ASU Scholarship Showcase

Background: Meiotic recombination has traditionally been explained based on the structural requirement to stabilize homologous chromosome pairs to ensure their proper meiotic segregation. Competing hypotheses seek to explain the emerging findings of significant heterogeneity in recombination rates within and between genomes, but intraspecific comparisons of genome-wide recombination patterns are rare. The honey bee (Apis mellifera) exhibits the highest rate of genomic recombination among multicellular animals with about five cross-over events per chromatid.

Results: Here, we present a comparative analysis of recombination rates across eight genetic linkage maps of the honey bee genome to investigate which genomic sequence features are correlated with recombination rate and with its variation across the eight data sets, ranging in average marker spacing ranging from 1 Mbp to 120 kbp. Overall, we found that GC content explained best the variation in local recombination rate along chromosomes at the analyzed 100 kbp scale. In contrast, variation among the different maps was correlated to the abundance of microsatellites and several specific tri- and tetra-nucleotides.

Conclusions: The combined evidence from eight medium-scale recombination maps of the honey bee genome suggests that recombination rate variation in this highly recombining genome might be due to the DNA configuration instead of distinct sequence motifs. However, more fine-scale analyses are needed. The empirical basis of eight differing genetic maps allowed for robust conclusions about the correlates of the local recombination rates and enabled the study of the relation between DNA features and variability in local recombination rates, which is particularly relevant in the honey bee genome with its exceptionally high recombination rate.

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.

Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.

Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.

This paper considers the changes in education and capacity building that are needed in response to environmental and social challenges of the 21st Century. We argue that such changes will require more than adjustments in current educational systems, research funding strategies, and interdisciplinary collaborations. Instead, it calls for a deeper questioning of the assumptions and beliefs that frame both problems and solutions. We first discuss the challenges of transforming education and capacity building within five key arenas: interdisciplinary research; university education systems; primary and secondary education systems; researchers from the developing world; and the public at large and politicians. Our starting point is that any type of revolution that is proposed in response to global change is likely to reflect the educational perspectives and paradigms of those calling for the revolution. We differentiate between a circular revolution (as in the "plan-do-check-act cycle" often used in change management) versus an axial revolution (moving to a different way of thinking about the issues), arguing that the latter is a more appropriate response to the complex transdisciplinary challenges posed by global environmental change. We present some potential tools to promote an axial revolution, and consider the limits to this approach. We conclude that rather than promoting one large and ideologically homogenous revolution in education and capacity building, there is a need for a revolution in the way that leaders working with education and capacity building look at systems and processes of change. From this perspective, transformative learning may not only be desirable, but critical in responding to the challenges posed by global environmental change.

The effects of urbanization on ozone levels have been widely investigated over cities primarily located in temperate and/or humid regions. In this study, nested WRF-Chem simulations with a finest grid resolution of 1 km are conducted to investigate ozone concentrations O₃ due to urbanization within cities in arid/semi-arid environments. First, a method based on a shape preserving Monotonic Cubic Interpolation (MCI) is developed and used to downscale anthropogenic emissions from the 4 km resolution 2005 National Emissions Inventory (NEI05) to the finest model resolution of 1 km. Using the rapidly expanding Phoenix metropolitan region as the area of focus, we demonstrate the proposed MCI method achieves ozone simulation results with appreciably improved correspondence to observations relative to the default interpolation method of the WRF-Chem system. Next, two additional sets of experiments are conducted, with the recommended MCI approach, to examine impacts of urbanization on ozone production: (1) the urban land cover is included (i.e., urbanization experiments) and, (2) the urban land cover is replaced with the region's native shrubland. Impacts due to the presence of the built environment on O₃ are highly heterogeneous across the metropolitan area. Increased near surface O₃ due to urbanization of 10–20 ppb is predominantly a nighttime phenomenon while simulated impacts during daytime are negligible. Urbanization narrows the daily O₃ range (by virtue of increasing nighttime minima), an impact largely due to the region's urban heat island. Our results demonstrate the importance of the MCI method for accurate representation of the diurnal profile of ozone, and highlight its utility for high-resolution air quality simulations for urban areas.

Studies in both terrestrial and aquatic ecosystems have documented the potential importance of consumers on ecosystem-level nutrient dynamics. This is especially true when aggregations of organisms create biogeochemical hotspots through nutrient consumption, assimilation, and remineralization via excretion and egestion. Here, we focused on aggregations of humans in cities to examine how diet and waste management interact to drive nitrogen- (N) and phosphorus- (P) fluxes into nutrient pollution, inert forms, and nutrient recycling. We constructed six diet patterns (five US-based and one developing nation) to examine N- and P-consumption and excretion, and explored their implications for human health. Next, we constructed six waste-management patterns (three US and three for developing nations) to model how decisions at household and city scales determine the eventual fates of N and P. When compared to the US Recommended Daily Intake, all US diet patterns exceeded N and P requirements. Other than the “enriched CO₂ environment scenario” diet, the typical US omnivore had the greatest excess (37% N and 62% P). Notably, P from food additives could account for all of the excess P found in US omnivore and vegetarian diets. Across all waste-management approaches, a greater proportion of P was stored or recycled (0 to > 100% more P than N) and a greater proportion of N was released as effluent (20 to > 100% more N than P) resulting in pollution enriched with N and a recycling stream enriched with P. In developing nations, 60% of N and 50% of P from excreta entered the environment as pollution because of a lack of sanitation infrastructure. Our study demonstrates a novel addition to modeling sustainable scenarios for urban N- and P-budgets by linking human diets and waste management through socio-ecological systems.

Honeybee workers are essentially sterile female helpers that make up the majority of individuals in a colony. Workers display a marked change in physiology when they transition from in-nest tasks to foraging. Recent technological advances have made it possible to unravel the metabolic modifications associated with this transition. Previous studies have revealed extensive remodeling of brain, thorax, and hypopharyngeal gland biochemistry. However, data on changes in the abdomen is scarce. To narrow this gap we investigated the proteomic composition of abdominal tissue in the days typically preceding the onset of foraging in honeybee workers.

In order to get a broader representation of possible protein dynamics, we used workers of two genotypes with differences in the age at which they initiate foraging. This approach was combined with RNA interference-mediated downregulation of an insulin/insulin-like signaling component that is central to foraging behavior, the insulin receptor substrate (irs), and with measurements of glucose and lipid levels.
Our data provide new insight into the molecular underpinnings of phenotypic plasticity in the honeybee, invoke parallels with vertebrate metabolism, and support an integrated and irs-dependent association of carbohydrate and lipid metabolism with the transition from in-nest tasks to foraging.

n public planning processes for sustainable urban development, planners and experts often face the challenge of engaging a public that is not familiar with sustainability principles or does not subscribe to sustainability values. Although there are calls to build the public’s sustainability literacy through social learning, such efforts require sufficient time and other resources that are not always available. Alternatively, public participation processes may be realigned with the sustainability literacy the participants possess, and their capacity can modestly be built during the engagement. Asking what tools might successfully align public participation with participants’ sustainability literacy, this article describes and evaluates a public participation process in Phoenix, Arizona, in which researchers, in collaboration with city planners, facilitated sustainability conversations as part of an urban development process. The tool employed for Visually Enhanced Sustainability Conversation (VESC) was specifically designed to better align public participation with stakeholders’ sustainability literacy. We tested and evaluated VESC through interviews with participants, city planners, and members of the research team, as well as an analysis of project reports. We found that the use of VESC successfully facilitated discussions on pertinent sustainability issues and embedded sustainability objectives into the project reports. We close with recommendations for strengthening tools like VESC for future public engagements.

Successful careers in sustainability are determined by positive real-world change towards sustainability. This success depends heavily on professional skills in effective and compassionate communication, collaborative teamwork, or impactful stakeholder engagement, among others. These professional skills extend beyond content knowledge and methodical expertise. Current sustainability programs do not sufficiently facilitate students’ acquisition of such skills. This article presents a brief summary of professional skills, synthesized from the literature, and why they are relevant for sustainability professionals. Second, it presents how these skills have been taught in an undergraduate course in sustainability at Arizona State University, USA. Third, it critically discusses the effectiveness and challenges of that exemplary course. Finally, the article concludes with outlining the lessons learned that should be incorporated into future course offerings.

Resilience can have desirable and undesirable consequences. Thus, resilience should not be viewed as a normative desirable goal, but as a descriptor of complex systems dynamics. From this perspective, we apply resilience thinking concepts to assess the dynamics of inequality, spatial segregation, and sustainability in Chile’s capital city of Santiago. Chile’s economy boosted since democracy was restored in 1990, but continuity of neoliberal reforms and transformations of Pinochet’s dictatorship (1973–1990) seem to have locked Chilean cities in resilient, albeit unsustainable, patterns of uneven development. Socio-economic data from Santiago shows highly resilient patterns of urban inequality and segregation from 1992 to 2009 despite democratic efforts, political agendas and discourses packed with calls for reducing poverty and inequality. We present a conceptual model based on the notion of stability landscapes to explore potential trade-offs between resilience and sustainable development. We mapped Santiago’s spatio-temporal inequality trends and explored if these patterns support an inequality-resilience stability landscape. Analysis of temporal and spatial distribution of development assets across four human development dimensions (i.e., income, education, health, democracy) revealed potential socio-political and spatial feedbacks supporting the resilience of inequality and segregation in Santiago. We argue that urban sustainability may require breaking this resilience, a process where bottom-up stressors such as social movements could play a key role.

Background: Gene bodies are the most evolutionarily conserved targets of DNA methylation in eukaryotes. However, the regulatory functions of gene body DNA methylation remain largely unknown. DNA methylation in insects appears to be primarily confined to exons. Two recent studies in Apis mellifera (honeybee) and Nasonia vitripennis (jewel wasp) analyzed transcription and DNA methylation data for one gene in each species to demonstrate that exon-specific DNA methylation may be associated with alternative splicing events. In this study we investigated the relationship between DNA methylation, alternative splicing, and cross-species gene conservation on a genome-wide scale using genome-wide transcription and DNA methylation data.

Results: We generated RNA deep sequencing data (RNA-seq) to measure genome-wide mRNA expression at the exon- and gene-level. We produced a de novo transcriptome from this RNA-seq data and computationally predicted splice variants for the honeybee genome. We found that exons that are included in transcription are higher methylated than exons that are skipped during transcription. We detected enrichment for alternative splicing among methylated genes compared to unmethylated genes using fisher’s exact test. We performed a statistical analysis to reveal that the presence of DNA methylation or alternative splicing are both factors associated with a longer gene length and a greater number of exons in genes. In concordance with this observation, a conservation analysis using BLAST revealed that each of these factors is also associated with higher cross-species gene conservation.

Conclusions: This study constitutes the first genome-wide analysis exhibiting a positive relationship between exon-level DNA methylation and mRNA expression in the honeybee. Our finding that methylated genes are enriched for alternative splicing suggests that, in invertebrates, exon-level DNA methylation may play a role in the construction of splice variants by positively influencing exon inclusion during transcription. The results from our cross-species homology analysis suggest that DNA methylation and alternative splicing are genetic mechanisms whose utilization could contribute to a longer gene length and a slower rate of gene evolution.