Matching Items (112)
Description
Background: Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer deaths in females worldwide, accounting for 23% of all new cancer cases and 14% of all total cancer deaths in 2008. Five tumor-normal pairs of primary breast epithelial cells were treated for infinite proliferation by using a ROCK inhibitor and mouse feeder cells. Methods: Raw paired-end, 100x coverage RNA-Seq data was aligned to the Human Reference Genome Version 19 using BWA and Tophat. Gene differential expression analysis was completed using Cufflinks and Cuffdiff. Interactive Genome Viewer was used for data visualization. Results: 15 genes were found to be down-regulated by at least one log-fold change in 4/5 of tumor samples. 75 genes were found to be down-regulated in 3/5 of our tumor samples by at least one log-fold change. 11 genes were found to be up-regulated in 4/5 of our tumor samples, and 68 genes were identified to be up-regulated in 3/5 of the tumor samples by at least one-fold change. Conclusion: Expression changes in genes such as AZGP1, AGER, ALG11, and S1007 suggest a disruption in the glycosylation pathway. No correlation was found between Cufflink's Her2 gene-expression and DAKO score classification.
ContributorsHernandez, Fernando (Author) / Anderson, Karen (Thesis director) / Mangone, Marco (Committee member) / Park, Jin (Committee member) / Barrett, The Honors College (Contributor) / Department of Information Systems (Contributor)
Created2013-05
Description
miRNAs are short non-coding regulatory RNAs that have an important roles in a wide range of biological processes. Dysfunction of miRNA regulation has also been shown to occur in diseases such as cancer. Despite the widespread influence of miRNAs in these contexts, the vast majority of miRNA targets are poorly characterized. The aim of this research project was to gain a better understating of miRNA targeting by using the model organism C. elegans. In order to do this I adapted a novel high-throughput assay to detect miRNA targets for use with the C. elegans 3`UTRome. As a proof of principle I performed this assay on 96 C. elegans 3`UTRs using high-throughput techniques. The results revealed miRNA interactions with two predicted 3`UTR targets for the miRNA lin-4 and ten unpredicted targets. The results also corroborated previous findings that certain worm miRNAs require special modifications to be expressed in human cells.
ContributorsKotagama, Kasuen Indrajith Bandara (Author) / Mangone, Marco (Thesis director) / Anderson, Karen (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2013-12
Description
Alternative polyadenylation (APA) is the biological mechanism in which the same gene can have multiple 3'untranslated region (3'UTR) isoforms due to the presence of multiple polyadenylation signal (PAS) elements within the pre mRNAs. Because APA produces mRNA transcripts that have different 3'UTR isoforms, certain transcripts may be subject to post-transcriptional regulation by regulatory non-coding RNAs, such as microRNAs or RNA binding proteins defects of which have been implicated in diseases such as cancer. Despite the increasing level of information, functional understanding of the molecular mechanisms involved in transcription is still poorly understood, nor is it clear why APA is necessary at a cell or tissue-specific level. To address these questions I wanted to develop a set of sensor strain plasmids capable of detecting cleavage and polyadenylation in vivo, inject the complete sensor strain plasmid into C. elegans and prepare stable transgenic lines, and perform proof-of-principle RNAi feeding experiments targeting genes associated with the cleavage and polyadenylation complex machinery. I demonstrated that it was possible to create a plasmid capable of detecting cleavage and polyadenylation in C. elegans; however, issues arose during the RNAi assays indicating the sensor strain plasmid was not sensitive enough to the RNAi to effectively detect in the worms. Once the problems involved with sensitivity and variability in the RNAi effects are resolved, the plasmid would be able to better address questions regarding the functional understanding of molecular mechanisms involved in transcription termination.
ContributorsWilky, Henry Patrick (Author) / Mangone, Marco (Thesis director) / Newbern, Jason (Committee member) / Blazie, Stephen (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
We, a team of students and faculty in the life sciences at Arizona State University (ASU), currently teach an Introduction to Biology course in a Level 5, or maximum-security unit with the support of the Arizona Department of Corrections and the Prison Education Program at ASU. This course aims to enhance current programs at the unit by offering inmates an opportunity to practice literacy and math skills, while also providing exposure to a new academic field (science, and specifically biology). Numerous studies, including a 2005 study from the Arizona Department of Corrections (ADC), have found that vocational programs, including prison education programs, reduce recidivism rates (ADC 2005, Esperian 2010, Jancic 1988, Steurer et al. 2001, Ubic 2002) and may provide additional benefits such as engagement with a world outside the justice system (Duguid 1992), the opportunity for inmates to revise personal patterns of rejecting education that they may regret, and the ability of inmate parents to deliberately set a good example for their children (Hall and Killacky 2008). Teaching in a maximum security prison unit poses special challenges, which include a prohibition on most outside materials (except paper), severe restrictions on student-teacher and student-student interactions, and the inability to perform any lab exercises except limited computer simulations. Lack of literature discussing theoretical and practical aspects of teaching science in such environment has prompted us to conduct an ongoing study to generate notes and recommendations from this class through the use of surveys, academic evaluation of students' work and ongoing feedback from both teachers and students to inform teaching practices in future science classes in high-security prison units.
ContributorsLarson, Anika Jade (Author) / Mor, Tsafrir (Thesis director) / Brownell, Sara (Committee member) / Lockard, Joe (Committee member) / Barrett, The Honors College (Contributor) / School of Politics and Global Studies (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
The WalkIT Study is a mobile health study examining the efficacy of a four month text message-based intervention for increasing physical activity among 96 overweight adults. The purpose of this thesis is to examine the potency of the different types of motivational prompt-to-action text messages used in the WalkIT Study for increasing steps per day by examining the individual messages, creating qualitative themes and comparing themed groups, and evaluating the interaction between demographic subgroups and themed groups. A total of nine themes was created. The results found that Message 13, “It doesn't matter how old you are – it's never too early or too late to become physically active so start today; only then will you start to see results!”, had the highest median step count (7129 steps) and Message 71, “It's ok if you can't reach your goal today. Just push yourself more tomorrow.”, had the lowest median step count (5054 steps). For themes, the highest median step count (6640 steps) was found in Theme 6, Challenges, and the lowest median step count (5450 steps) was found in Theme 9, Unconditional Feedback. Theme 6 (Challenges) had the highest median step count for females, Theme 7 (Everyday Tips) had the highest median step count for males, Theme 4 (Nutrition) had the highest median step count for the 18-42 group, Theme 6 (Challenges) had the highest median step count for the 43-61 group, and Theme 9 (Unconditional Feedback) had the lowest median step count for both genders and both age groups. The results suggest the usefulness of analyzing the effectiveness of individual motivational text messages, themes, and the interaction between demographic groups and themes in physical activity interventions.
ContributorsBhuiyan, Nishat Anjum (Author) / Adams, Marc (Thesis director) / Ainsworth, Barbara (Committee member) / Barrett, The Honors College (Contributor) / School of Nutrition and Health Promotion (Contributor)
Created2015-05
Description
The SARS-CoV-2 (Covid-19) virus has had severe impacts on college students' ways of life. To examine how students were coping and perceiving the Covid-19 pandemic, a secondary analysis of an online survey across the three Arizona public universities investigated students’ knowledge about Covid-19, engagement with preventive strategies, pandemic preparedness and gauged their risk perception. Results from our analysis indicate that the students were knowledgeable about Covid-19 and were changing their habits and engaging with preventive measures. Results further suggest that students were prepared for the pandemic in terms of resources and were exhibiting high-risk perceptions. The data also revealed that students who were being cautious and engaging with preventive behaviors had a higher risk-perception than individuals who were not. As for individuals who were prepared for the pandemic in terms of supplies, their risk perception was similar to those who did not have supplies. Individuals who were prepared and capable of providing a single caretaker to tend to their sick household members and isolate them in a separate room had a higher risk perception than those who could not. These results can help describe how college students will react to a future significant event, what resources students may be in need of, and how universities can take additional steps to keep their students safe and healthy. The results from this study and recommendations will provide for a stronger and more understanding campus community during times of distress and can improve upon already established university protocols for health crises and even natural disasters.
ContributorsNaqvi, Avina Itrat (Co-author) / Shaikh, Sara (Co-author) / Jehn, Megan (Thesis director) / Adams, Marc (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution & Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
The SARS-CoV-2 (Covid-19) virus has had severe impacts on college students' ways of life. To examine how students were coping and perceiving the Covid-19 pandemic, a secondary analysis of an online survey across the three Arizona public universities investigated students’ knowledge about Covid-19, engagement with preventive strategies, pandemic preparedness and gauged their risk-perception. Results from our analysis indicate that the students were knowledgeable about Covid-19 and were changing their habits and engaging with preventive measures. Results further suggest that students were prepared for the pandemic in terms of resources and were exhibiting high-risk perceptions. The data also revealed that students who were being cautious and engaging with preventive behaviors had a higher risk-perception than individuals who were not. As for individuals who were prepared for the pandemic in terms of supplies, their risk perception was similar to those who did not have supplies. Individuals who were prepared and capable of providing a single caretaker to tend to their sick household members and isolate them in a separate room had a higher risk perception than those who could not. These results can help describe how college students will react to a future significant event, what resources students may be in need of, and how universities can take additional steps to keep their students safe and healthy. The results from this study and recommendations will provide for a stronger and more understanding campus community during times of distress and can improve upon already established university protocols for health crises and even natural disasters.
ContributorsShaikh, Sara (Co-author) / Naqvi, Avina (Co-author) / Jehn, Megan (Thesis director) / Adams, Marc (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution & Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Background: National and international strategies to increase physical activity emphasize environmental and policy changes that can have widespread and long-lasting impact. Evidence from multiple countries using comparable methods is required to strengthen the evidence base for such initiatives. Because some environment and policy changes could have generalizable effects and others may depend on each country's context, only international studies using comparable methods can identify the relevant differences. Methods: Currently 12 countries are participating in the International Physical Activity and the Environment Network (IPEN) study. The IPEN Adult study design involves recruiting adult participants from neighborhoods with wide variations in environmental walkability attributes and socioeconomic status (SES). Results: Eleven of twelve countries are providing accelerometer data and 11 are providing GIS data. Current projections indicate that 14,119 participants will provide survey data on built environments and physical activity and 7145 are likely to provide objective data on both the independent and dependent variables. Though studies are highly comparable, some adaptations are required based on the local context. Conclusions: This study was designed to inform evidence-based international and country-specific physical activity policies and interventions to help prevent obesity and other chronic diseases that are high in developed countries and growing rapidly in developing countries.
ContributorsKerr, Jacqueline (Author) / Sallis, James F. (Author) / Owen, Neville (Author) / De Bourdeaudhuij, Ilse (Author) / Cerin, Ester (Author) / Sugiyama, Takemi (Author) / Reis, Rodrigo (Author) / Sarmiento, Olga (Author) / Froemel, Karel (Author) / Mitas, Josef (Author) / Troelsen, Jens (Author) / Christiansen, Lars Breum (Author) / Macfarlane, Duncan (Author) / Salvo, Deborah (Author) / Schofield, Grant (Author) / Badland, Hannah (Author) / Guillen-Grima, Francisco (Author) / Aguinaga-Ontoso, Ines (Author) / Davey, Rachel (Author) / Bauman, Adrian (Author) / Saelens, Brian (Author) / Riddoch, Chris (Author) / Ainsworth, Barbara (Author) / Pratt, Michael (Author) / Schmidt, Tom (Author) / Frank, Lawrence (Author) / Adams, Marc (Author) / Conway, Terry (Author) / Cain, Kelli (Author) / Van Dyck, Delfien (Author) / Bracy, Nicole (Author) / College of Health Solutions (Contributor) / School of Nutrition and Health Promotion (Contributor)
Created2013
Description
This thesis contains three chapters, all of which involve using culturally inclusive education to explore the experiences of religious undergraduate biology students. The first chapter is an essay entitled "Toward Culturally Inclusive Undergraduate Biology Education," which describes a literature review performed with the aim of characterizing the landscape of cultural competence and related terms for biology educators and biology education researchers. This chapter highlights the use of 16 different terms related to cultural competence and presents these terms, their definitions, and highlights their similarities and differences. This chapter also identifies gaps in the cultural competence literature, and presents a set of recommendations to support better culturally inclusive interventions in undergraduate science education. The second chapter, entitled "Different Evolution Acceptance Instruments Lead to Different Research Findings," describes a study in which the source of 30 years of conflicting research on the relationship between evolution acceptance and evolution understanding was determined. The results of this study showed that different instruments used to measure evolution acceptance sometimes lead to different research results and conclusions. The final chapter, entitled "Believing That Evolution is Atheistic is Associated with Poor Evolution Education Outcomes Among Religious College Students," describes a study characterizing definitions of evolution that religious undergraduate biology students may hold, and examines the impact that those definitions of evolution have on multiple outcome variables. In this study, we found that among the most religious students, those who thought evolution is atheistic were less accepting of evolution, less comfortable learning evolution, and perceived greater conflict between their personal religious beliefs and evolution than those who thought evolution is agnostic.
ContributorsDunlop, Hayley Marie (Author) / Brownell, Sara (Thesis director) / Collins, James (Committee member) / Barnes, M. Elizabeth (Committee member) / School of Human Evolution & Social Change (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
In eukaryotes, most messenger RNA precursors (pre-mRNA) undergo extensive processing, leading to the cleavage of the transcript followed by the addition of a poly(A) tail. This process is executed by a large complex known as the Cleavage and Polyadenylation Complex (CPC). Its central subcomplex, the Cleavage and Polyadenylation Specificity Factor (CPSF) complex is responsible for recognizing a short hexameric element AAUAAA located at the 3’end in the nascent mRNA molecule and catalyzing the pre-mRNA cleavage. In the round nematode C. elegans, the cleavage reaction is executed by a subunit of this complex named CPSF3, a highly conserved RNA endonuclease. While the crystal structure of its human ortholog CPSF73 has been recently identified, we still do not understand the molecular mechanisms and sequence specificity used by this protein to induce cleavage, which in turn would help to understand how this process is executed in detail. Additionally, we do not understand in additional factors are needed for this process. In order to address these issues, we performed a comparative analysis of the CPSF3 protein in higher eukaryotes to identify conserved functional domains. The overall percent identities for members of the CPSF complex range from 33.68% to 56.49%, suggesting that the human and C. elegans orthologs retain a high level of conservation. CPSF73 is the protein with the overall highest percent identity of the CPSF complex, with its active site-containing domain possessing 74.60% identity with CPSF3. Additionally, we gathered and expressed using a bacterial expression system CPSF3 and a mutant, which is unable to perform the cleavage reaction, and developed an in vitro cleavage assay to test whether CPSF3 activity is necessary and sufficient to induce nascent mRNA cleavage. This project establishes tools to better understand how CPSF3 functions within the CPC and sheds light on the biology surrounding the transcription process as a whole.
ContributorsGallante, Christina (Author) / Mangone, Marco (Thesis director) / Sharma, Shalini (Committee member) / Hrach, Heather (Committee member) / School of Life Sciences (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05