ASU Scholarship Showcase
This growing collection consists of scholarly works authored by ASU-affiliated faculty, staff, and community members, and it contains many open access articles. ASU-affiliated authors are encouraged to Share Your Work in KEEP.
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- Creators: College of Health Solutions
- Creators: Mangone, Marco
Background: 3′untranslated regions (3′UTRs) are poorly understood portions of eukaryotic mRNAs essential for post-transcriptional gene regulation. Sequence elements in 3′UTRs can be target sites for regulatory molecules such as RNA binding proteins and microRNAs (miRNAs), and these interactions can exert significant control on gene networks. However, many such interactions remain uncharacterized due to a lack of high-throughput (HT) tools to study 3′UTR biology. HT cloning efforts such as the human ORFeome exemplify the potential benefits of genomic repositories for studying human disease, especially in relation to the discovery of biomarkers and targets for therapeutic agents. Currently there are no publicly available human 3′UTR libraries. To address this we have prepared the first version of the human 3′UTRome (h3′UTRome v1) library. The h3′UTRome is produced to a single high quality standard using the same recombinational cloning technology used for the human ORFeome, enabling universal operating methods and high throughput experimentation. The library is thoroughly sequenced and annotated with simple online access to information, and made publicly available through gene repositories at low cost to all scientists with minimal restriction.
Results: The first release of the h3′UTRome library comprises 1,461 human 3′UTRs cloned into Gateway® entry vectors, ready for downstream analyses. It contains 3′UTRs for 985 transcription factors, 156 kinases, 171 RNA binding proteins, and 186 other genes involved in gene regulation and in disease. We demonstrate the feasibility of the h3′UTRome library by screening a panel of 87 3′UTRs for targeting by two miRNAs: let-7c, which is implicated in tumorigenesis, and miR-221, which is implicated in atherosclerosis and heart disease. The panel is enriched with genes involved in the RAS signaling pathway, putative novel targets for the two miRNAs, as well as genes implicated in tumorigenesis and heart disease.
Conclusions: The h3′UTRome v1 library is a modular resource that can be utilized for high-throughput screens to identify regulatory interactions between trans-acting factors and 3′UTRs, Importantly, the library can be customized based on the specifications of the researcher, allowing the systematic study of human 3′UTR biology.
Background: Public parks can be an important setting for physical activity promotion, but to increase park use and the activity levels of park users, the crucial attributes related to active park use need to be defined. Not only user characteristics and structural park attributes, but also characteristics of the surrounding neighborhood are important to examine. Furthermore, internationally comparable studies are needed, to find out if similar intervention strategies might be effective worldwide. The main aim of this study was to examine whether the overall number of park visitors and their activity levels depend on study site, neighborhood walkability and neighborhood income.
Methods: Data were collected in 20 parks in Ghent, Belgium and San Diego, USA. Two trained observers systematically coded park characteristics using the Environmental Assessment of Public Recreation Spaces (EAPRS) tool, and park user characteristics using the System for Observing Play and recreation in Communities (SOPARC) tool. Multilevel multiple regression models were conducted in MLwiN 2.25.
Results: In San Diego parks, activity levels of park visitors and number of vigorously active visitors were higher than in Ghent, while the number of visitors walking and the overall number of park visitors were lower. Neighborhood walkability was positively associated with the overall number of visitors, the number of visitors walking, number of sedentary visitors and mean activity levels of visitors. Neighborhood income was positively associated with the overall number of visitors, but negatively with the number of visitors being vigorously active.
Conclusions: Neighborhood characteristics are important to explain park use. Neighborhood walkability-related attributes should be taken into account when promoting the use of existing parks or creating new parks. Because no strong differences were found between parks in high- and low-income neighborhoods, it seems that promoting park use might be a promising strategy to increase physical activity in low-income populations, known to be at higher risk for overweight and obesity.
Background: Aspects of the food environment such as the availability of different types of food stores have recently emerged as key modifiable factors that may contribute to the increased prevalence of obesity. Given that many of these studies have derived their results based on secondary datasets and the relationship of food stores with individual weight outcomes has been reported to vary by store type, it is important to understand the extent to which often-used secondary data correctly classify food stores. We evaluated the classification bias of food stores in Dun & Bradstreet (D&B) and InfoUSA commercial business lists.
Methods: We performed a full census in 274 randomly selected census tracts in the Chicago metropolitan area and collected detailed store attributes inside stores for classification. Store attributes were compared by classification match status and store type. Systematic classification bias by census tract characteristics was assessed in multivariate regression.
Results: D&B had a higher classification match rate than InfoUSA for supermarkets and grocery stores, while InfoUSA was higher for convenience stores. Both lists were more likely to correctly classify large supermarkets, grocery stores, and convenience stores with more cash registers and different types of service counters (supermarkets and grocery stores only). The likelihood of a correct classification match for supermarkets and grocery stores did not vary systemically by tract characteristics whereas convenience stores were more likely to be misclassified in predominately Black tracts.
Conclusion: Researches can rely on classification of food stores in commercial datasets for supermarkets and grocery stores whereas classifications for convenience and specialty food stores are subject to some systematic bias by neighborhood racial/ethnic composition.
Background: Tissue-specific RNA plasticity broadly impacts the development, tissue identity and adaptability of all organisms, but changes in composition, expression levels and its impact on gene regulation in different somatic tissues are largely unknown. Here we developed a new method, polyA-tagging and sequencing (PAT-Seq) to isolate high-quality tissue-specific mRNA from Caenorhabditis elegans intestine, pharynx and body muscle tissues and study changes in their tissue-specific transcriptomes and 3’UTRomes.
Results: We have identified thousands of novel genes and isoforms differentially expressed between these three tissues. The intestine transcriptome is expansive, expressing over 30% of C. elegans mRNAs, while muscle transcriptomes are smaller but contain characteristic unique gene signatures. Active promoter regions in all three tissues reveal both known and novel enriched tissue-specific elements, along with putative transcription factors, suggesting novel tissue-specific modes of transcription initiation. We have precisely mapped approximately 20,000 tissue-specific polyadenylation sites and discovered that about 30% of transcripts in somatic cells use alternative polyadenylation in a tissue-specific manner, with their 3’UTR isoforms significantly enriched with microRNA targets.
Conclusions: For the first time, PAT-Seq allowed us to directly study tissue specific gene expression changes in an in vivo setting and compare these changes between three somatic tissues from the same organism at single-base resolution within the same experiment. We pinpoint precise tissue-specific transcriptome rearrangements and for the first time link tissue-specific alternative polyadenylation to miRNA regulation, suggesting novel and unexplored tissue-specific post-transcriptional regulatory networks in somatic cells.
Background: The field of cancer genomics has rapidly adopted next-generation sequencing (NGS) in order to study and characterize malignant tumors with unprecedented resolution. In particular for cancer, one is often trying to identify somatic mutations--changes specific to a tumor and not within an individual's germline. However, false positive and false negative detections often result from lack of sufficient variant evidence, contamination of the biopsy by stromal tissue, sequencing errors, and the erroneous classification of germline variation as tumor-specific.
Results: We have developed a generalized Bayesian analysis framework for matched tumor/normal samples with the purpose of identifying tumor-specific alterations such as single nucleotide mutations, small insertions/deletions, and structural variation. We describe our methodology, and discuss its application to other types of paired-tissue analysis such as the detection of loss of heterozygosity as well as allelic imbalance. We also demonstrate the high level of sensitivity and specificity in discovering simulated somatic mutations, for various combinations of a) genomic coverage and b) emulated heterogeneity.
Conclusion: We present a Java-based implementation of our methods named Seurat, which is made available for free academic use. We have demonstrated and reported on the discovery of different types of somatic change by applying Seurat to an experimentally-derived cancer dataset using our methods; and have discussed considerations and practices regarding the accurate detection of somatic events in cancer genomes. Seurat is available at https://sites.google.com/site/seuratsomatic.
Background: Opioid peptides, including dynorphin A, besides their analgesic action in the nervous system, exert a broad spectrum of effects on cells of the immune system, including leukocyte migration, degranulation and cytokine production. The mechanisms whereby opioid peptides induce leukocyte responses are poorly understood. The integrin Mac-1 (alpha(M)beta(2), CD11b/CD18) is a multiligand receptor which mediates numerous reactions of neutrophils and monocyte/macrophages during the immune-inflammatory response. Our recent elucidation of the ligand recognition specificity of Mac-1 suggested that dynorphin A and dynorphin B contain Mac-1 recognition motifs and can potentially interact with this receptor.
Results: In this study, we have synthesized the peptide library spanning the sequence of dynorphin AB, containing dynorphin A and B, and showed that the peptides bound recombinant alpha I-M-domain, the ligand binding region of Mac-1. In addition, immobilized dynorphins A and B supported adhesion of the Mac-1-expressing cells. In binding to dynorphins A and B, Mac-1 cooperated with cell surface proteoglycans since both anti-Mac-1 function-blocking reagents and heparin were required to block adhesion. Further focusing on dynorphin A, we showed that its interaction with the alpha I-M-domain was activation independent as both the alpha 7 helix-truncated (active conformation) and helix-extended (nonactive conformation) alpha I-M-domains efficiently bound dynorphin A. Dynorphin A induced a potent migratory response of Mac-1-expressing, but not Mac-1-deficient leukocytes, and enhanced Mac-1-mediated phagocytosis of latex beads by murine IC-21 macrophages.
Conclusions: Together, the results identify dynorphins A and B as novel ligands for Mac-1 and suggest a role for the Dynorphin A-Mac-1 interactions in the induction of nonopiod receptor-dependent effects in leukocytes.
The broad recognition specificity exhibited by integrin αMβ2 (Mac-1, CD11b/CD18) has allowed this adhesion receptor to play innumerable roles in leukocyte biology, yet we know little about how and why αMβ2 binds its multiple ligands. Within αMβ2, the αMI-domain is responsible for integrin’s multiligand binding properties. To identify its recognition motif, we screened peptide libraries spanning sequences of many known protein ligands for αMI-domain binding and also selected the αM I-domain recognition sequences by phage display. Analyses of >1400 binding and nonbinding peptides derived from peptide libraries showed that a key feature of the αMI-domain recognition motif is a small core consisting of basic amino acids flanked by hydrophobic residues. Furthermore, the peptides selected by phage display conformed to a similar pattern. Identification of the recognition motif allowed the construction of an algorithm that reliably predicts the αMI-domain binding sites in the αMβ2 ligands. The recognition specificity of the αMI-domain resembles that of some chaperones, which allows it to bind segments exposed in unfolded proteins. The disclosure of the αMβ2 binding preferences allowed the prediction that cationic host defense peptides, which are strikingly enriched in the αMI-domain recognition motifs, represent a new class of αMβ2 ligands. This prediction has been tested by examining the interaction of αMβ2 with the human cathelicidin peptide LL-37. LL-37 induced a potent αMβ2-dependent cell migratory response and caused activation of αMβ2 on neutrophils. The newly revealed recognition specificity of αMβ2 toward unfolded protein segments and cationic proteins and peptides suggests that αMβ2 may serve as a previously proposed “alarmin” receptor with important roles in innate host defense.
The aim of this article was to study sound source localization by cochlear implant (CI) listeners with low-frequency (LF) acoustic hearing in both the operated ear and in the contralateral ear. Eight CI listeners had symmetrical LF acoustic hearing and 4 had asymmetrical LF acoustic hearing. The effects of two variables were assessed: (i) the symmetry of the LF thresholds in the two ears and (ii) the presence/absence of bilateral acoustic amplification. Stimuli consisted of low-pass, high-pass, and wideband noise bursts presented in the frontal horizontal plane. Localization accuracy was 23° of error for the symmetrical listeners and 76° of error for the asymmetrical listeners. The presence of a unilateral CI used in conjunction with bilateral LF acoustic hearing does not impair sound source localization accuracy, but amplification for acoustic hearing can be detrimental to sound source localization accuracy.