Using the Stroop Effect to Examine the Effect of Words to Which Humans are Sensitive on Cognitive Conflict

The purpose of experiment one was to test the effects of drink consumed (glucose, artificial sweetener, or water) and stimuli (food or non-food) on cognitive conflict. Glucose has been known to better cognitive functioning, and preoccupation with food worsens cognitive functioning on a food-related task. We hypothesized that participants who received glucose and non-food stimuli will perform best on the cognitive tests, and participants who received aspartame and food-stimuli will perform worst on the cognitive tests. Participants were each given an 8 oz. drink to consume, shown six minutes of stimuli, performed an “X-word” Stroop test, shown six more minutes of stimuli, and finally, performed a “Food-word” Stroop test. There was a significant effect of stimulus shown on reaction time. The purpose of experiment two was to test the effects of stimuli, emotionally positive or negative, on cognitive conflict. The lateral prefrontal cortex shows a crossover between emotion and cognition, predicting behavioral performance. We hypothesized that participants who are shown positive emotion-evoking pictures will have a larger Stroop effect on a “Positive-word” Stroop and participants who are shown negative emotion-evoking pictures will have a larger Stroop effect on a “Negative-word” Stroop. Participants were shown four minutes of assigned stimuli, given a basic “X-word” Stroop test, shown four more minutes of stimuli, given either a “Positive-word” or “Negative-word” Stroop test, shown four more minutes of stimuli, and given the final Stroop test they had not yet taken. No significant results regarding a difference between positive and negative stimuli were found

Repertoire of microRNAs in Epithelial Ovarian Cancer as Determined by Next Generation Sequencing of Small RNA cDNA Libraries

MicroRNAs (miRNAs) are small regulatory RNAs that are implicated in cancer pathogenesis and have recently shown promise as blood-based biomarkers for cancer detection. Epithelial ovarian cancer is a deadly disease for which improved outcomes could be achieved by successful early detection and enhanced understanding of molecular pathogenesis that leads to improved therapies. A critical step toward these goals is to establish a comprehensive view of miRNAs expressed in epithelial ovarian cancer tissues as well as in normal ovarian surface epithelial cells.We used massively parallel pyrosequencing (i.e., "454 sequencing") to discover and characterize novel and known miRNAs expressed in primary cultures of normal human ovarian surface epithelium (HOSE) and in tissue from three of the most common histotypes of ovarian cancer. Deep sequencing of small RNA cDNA libraries derived from normal HOSE and ovarian cancer samples yielded a total of 738,710 high-quality sequence reads, generating comprehensive digital profiles of miRNA expression. Expression profiles for 498 previously annotated miRNAs were delineated and we discovered six novel miRNAs and 39 candidate miRNAs. A set of 124 miRNAs was differentially expressed in normal versus cancer samples and 38 miRNAs were differentially expressed across histologic subtypes of ovarian cancer. Taqman qRT-PCR performed on a subset of miRNAs confirmed results of the sequencing-based study.This report expands the body of miRNAs known to be expressed in epithelial ovarian cancer and provides a useful resource for future studies of the role of miRNAs in the pathogenesis and early detection of ovarian cancer

DU Undergraduate Showcase: Research, Scholarship, and Creative Works

DU Undergraduate Showcase: Research, Scholarship, and Creative Work

Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity

Modification of microRNA sequences by the 3′ addition of nucleotides to generate so-called “isomiRs” adds to the complexity of miRNA function, with recent reports showing that 3′ modifications can influence miRNA stability and efficiency of target repression. Here, we show that the 3′ modification of miRNAs is a physiological and common post-transcriptional event that shows selectivity for specific miRNAs and is observed across species ranging from C. elegans to human. The modifications result predominantly from adenylation and uridylation and are seen across tissue types, disease states, and developmental stages. To quantitatively profile 3′ nucleotide additions, we developed and validated a novel assay based on NanoString Technologies' nCounter platform. For certain miRNAs, the frequency of modification was altered by processes such as cell differentiation, indicating that 3′ modification is a biologically regulated process. To investigate the mechanism of 3′ nucleotide additions, we used RNA interference to screen a panel of eight candidate miRNA nucleotidyl transferases for 3′ miRNA modification activity in human cells. Multiple enzymes, including MTPAP, PAPD4, PAPD5, ZCCHC6, ZCCHC11, and TUT1, were found to govern 3′ nucleotide addition to miRNAs in a miRNA-specific manner. Three of these enzymes–MTPAP, ZCCHC6, and TUT1–have not previously been known to modify miRNAs. Collectively, our results indicate that 3′ modification observed in next-generation small RNA sequencing data is a biologically relevant process, and identify enzymatic mechanisms that may lead to new approaches for modulating miRNA activity in vivo

MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries

We used massively parallel pyrosequencing to discover and characterize microRNAs (miRNAs) expressed in human embryonic stem cells (hESC). Sequencing of small RNA cDNA libraries derived from undifferentiated hESC and from isogenic differentiating cultures yielded a total of 425,505 high-quality sequence reads. A custom data analysis pipeline delineated expression profiles for 191 previously annotated miRNAs, 13 novel miRNAs and 56 candidate miRNAs. Further characterization of a subset of the novel miRNAs in Dicer-knockdown hESC demonstrated Dicer-dependent expression, providing additional validation of our results. A set of 14 miRNAs (9 known and 5 novel) were noted to be expressed in undifferentiated hESC and then strongly down-regulated with differentiation. Functional annotation analysis of predicted targets of these miRNAs and comparison to a null model using non-hESC-expressed miRNAs identified statistically enriched functional categories, including chromatin remodeling and lineage-specific differentiation annotations. Finally, integration of our data with genome-wide chromatin immunoprecipitation data on OCT4, SOX2 and NANOG binding sites implicates these transcription factors in the regulation of nine of the novel/candidate miRNAs identified here. Comparison of our results to those of recent deep sequencing studies in mouse ESC and human ESC show that most of the novel/candidate miRNAs found here were not identified in the other studies. The data indicate that hESC express a larger complement of miRNAs than previously appreciated, and provide a resource for further studies of miRNA regulation of hESC physiology