Skip to main content

ASU Scholarship Showcase


This growing collection consists of scholarly works authored by ASU-affiliated faculty, students and community members, and contains many open access articles. ASU-affiliated authors are encouraged to Share Your Work in the ASU Digital Repository.


Contributor
Date Range
2010 2017


Inbreeding in hermaphroditic plants can occur through two different mechanisms: biparental inbreeding, when a plant mates with a related individual, or self-fertilization, when a plant mates with itself. To avoid inbreeding, many hermaphroditic plants have evolved self-incompatibility (SI) systems which prevent or limit self-fertilization. One particular SI system—homomorphic SI—can also reduce biparental inbreeding. Homomorphic SI is found in many angiosperm species, and it is often assumed that the additional benefit of reduced biparental inbreeding may be a factor in the success of this SI system. To test this assumption, we developed a spatially-explicit, individual-based simulation of plant populations that displayed …

Contributors
Furstenau, Tara, Cartwright, Reed, Biodesign Institute, et al.
Created Date
2017-11-24

Mutation is the ultimate source of all genetic variation and is, therefore, central to evolutionary change. Previous work on Paramecium tetraurelia found an unusually low germline base-substitution mutation rate in this ciliate. Here, we tested the generality of this result among ciliates using Tetrahymena thermophila. We sequenced the genomes of 10 lines of T. thermophila that had each undergone approximately 1,000 generations of mutation accumulation (MA). We applied an existing mutation-calling pipeline and developed a new probabilistic mutation detection approach that directly models the design of an MA experiment and accommodates the noise introduced by mismapped reads. Our probabilistic mutation-calling …

Contributors
Long, Hongan, Winter, David, Chang, Allan Y.-C., et al.
Created Date
2016-09-15

Human milk contains essential micronutrients for growth and development during early life. Environmental pollutants, such as potentially toxic metals, can also be transferred to the infant through human milk. These elements have been well-studied, but changing diets and environments and advances in laboratory technology require re-examining these elements in a variety of settings. The aim of this study was to characterize the concentrations of essential and toxic metals in human milk from four diverse populations. Human milk samples (n = 70) were collected in Argentina (n = 21), Namibia (n = 6), Poland (n = 23), and the United States …

Contributors
Klein, Laura D., Breakey, Alicia A., Scelza, Brooke, et al.
Created Date
2017-08-17

Active learning in college classes and participation in the workforce frequently hinge on small group work. However, group dynamics vary, ranging from equitable collaboration to dysfunctional groups dominated by one individual. To explore how group dynamics impact student learning, we asked students in a large-enrollment university biology class to self-report their experience during in-class group work. Specifically, we asked students whether there was a friend in their group, whether they were comfortable in their group, and whether someone dominated their group. Surveys were administered after students participated in two different types of intentionally constructed group activities: 1) a loosely-structured activity …

Contributors
Theobald, Elli J., Eddy, Sarah L., Grunspan, Daniel, et al.
Created Date
2017-07-20

Background In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. Methods A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using …

Contributors
Boukari, Wardatou, Alcala-Briseno, Ricardo I., Kraberger, Simona Joop, et al.
Created Date
2017-07-28

Bacteriophages are ideal candidates for pathogen biocontrol to mitigate outbreaks of prevalent foodborne pathogens, such as Escherichia coli. We identified a bacteriophage (AAPEc6) from wastewater that infects E. coli O45:H10. The AAPEc6 genome sequence shares 93% identity (with 92% coverage) to enterobacterial phage K1E (Sp6likevirus) in the Autographivirinae subfamily (Podoviridae).

Contributors
Nonis, Judith, Premaratne, Aruni, Billington, Craig, et al.
Created Date
2017-08-03

STEM classrooms (science, technology, engineering, and mathematics) in postsecondary education are rapidly improved by the proper use of active learning techniques. These techniques occupy a descriptive spectrum that transcends passive teaching toward active, constructive, and, finally, interactive methods. While aspects of this framework have been examined, no large-scale or actual classroom-based data exist to inform postsecondary education STEM instructors about possible learning gains. We describe the results of a quasi-experimental study to test the apex of the ICAP framework (interactive, constructive, active, and passive) in this ecological classroom environment. Students in interactive classrooms demonstrate significantly improved learning outcomes relative to …

Contributors
Wiggins, Benjamin L., Eddy, Sarah L., Grunspan, Daniel, et al.
Created Date
2017-04-01

Social monogamy at its most basic is a group structure in which two adults form a unit and share a territory. However, many socially monogamous pairs display attachment relationships known as pair bonds, in which there is a mutual preference for the partner and distress upon separation. The neural and hormonal basis of this response to separation from the adult pair mate is under-studied. In this project, we examined this response in male titi monkeys (Callicebus cupreus), a socially monogamous New World primate. Males underwent a baseline scan, a short separation (48 h), a long separation (approximately 2 weeks), a …

Contributors
Hinde, Katie, Muth, Chelsea, Maninger, Nicole, et al.
Created Date
2016-11-14

With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2–2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family. Genomoviruses display ∼47% sequence diversity, which is very similar to that within the well-established and extensively studied family Geminiviridae (46% diversity). Based on our analysis, we …

Contributors
Varsani, Arvind, Krupovic, Mart, Biodesign Institute, et al.
Created Date
2017-02-02

The most common evolutionary events at the molecular level are single-base substitutions, as well as insertions and deletions (indels) of short DNA segments. A large body of research has been devoted to develop probabilistic substitution models and to infer their parameters using likelihood and Bayesian approaches. In contrast, relatively little has been done to model indel dynamics, probably due to the difficulty in writing explicit likelihood functions. Here, we contribute to the effort of modeling indel dynamics by presenting SpartaABC, an approximate Bayesian computation (ABC) approach to infer indel parameters from sequence data (either aligned or unaligned). SpartaABC circumvents the …

Contributors
Levy Karin, Eli, Shkedy, Dafna, Ashkenazy, Haim, et al.
Created Date
2017-05-01