimated by the eigenvectors of a consistent estimator of the spectral density matrix, which is a matrix depending only on the frequency. In the evolutionary framework the dynamics of the model is explained by a time-varying spectral density matrix. This operator is a function of time as well as of the frequency. In this chapter we show that the common components of a locally stationary dynamic factor model can be estimated consistently by the eigenvectors of a consistent estimator of the time-varying spectral density matrix. In Chapter 4 we apply our theoretical results to real data and compare the performance of our approach with that based on standard techniques. Chapter 6 concludes and mention the main questions for future research.

Au travers d’études cliniques et biologiques, de méta-analyses et de revues systématiques de la littérature, nous avons étudié les CBNPC de stade III sur le plan thérapeutique et cherché des facteurs pronostiques pour la survie dans le but d’améliorer la classification internationale et, à terme, de permettre une meilleure prise en charge des patients inclus dans ce groupe hétérogène de tumeurs. Dans le cadre d’essais randomisés, nous avons montré qu’un abord multimodal et multidisciplinaire permettait d’améliorer le pronostic des patients atteints d’un CBNPC de stade III. Le traitement des tumeurs non résécables implique une combinaison de chimiothérapie et de radiothérapie, dont l’administration concomitante doit être proposée aux patients aptes à la tolérer. La chimiothérapie doit être incluse dans le schéma thérapeutique des tumeurs potentiellement résécables. Elle permet une résection chirurgicale complète chez des patients sélectionnés dont la tumeur était initialement non résécable. Nous avons déterminé que des caractéristiques cliniques (l’indice de performance et l’âge), biologiques (les taux sanguins de polynucléaires neutrophiles, d’hémoglobine et de plaquettes, la bilirubinémie) et propres à la tumeur (l’extension locale [T3-4] et ganglionnaire [N3]) avaient une valeur pronostique indépendante pour la survie. Ceci nous a permis d’aboutir à une proposition de modification de la classification internationale concernant les CBNPC de stade III. Bien que pris individuellement, les facteurs biologiques que nous avons étudiés (p53, EGF-R, TTF-1, Mdm2) n’aient pas de valeur pronostique pour la survie, nous avons montré que la combinaison EGF-R+/TTF1- était un facteur pronostique indépendant en analyse multivariée pour la survie spécifique au cancer bronchique. Nous avons finalement évalué le rôle pronostique de la tomodensitométrie par émission de positrons et de la mesure semi-quantitative de captation du 18F-FDG (SUV) sur la survie des patients atteints de CBNPC et montré qu’un SUV élevé était un facteur de mauvais pronostic pour la survie.

Childhood overweight and obesity is a significant public health concern, especially among children of different racial and socioeconomic backgrounds. This dissertation provides insight into one such population: Asian youth in the U.S. Three studies - two literature reviews and one quantitative study - compose this dissertation, which aims to understand dietary behaviors of Asian-American youths using a theoretical framework. The first study is a systematic literature review of existing health education/promotion theories and models used to study eating/feeding practices for preschool-aged children. The main purpose of this study was to review and critique theories and constructs utilized in nutrition research on preschool-aged children, while also providing recommendations for strengthening theory utilization and diversifying nutrition research in the future. Forty articles were included, of which 43% had clear identification of theory/constructs and a strong theoretical framework. The most common finding was modeling's effect on children's dietary behaviors, followed by the relationship between parental restriction/control and children's dietary behaviors. The second study was a systematic literature review of dietary behaviors of children of Asian background in the U.S. The aims of this review were three-fold: (a) to review literature regarding Asian-American youths' dietary behaviors, (b) to critically evaluate the methodological quality of such research, and (c) provide recommendations for future nutrition-related research on Asian-American youths. Fifteen articles were included. Major findings included: (a) frequent consumption of milk, fruit, meat, unenriched white rice, vegetables, and high-fat and high-sugar items among Asian-American children and (b) acculturation's effect on Asian-American youths' dietary behaviors. The third study was an investigation of cognitive, behavioral, and environmental influences on dietary behaviors of Asian-American preschool-aged children on WIC using Social Cognitive Theory. Analyses included descriptive statistics and multiple linear regression on a sample of 68 Asian caregiver-child pairs in Texas. Results revealed consumption of 100% juices, fruits, vegetables, and white rice. In addition, adult fruit consumption frequency, adult potato consumption frequency, adult other vegetable consumption frequency, and outcome expectancies were statistically significant predictors of child's fruit and vegetable consumption. The findings from this dissertation will help nutrition education and health professionals culturally tailor obesity prevention programs for Asian Americans.

Polymorphisms in the interferon regulatory factor 5 (IRF5) gene have been consistently replicated and shown to confer risk for or protection from the development of systemic lupus erythematosus (SLE). IRF5 expression is significantly upregulated in SLE patients and upregulation associates with IRF5-SLE risk haplotypes. IRF5 alternative splicing has also been shown to be elevated in SLE patients. Given that human IRF5 exists as multiple alternatively spliced transcripts with distinct function(s), it is important to determine whether the IRF5 transcript profile expressed in healthy donor immune cells is different from that expressed in SLE patients. Moreover, it is not currently known whether an IRF5-SLE risk haplotype defines the profile of IRF5 transcripts expressed. Using standard molecular cloning techniques, we identified and isolated 14 new differentially spliced IRF5 transcript variants from purified monocytes of healthy donors and SLE patients to generate an IRF5 variant transcriptome. Next-generation sequencing was then used to perform in-depth and quantitative analysis of full-length IRF5 transcript expression in primary immune cells of SLE patients and healthy donors by next-generation sequencing. Evidence for additional alternatively spliced transcripts was obtained from de novo junction discovery. Data from these studies support the overall complexity of IRF5 alternative splicing in SLE. Results from next-generation sequencing correlated with cloning and gave similar abundance rankings in SLE patients thus supporting the use of this new technology for in-depth single gene transcript profiling. Results from this study provide the first proof that 1) SLE patients express an IRF5 transcript signature that is distinct from healthy donors, 2) an IRF5-SLE risk haplotype defines the top four most abundant IRF5 transcripts expressed in SLE patients, and 3) an IRF5 transcript signature enables clustering of SLE patients with the H2 risk haplotype.

Embryonic stem cells (ESCs) represent a promising source of cells for cell replacement therapy in the context of muscle diseases; however, before ESC-based cell therapy can be translated to the clinic, we must learn to modulate cell-fate decisions in order to maximize the yield of myocytes from this systems. In order to gain a better understanding of the myogenic cell fate, we sought to define the molecular mechanisms underlying the specification and differentiation of ESCs into cardiac and skeletal muscle. More specifically, the central hypothesis of the thesis is that myogenic signalling cascades modulate cell fate via regulation of transcription factors. Retinoic acid (RA) is known to promote skeletal myogenesis, however the molecular basis for this remains unknown. We showed that RA expands the premyogenic progenitor population in mouse stem cells by directly activating pro-myogenic transcription factors such as Pax3 and Meox1. RA also acts indirectly by activating the pro-myogenic Wnt signalling cascade while simultaneously inhibiting the anti-myogenic influence of BMP4. This ultimately resulted in a significant enhancement of skeletal myogenesis. Furthermore, we showed that this effect was conserved in human embryonic stem cells, with implications for directed differentiation and cell therapy. The regulation of cardiomyogenesis by the Wnt pathway was also investigated. We identified a novel interaction between the cardiomyogenic transcription factor Nkx2.5 and the myosin phosphatase (MP) enzyme complex. Interaction with MP resulted in exclusion of Nkx2.5 from the nucleus and inhibition of its transcriptional activity. Finally, we showed that this interaction was modulated by phosphorylation of the Mypt1 subunit of MP by ROCK, downstream of Wnt3a. Treatment of differentiating mouse ESCs with Wnt3a resulted in exclusion of Nkx2.5 from the nucleus and a subsequent failure to undergo terminal differentiation into cardiomyocytes. This likely represents part of the molecular basis for Wnt-mediated inhibition of terminal differentiation of cardiomyocytes. Taken together, our results provide novel insight into the relationship between myogenic signalling cascades and downstream transcription factors and into how they function together to orchestrate the myogenic cell fate in stem cells.

Versican, a chondroitin sulfate proteoglycan, is one of the main components of the extracellular matrix and hence plays a central role in tissue morphogenesis and a number of pathologic processes. My main goal has been to investigate the mechanisms of versican gene regulation, focusing on the signal transduction pathways, promoter regions, cis-acting elements,and trans- factors. This thesis puts forth new knowledge regarding transcriptional regulation of the human versican gene. In chapter III, I present the cloning of a 752-bp fragment of the human versican promoter (- 634/+118 bp) and nine stepwise 5' deletion fragments in the PGL3-luciferase reporter plasmid. Furthermore, I identify three potential enhancer and two repressor regions in this promoter. I also demonstrate that both cAMP and C/EBPf3 enhanced and repressed versican transcription in HeLa cells and rat aortic smooth muscle cells (SMC),respectively, suggesting that versican transcription is differentially regulated by the respective mediator and transcription factor in epithelial cells and SMC. In chapter IV, I reveal the role ofPI3K/PKB/GSK-30 signaling pathway in regulating versican promoter activity and transcription. Furthermore, I identify that the 0-catenin/TCF-4 transcription factor complex, one of the downstream targets of GSK-3[3, mediates versican promoter activity and transcription. In chapter V, I identify that variations in C-terminal regions of TCF family members determine the irrepressor or enhancer properties on Wnt target genes. Furthermore, I show that curcumin is a strong inhibitor of the P-catenin/TCF-p300 mediated gene expression. In chapter VI, I demonstrate that the androgen receptor trans-activates versican transcription in prostate cancer cells. Furthermore, I show cross-talk between the androgen receptor and 13-catenin in regulating versican transcription in prostate stromal fibroblasts. Overall, this study charts previously uncharacterized promoter elements, transcription factors, and signal transduction pathways involved in regulation of the versican gene.