Exploring the Association Between Household Food Insecurity, Parental Self-Efficacy, and Fruit and Vegetable Parenting Practices Among Parents of 5- to 8-Year-Old Overweight Children

Background: Food insecurity may negatively impact children’s nutritional status by affecting parenting quality. Because parents have a strong influence on their children’s eating and food choices, examining the effects of food insecurity on parenting may provide important insights into obesity prevention efforts. Objectives: This study explored whether food insecurity was associated with parental self-efficacy and parenting practices related to fruit and vegetable consumption. Methods: Secondary analysis was performed using baseline data from 31 mothers of 5-8 year old overweight or obese children who had participated in a pilot obesity treatment program. Household food security status, fruit and vegetable parental self-efficacy (modeling/socialization, planning/encouraging and availability/accessibility) and fruit and vegetable parenting practices (structure, responsiveness, non-directive control, and external control) were assessed using validated measures. Students' t-test investigated differences in subscales by food security status. Results: There were no significant differences in fruit and vegetable parenting practices and parental self-efficacy between food secure and insecure groups. There was a trend towards a decrease in parental self-efficacy for making fruit and vegetables available in the home among food insecure parents (p=.06). Conclusions: In this small sample no significant associations were found between food insecurity and fruit and vegetable parenting practices and parental self-efficacy. However, the trend observed in this exploratory analysis supports further hypothesis-driven research with a larger sample size able to detect more subtle differences.

Fate and effects of drilling wastes in a shallow estuarine mesocosm

To address concerns expressed about the possible effect of drilling mud discharges on shallow, low-energy estuarine ecosystems, a 12 month study was designed to detect alterations in water quality and sediment geochemistry. Each drilling mud used in the study and sediments from the study site were analyzed in the laboratory for chemical and physical characteristics. Potential water quality impacts were simulated by the EPA-COE elutriation test procedure. Mud toxicity was measured by acute and chronic bioassays with Mysidopsis bahia, Mercenaria mercenaria, and Nereis virens.^ For the field study, a relatively pristine, shallow (1.2 m) estuary (Christmas Bay, TX) without any drilling activity for the last 30 years was chosen for the study site. After a three month baseline study, three stations were selected. Station 1 was an external control. At each treatment station (2, 3), mesocosms were constructed to enclose a 3.5 m$\sp3$ water column. Each treatment station included an internal control site also. Each in situ mesocosm, except the controls, was successively dosed at a mesocosm-specific dose (1:100; 1:1,000; or 1:10,000 v/v) with 4 field collected drilling muds (spud, nondispersed, lightly-treated, and heavily-treated lignosulfonate) in sequential order over 1.5 months. Twenty-four hours after each dose, water exchange was allowed until the next treatment. Station 3 was destroyed by a winter storm. After the last treatment, the enclosures were removed and the remaining sites monitored for 6 months. One additional site was similarly dosed (1:100 v/v) with clean dredged sediment from Christmas Bay for comparison between dredged sediments and drilling muds.^ Results of the analysis of the water samples and field measurements showed that water quality was impacted during the discharges, primarily at the highest dose (1:100 v/v), but that elevated levels of C, Cr (T,F), Cr$\sp{+3}$ (T, F), N, Pb, and Zn returned to ambient levels before the end of the 24 hour exposure period or immediately after water exchange was allowed (Al, Ba(T), Chlorophyll ABC, SS, %T). Barium, from the barite, was used as a geochemical tracer in the sediments to confirm estimated doses by mass balance calculations. Barium reached a maximum of 166x background levels at the high dose mesocosm. Barium levels returned to ambient or only slightly elevated levels at the end of the 6 month monitoring period due to sediment deposition, resuspension, and bioturbation. QA/QC results using blind samples consisting of lab standards and spiked samples for both water and sediment matrices were within acceptable coefficients of variation.^ In order to avoid impacts on water quality and sediment geochemistry in a shallow estuarine ecosystem, this study concluded that a minimal dilution of 1:1,000 (v/v) would be required in addition to existing regulatory constraints. ^

RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION

My dissertation focuses on two aspects of RNA sequencing technology. The first is the methodology for modeling the overdispersion inherent in RNA-seq data for differential expression analysis. This aspect is addressed in three sections. The second aspect is the application of RNA-seq data to identify the CpG island methylator phenotype (CIMP) by integrating datasets of mRNA expression level and DNA methylation status. Section 1: The cost of DNA sequencing has reduced dramatically in the past decade. Consequently, genomic research increasingly depends on sequencing technology. However it remains elusive how the sequencing capacity influences the accuracy of mRNA expression measurement. We observe that accuracy improves along with the increasing sequencing depth. To model the overdispersion, we use the beta-binomial distribution with a new parameter indicating the dependency between overdispersion and sequencing depth. Our modified beta-binomial model performs better than the binomial or the pure beta-binomial model with a lower false discovery rate. Section 2: Although a number of methods have been proposed in order to accurately analyze differential RNA expression on the gene level, modeling on the base pair level is required. Here, we find that the overdispersion rate decreases as the sequencing depth increases on the base pair level. Also, we propose four models and compare them with each other. As expected, our beta binomial model with a dynamic overdispersion rate is shown to be superior. Section 3: We investigate biases in RNA-seq by exploring the measurement of the external control, spike-in RNA. This study is based on two datasets with spike-in controls obtained from a recent study. We observe an undiscovered bias in the measurement of the spike-in transcripts that arises from the influence of the sample transcripts in RNA-seq. Also, we find that this influence is related to the local sequence of the random hexamer that is used in priming. We suggest a model of the inequality between samples and to correct this type of bias. Section 4: The expression of a gene can be turned off when its promoter is highly methylated. Several studies have reported that a clear threshold effect exists in gene silencing that is mediated by DNA methylation. It is reasonable to assume the thresholds are specific for each gene. It is also intriguing to investigate genes that are largely controlled by DNA methylation. These genes are called “L-shaped” genes. We develop a method to determine the DNA methylation threshold and identify a new CIMP of BRCA. In conclusion, we provide a detailed understanding of the relationship between the overdispersion rate and sequencing depth. And we reveal a new bias in RNA-seq and provide a detailed understanding of the relationship between this new bias and the local sequence. Also we develop a powerful method to dichotomize methylation status and consequently we identify a new CIMP of breast cancer with a distinct classification of molecular characteristics and clinical features.