ASU Scholarship Showcase

Through the mathematical study of two models we quantify some of the theories of co-development and co-existence of focused groups in the social sciences. This work attempts to develop the mathematical framework behind the social sciences of community formation. By using well developed theories and concepts from ecology and epidemiology we hope to extend the theoretical framework of organizing and self-organizing social groups and communities, including terrorist groups. The main goal of our work is to gain insight into the role of recruitment and retention in the formation and survival of social organizations. Understanding the underlining mechanisms of the spread of ideologies under competition is a fundamental component of this work. Here contacts between core and non-core individuals extend beyond its physical meaning to include indirect interaction and spread of ideas through phone conversations, emails, media sources and other similar mean.

This work focuses on the dynamics of formation of interest groups, either ideological, economical or ecological and thus we explore the questions such as, how do interest groups initiate and co-develop by interacting within a common environment and how do they sustain themselves? Our results show that building and maintaining the core group is essential for the existence and survival of an extreme ideology. Our research also indicates that in the absence of competitive ability (i.e., ability to take from the other core group or share prospective members) the social organization or group that is more committed to its group ideology and manages to strike the right balance between investment in recruitment and retention will prevail. Thus under no cross interaction between two social groups a single trade-off (of these efforts) can support only a single organization. The more efforts that an organization implements to recruit and retain its members the more effective it will be in transmitting the ideology to other vulnerable individuals and thus converting them to believers.

Background: Microalgae are promising feedstock for production of lipids, sugars, bioactive compounds and in particular biofuels, yet development of sensitive and reliable phylotyping strategies for microalgae has been hindered by the paucity of phylogenetically closely-related finished genomes.

Results: Using the oleaginous eustigmatophyte Nannochloropsis as a model, we assessed current intragenus phylotyping strategies by producing the complete plastid (pt) and mitochondrial (mt) genomes of seven strains from six Nannochloropsis species. Genes on the pt and mt genomes have been highly conserved in content, size and order, strongly negatively selected and evolving at a rate 33% and 66% of nuclear genomes respectively. Pt genome diversification was driven by asymmetric evolution of two inverted repeats (IRa and IRb): psbV and clpC in IRb are highly conserved whereas their counterparts in IRa exhibit three lineage-associated types of structural polymorphism via duplication or disruption of whole or partial genes. In the mt genomes, however, a single evolution hotspot varies in copy-number of a 3.5 Kb-long, cox1-harboring repeat. The organelle markers (e.g., cox1, cox2, psbA, rbcL and rrn16_mt) and nuclear markers (e.g., ITS2 and 18S) that are widely used for phylogenetic analysis obtained a divergent phylogeny for the seven strains, largely due to low SNP density. A new strategy for intragenus phylotyping of microalgae was thus proposed that includes (i) twelve sequence markers that are of higher sensitivity than ITS2 for interspecies phylogenetic analysis, (ii) multi-locus sequence typing based on rps11_mt-nad4, rps3_mt and cox2-rrn16_mt for intraspecies phylogenetic reconstruction and (iii) several SSR loci for identification of strains within a given species.

Conclusion: This first comprehensive dataset of organelle genomes for a microalgal genus enabled exhaustive assessment and searches of all candidate phylogenetic markers on the organelle genomes. A new strategy for intragenus phylotyping of microalgae was proposed which might be generally applicable to other microalgal genera and should serve as a valuable tool in the expanding algal biotechnology industry.

MALDI-TOF MS has been shown capable of rapidly and accurately characterizing bacteria. Highly reproducible spectra are required to ensure reliable characterization. Prior work has shown that spectra acquired manually can have higher reproducibility than those acquired automatically. For this reason, the objective of this study was to optimize automated data acquisition to yield spectra with reproducibility comparable to those acquired manually. Fractional factorial design was used to design experiments for robust optimization of settings, in which values of five parameters (peak selection mass range, signal to noise ratio (S:N), base peak intensity, minimum resolution and number of shots summed) commonly used to facilitate automated data acquisition were varied. Pseudomonas aeruginosa was used as a model bacterium in the designed experiments, and spectra were acquired using an intact cell sample preparation method. Optimum automated data acquisition settings (i.e., those settings yielding the highest reproducibility of replicate mass spectra) were obtained based on statistical analysis of spectra of P. aeruginosa. Finally, spectrum quality and reproducibility obtained from non-optimized and optimized automated data acquisition settings were compared for P. aeruginosa, as well as for two other bacteria, Klebsiella pneumoniae and Serratia marcescens. Results indicated that reproducibility increased from 90% to 97% (p-value [~ over =] 0.002) for P. aeruginosa when more shots were summed and, interestingly, decreased from 95% to 92% (p-value [~ over =] 0.013) with increased threshold minimum resolution. With regard to spectrum quality, highly reproducible spectra were more likely to have high spectrum quality as measured by several quality metrics, except for base peak resolution. Interaction plots suggest that, in cases of low threshold minimum resolution, high reproducibility can be achieved with fewer shots. Optimization yielded more reproducible spectra than non-optimized settings for all three bacteria.

Urban areas consume more than 66% of the world’s energy and generate more than 70% of global greenhouse gas emissions. With the world’s population expected to reach 10 billion by 2100, nearly 90% of whom will live in urban areas, a critical question for planetary sustainability is how the size of cities affects energy use and carbon dioxide (CO₂) emissions. Are larger cities more energy and emissions efficient than smaller ones? Do larger cities exhibit gains from economies of scale with regard to emissions? Here we examine the relationship between city size and CO₂ emissions for U.S. metropolitan areas using a production accounting allocation of emissions. We find that for the time period of 1999–2008, CO₂ emissions scale proportionally with urban population size. Contrary to theoretical expectations, larger cities are not more emissions efficient than smaller ones.

The unicellular green microalga Desmodesmus sp. S1 can produce more than 50% total lipid of cell dry weight under high light and nitrogen-limitation conditions. After irradiation by heavy ¹²C⁶⁺ ion beam of 10, 30, 60, 90 or 120 Gy, followed by screening of resulting mutants on 24-well microplates, more than 500 mutants were obtained. One of those, named D90G-19, exhibited lipid productivity of 0.298 g L^-1⋅d^-1, 20.6% higher than wild type, likely owing to an improved maximum quantum efficiency (Fv/Fm) of photosynthesis under stress. This work demonstrated that heavy-ion irradiation combined with high-throughput screening is an effective means for trait improvement. The resulting mutant D90G-19 may be used for enhanced lipid production.

The production, characterization, and antioxidant capacity of the carotenoid fucoxanthin from the marine diatom Odontella aurita were investigated. The results showed that low light and nitrogen-replete culture medium enhanced the biosynthesis of fucoxanthin. The maximum biomass concentration of 6.36 g L^-1 and maximum fucoxanthin concentration of 18.47 mg g^-1 were obtained in cultures grown in a bubble column photobioreactor (Ø 3.0 cm inner diameter), resulting in a fucoxanthin volumetric productivity of 7.96 mg L^-1 day^-1. A slight reduction in biomass production was observed in the scaling up of O. aurita culture in a flat plate photobioreactor, yet yielded a comparable fucoxanthin volumetric productivity. A rapid method was developed for extraction and purification of fucoxanthin. The purified fucoxanthin was identified as all-trans-fucoxanthin, which exhibited strong antioxidant properties, with the effective concentration for 50% scavenging (EC₅₀) of 1,1-dihpenyl-2-picrylhydrazyl (DPPH) radical and 2,2′-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid (ABTS) radical being 0.14 and 0.03 mg mL^-1, respectively. Our results suggested that O. aurita can be a natural source of fucoxanthin for human health and nutrition.

Restoration projects can have varying goals, depending on the specific focus, rationale, and aims for restoration. When restoration projects use project-specific goals to define activities and gauge success without considering broader ecological context, determination of project implications and success can be confounding. We used case studies from the Middle Rio Grande (MRG), southwest USA, to demonstrate how restoration outcomes can rank inconsistently when narrowly-based goals are used. Resource managers have chosen MRG for restoration due to impacts to the natural flood regime, reduced native tree recruitment, and establishment of non-native plants. We show restoration “success” ranks differently based upon three goals: increasing biodiversity, increasing specific ecosystem functions, or restoring native communities. We monitored 12 restored and control sites for seven years. Treatments ranked higher in reducing exotic woody populations, and increasing proportions of native plants and groundwater salvage, but generally worse at removing fuels, and increasing species and habitat structural diversity. Managers cannot rely on the term “restoration” to sufficiently describe a project’s aim. Specific desired outcomes must be defined and monitored. Long-term planning should include flexibility to incorporate provisions for adaptive management to refine treatments to avoid unintended ecological consequences.

Working towards sustainable solutions requires involving professionals and stakeholders from all sectors of society into research and teaching. This often presents a challenge to scholars at universities, as they lack capacity and time needed for negotiating different agendas, languages, competencies, and cultures among faculty, students, and stakeholders. Management approaches and quality criteria have been developed to cope with this challenge, including concepts of boundary organizations, transdisciplinary research, transition management, and interface management. However, few of these concepts present comprehensive proposals how to facilitate research with stakeholder participation while creating educational opportunities along the lifecycle of a project. The article focuses on the position of a transacademic interface manager (TIM) supporting participatory sustainability research and education efforts. We conceptualize the task portfolio of a TIM; outline the capacities a TIM needs to possess in order to successfully operate; and propose an educational approach for how to train students in becoming a TIM. For this, we review the existing literature on TIMs and present insights from empirical sustainability research and educational projects that involved TIMs in different functions. The article provides practical guidance to universities on how to organize these critical endeavors more effectively and to offer students an additional career perspective.

Jewish observance of shmita (alternatively spelled shemitah)—the sabbatical year, or seventh (sheviit) year—is changing. Historically rooted in agriculture, modern Jewish environmentalists are seizing upon the long-ignored environmental and social justice (tikkun olam) aspects of shmita as originally described in the five books of Moses, the Torah in the Hebrew Bible, the basis of Jewish law. Primary research was conducted through key-stakeholder interviews with leading American and Israeli Jewish environmentalists and thought leaders. They see shmita as a core Jewish value—one that, like Shabbat, the Jewish sabbath, has the power to transform society. Their work has brought shmita from an obscure law dealt with mainly by Israel’s Orthodox to a new Jewish ethos being discussed across the United States, Europe, Israel, and even on the floor of Knesset, Israel’s parliament. This article also describes shmita as delineated in the Torah and through the rabbinic canon of halacha (Jewish law), and explains shmita practice from biblical times to the present day.

Background: Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome.

Results: Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable – estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation.

Conclusions: Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation.