ASU Scholarship Showcase

Biomarkers encompass a wide range of different measurable indicators, representing a tangible link to physiological changes occurring within the body. Accessibility, sensitivity, and specificity are significant factors in biomarker suitability. New biomarkers continue to be discovered, and questions over appropriate selection and assessment of their usefulness remain. If traditional markers of inflammation are not sufficiently robust in their specificity, then perhaps alternative means of detection may provide more information. Epigenetic drift (epigenetic modifications as they occur as a direct function with age), and its ancillary elements, including platelets, secreted microvesicles (MVs), and microRNA (miRNA), may hold enormous predictive potential. The majority of epigenetic drift observed in blood is independent of variations in blood cell composition, addressing concerns affecting traditional blood-based biomarker efficacy. MVs are found in plasma and other biological fluids in healthy individuals. Altered MV/miRNA profiles may also be found in individuals with various diseases. Platelets are also highly reflective of physiological and lifestyle changes, making them extremely sensitive biomarkers of human health. Platelets release increased levels of MVs in response to various stimuli and under a plethora of disease states, which demonstrate a functional effect on other cell types.

In Ritual and Religion in the Making of Humanity, Roy Rappaport misses an opportunity to more tightly theorize the synergistic relationship between concepts of the divine, the psyches of ritual participants, and the adaptive dynamics of religious sociality. This paper proposes such a theory by drawing on implicit features of Rappaport’s account, fulfilling his goal of a “cybernetics of the holy.” I argue that concepts of the divine, when made authoritative for participants through ritual, have three important effects: they invite intense and meaningful reconstructions of personal identity according to paradigmatic examples; they act as a form of encoded social memory by organizing human relationship according to a “spiritual map”; and they provide the cognitive framework that make religious community organization robust, adaptive, and reproductive. We can characterize divine concepts as “specified absences” that ground each of these effects and link them together in a mutually-reinforcing set.

The conscientious are morally conflicted when their moral dilemmas or incommensurabilities, real or apparent, have not been resolved. But such doublemindedness need not lead to ethical disintegration or moral insensitivity. For one may develop the moral virtue of doublemindedness, the settled power to deliberate and act well while morally conflicted. Such action will be accompanied by both moral loss (perhaps 'dirty hands') and ethical gain (salubrious agental stability). In explaining the virtue's moral psychology I show, among other things, its consistency with wholeheartedness and the unity of the virtues. To broaden its claim to recognition, I show the virtue's consistency with diverse models of practical reason. In conclusion, Michael Walzer's interpretation of Hamlet's attitude toward Gertrude exemplifies this virtue in a fragmentary but nonetheless praiseworthy form.

Rice is an essential crop in Ghana. Several aspects of rice have been studied to increase its production; however, the environmental aspects, including impact on climate change, have not been studied well. There is therefore a gap in knowledge, and hence the need for continuous research. By accessing academic portals, such as Springer Open, InTech Open, Elsevier, and the Kwame Nkrumah University of Science and Technology’s offline campus library, 61 academic publications including peer reviewed journals, books, working papers, reports, etc. were critically reviewed. It was found that there is a lack of data on how paddy rice production systems affect greenhouse gas (GHG) emissions, particularly emissions estimation, geographical location, and crops. Regarding GHG emission estimation, the review identified the use of emission factors calibrated using temperate conditions which do not suit tropical conditions. On location, most research on rice GHG emissions have been carried out in Asia with little input from Africa. In regard to crops, there is paucity of in-situ emissions data from paddy fields in Ghana. Drawing on the review, a conceptual framework is developed using Ghana as reference point to guide the discussion on fertilizer application, water management rice cultivars, and soil for future development of adaptation strategies for rice emission reduction.

Background: Lizards are evolutionarily the most closely related vertebrates to humans that can lose and regrow an entire appendage. Regeneration in lizards involves differential expression of hundreds of genes that regulate wound healing, musculoskeletal development, hormonal response, and embryonic morphogenesis. While microRNAs are able to regulate large groups of genes, their role in lizard regeneration has not been investigated.

Results: MicroRNA sequencing of green anole lizard (Anolis carolinensis) regenerating tail and associated tissues revealed 350 putative novel and 196 known microRNA precursors. Eleven microRNAs were differentially expressed between the regenerating tail tip and base during maximum outgrowth (25 days post autotomy), including miR-133a, miR-133b, and miR-206, which have been reported to regulate regeneration and stem cell proliferation in other model systems. Three putative novel differentially expressed microRNAs were identified in the regenerating tail tip.

Conclusions: Differentially expressed microRNAs were identified in the regenerating lizard tail, including known regulators of stem cell proliferation. The identification of 3 putative novel microRNAs suggests that regulatory networks, either conserved in vertebrates and previously uncharacterized or specific to lizards, are involved in regeneration. These findings suggest that differential regulation of microRNAs may play a role in coordinating the timing and expression of hundreds of genes involved in regeneration.

MicroRNAs (miRNAs) regulate gene output by targeting degenerate elements in mRNAs and have undergone drastic expansions in higher metazoan genomes. The evolutionary advantage of maintaining copies of highly similar miRNAs is not well understood, nor is it clear what unique functions, if any, miRNA family members possess. Here, we study evolutionary patterns of metazoan miRNAs, focusing on the targeting preferences of the let-7 and miR-10 families. These studies reveal hotspots for sequence evolution with implications for targeting and secondary structure. High-throughput screening for functional targets reveals that each miRNA represses sites with distinct features and regulates a large number of genes with cooperative function in regulatory networks. Unexpectedly, given the high degree of similarity, single-nucleotide changes grant miRNA family members with distinct targeting preferences. Together, our data suggest complex functional relationships among miRNA duplications, novel expression patterns, sequence change, and the acquisition of new targets.

mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3′untranslated region (3′UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3′UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3′UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis.

Foodways have been a component of archaeological research for decades. However, cooking and food preparation, as specific acts that could reveal social information about life beyond the kitchen, only became a focus of archaeological inquiry more recently. A review of the literature on cooking and food preparation reveals a shift from previous studies on subsistence strategies, consumption, and feasting. The new research is different because of the social questions that are asked, the change in focus to preparation and production rather than consumption, and the interest in highlighting marginalized people and their daily experiences. The theoretical perspectives the literature addresses revolve around practice, agency, and gender. As a result, this new focus of archaeological research on cooking and preparing food is grounded in anthropology.

Scholarly communication is at an unprecedented turning point created in part by the increasing saliency of data stewardship and data sharing. Formal data management plans represent a new emphasis in research, enabling access to data at higher volumes and more quickly, and the potential for replication and augmentation of existing research. Data sharing has recently transformed the practice, scope, content, and applicability of research in several disciplines, in particular in relation to spatially specific data. This lends exciting potentiality, but the most effective ways in which to implement such changes, particularly for disciplines involving human subjects and other sensitive information, demand consideration. Data management plans, stewardship, and sharing, impart distinctive technical, sociological, and ethical challenges that remain to be adequately identified and remedied. Here, we consider these and propose potential solutions for their amelioration.

MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene output at the post-transcriptional level by targeting degenerate elements primarily in 3′untranslated regions (3′UTRs) of mRNAs. Individual miRNAs can regulate networks of hundreds of genes, yet for the majority of miRNAs few, if any, targets are known. Misexpression of miRNAs is also a major contributor to cancer progression, thus there is a critical need to validate miRNA targets in high-throughput to understand miRNAs' contribution to tumorigenesis. Here we introduce a novel high-throughput assay to detect miRNA targets in 3′UTRs, called Luminescent Identification of Functional Elements in 3′UTRs (3′LIFE). We demonstrate the feasibility of 3′LIFE using a data set of 275 human 3′UTRs and two cancer-relevant miRNAs, let-7c and miR-10b, and compare our results to alternative methods to detect miRNA targets throughout the genome. We identify a large number of novel gene targets for these miRNAs, with only 32% of hits being bioinformatically predicted and 27% directed by non-canonical interactions. Functional analysis of target genes reveals consistent roles for each miRNA as either a tumor suppressor (let-7c) or oncogenic miRNA (miR-10b), and preferentially target multiple genes within regulatory networks, suggesting 3′LIFE is a rapid and sensitive method to detect miRNA targets in high-throughput.