ASU Scholarship Showcase

Background: Healthy individuals on the lower end of the insulin sensitivity spectrum also have a reduced gene expression response to exercise for specific genes. The goal of this study was to determine the relationship between insulin sensitivity and exercise-induced gene expression in an unbiased, global manner.

Methods and Findings: Euglycemic clamps were used to measure insulin sensitivity and muscle biopsies were done at rest and 30 minutes after a single acute exercise bout in 14 healthy participants. Changes in mRNA expression were assessed using microarrays, and miRNA analysis was performed in a subset of 6 of the participants using sequencing techniques. Following exercise, 215 mRNAs were changed at the probe level (Bonferroni-corrected P<0.00000115). Pathway and Gene Ontology analysis showed enrichment in MAP kinase signaling, transcriptional regulation and DNA binding. Changes in several transcription factor mRNAs were correlated with insulin sensitivity, including MYC, r=0.71; SNF1LK, r=0.69; and ATF3, r= 0.61 (5 corrected for false discovery rate). Enrichment in the 5’-UTRs of exercise-responsive genes suggested regulation by common transcription factors, especially EGR1. miRNA species of interest that changed after exercise included miR-378, which is located in an intron of the PPARGC1B gene.

Conclusions: These results indicate that transcription factor gene expression responses to exercise depend highly on insulin sensitivity in healthy people. The overall pattern suggests a coordinated cycle by which exercise and insulin sensitivity regulate gene expression in muscle.

A major challenge for biogeographers and conservation planners is to identify where to best locate or distribute high-priority areas for conservation and to explore whether these areas are well represented by conservation actions such as protected areas (PAs). We aimed to identify high-priority areas for conservation, expressed as hotpots of rarity-weighted richness (HRR)–sites that efficiently represent species–for birds across EU countries, and to explore whether HRR are well represented by the Natura 2000 network. Natura 2000 is an evolving network of PAs that seeks to conserve biodiversity through the persistence of the most patrimonial species and habitats across Europe. This network includes Sites of Community Importance (SCI) and Special Areas of Conservation (SAC), where the latter regulated the designation of Special Protected Areas (SPA). Distribution maps for 416 bird species and complementarity-based approaches were used to map geographical patterns of rarity-weighted richness (RWR) and HRR for birds. We used species accumulation index to evaluate whether RWR was efficient surrogates to identify HRRs for birds. The results of our analysis support the proposition that prioritizing sites in order of RWR is a reliable way to identify sites that efficiently represent birds. HRRs were concentrated in the Mediterranean Basin and alpine and boreal biogeographical regions of northern Europe. The cells with high RWR values did not correspond to cells where Natura 2000 was present. We suggest that patterns of RWR could become a focus for conservation biogeography. Our analysis demonstrates that identifying HRR is a robust approach for prioritizing management actions, and reveals the need for more conservation actions, especially on HRR.

Uncovering the chemical and physical links between natural environments and microbial communities is becoming increasingly amenable owing to geochemical observations and metagenomic sequencing. At the hot spring known as Bison Pool in Yellowstone National Park, the cooling of the water in the outflow channel is associated with an increase in oxidation potential estimated from multiple field-based measurements. Representative groups of proteins whose sequences were derived from metagenomic data also exhibit an increase in average oxidation state of carbon in the protein molecules with distance from the hot-spring source. The energetic requirements of reactions to form selected proteins used in the model were computed using amino-acid group additivity for the standard molal thermodynamic properties of the proteins, and the relative chemical stabilities of the proteins were investigated by varying temperature, pH and oxidation state, expressed as activity of dissolved hydrogen. The relative stabilities of the proteins were found to track the locations of the sampling sites when the calculations included a function for hydrogen activity that increases with temperature and is higher, or more reducing, than values consistent with measurements of dissolved oxygen, sulfide and oxidation-reduction potential in the field. These findings imply that spatial patterns in the amino acid compositions of proteins can be linked, through energetics of overall chemical reactions representing the formation of the proteins, to the environmental conditions at this hot spring, even if microbial cells maintain considerably different internal conditions. Further applications of the thermodynamic calculations are possible for other natural microbial ecosystems.

The role of ambiguity tolerance in career decision making was examined in a sample of college students (n = 275). Three hypotheses were proposed regarding the direct prediction of ambiguity tolerance on career indecision, the indirect prediction of ambiguity tolerance on career indecision through environmental and self explorations, and the moderation effect of ambiguity tolerance on the link of environmental and self explorations with career indecision. Results supported the significance of ambiguity tolerance with respect to career indecision, finding that it directly predicted general indecisiveness, dysfunctional beliefs, lack of information, and inconsistent information, and moderated the prediction of environmental exploration on inconsistent information. The implications of this study are discussed and suggestions for future research are provided.

Type 2 diabetes (T2D) is a complex metabolic disease that is more prevalent in ethnic groups such as Mexican Americans, and is strongly associated with the risk factors obesity and insulin resistance. The goal of this study was to perform whole genome gene expression profiling in adipose tissue to detect common patterns of gene regulation associated with obesity and insulin resistance. We used phenotypic and genotypic data from 308 Mexican American participants from the Veterans Administration Genetic Epidemiology Study (VAGES). Basal fasting RNA was extracted from adipose tissue biopsies from a subset of 75 unrelated individuals, and gene expression data generated on the Illumina BeadArray platform. The number of gene probes with significant expression above baseline was approximately 31,000. We performed multiple regression analysis of all probes with 15 metabolic traits. Adipose tissue had 3,012 genes significantly associated with the traits of interest (false discovery rate, FDR ≤ 0.05). The significance of gene expression changes was used to select 52 genes with significant (FDR ≤ 10^-4) gene expression changes across multiple traits. Gene sets/Pathways analysis identified one gene, alcohol dehydrogenase 1B (ADH1B) that was significantly enriched (P < 10^-60) as a prime candidate for involvement in multiple relevant metabolic pathways. Illumina BeadChip derived ADH1B expression data was consistent with quantitative real time PCR data. We observed significant inverse correlations with waist circumference (2.8 x 10[superscript -9]), BMI (5.4 x 10^-6), and fasting plasma insulin (P < 0.001). These findings are consistent with a central role for ADH1B in obesity and insulin resistance and provide evidence for a novel genetic regulatory mechanism for human metabolic diseases related to these traits.

Anthropogenic water sources (AWS) are developed water sources used as a management tool for desert wildlife species. Studies documenting the effects of AWS are often focused on game species; whereas, the effects on non-target wildlife are less understood. We used live trapping techniques to investigate rodent abundance, biomass, and diversity metrics near AWS and paired control sites; we sampled vegetation to determine rodent-habitat associations in the Sauceda Mountains of the Sonoran Desert in Arizona. A total of 370 individual mammals representing three genera and eight species were captured in 4,800 trap nights from winter 2011 to spring 2012.

A multi-response permutation procedure was used to identify differences in small mammal community abundance and biomass by season and treatment. Rodent abundance, biomass, and richness were greater at AWS compared to control sites. Patterns of abundance and biomass were driven by the desert pocket mouse (Chaetodipus penicillatus) which was the most common capture and two times more numerous at AWS compared to controls. Vegetation characteristics, explored using principal components analysis, were similar between AWS and controls. Two species that prefer vegetation structure, Bailey’s pocket mouse (C. baileyi) and white-throated woodrat (Neotoma albigula), had greater abundances and biomass near AWS and were associated with habitat having high cactus density. Although small mammals do not drink free-water, perhaps higher abundances of some species of desert rodents at AWS could be related to artificial structure associated with construction or other resources. Compared to the 30-year average of precipitation for the area, the period of our study occurred during a dry winter. During dry periods, perhaps AWS provide resources to rodents related to moisture.

Since nitrogen (N) is often limiting in permafrost soils, we investigated the N[subscript 2]-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N[subscript 2]-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.

Streamer biofilm communities (SBC) are often observed within chemosynthetic zones of Yellowstone hot spring outflow channels, where temperatures exceed those conducive to photosynthesis. Nearest the hydrothermal source (75–88°C) SBC comprise thermophilic Archaea and Bacteria, often mixed communities including Desulfurococcales and uncultured Crenarchaeota, as well as Aquificae and Thermus, each carrying diagnostic membrane lipid biomarkers. We tested the hypothesis that SBC can alternate their metabolism between autotrophy and heterotrophy depending on substrate availability. Feeding experiments were performed at two alkaline hot springs in Yellowstone National Park: Octopus Spring and “Bison Pool,” using various ¹³C-labeled substrates (bicarbonate, formate, acetate, and glucose) to determine the relative uptake of these different carbon sources. Highest ¹³C uptake, at both sites, was from acetate into almost all bacterial fatty acids, particularly into methyl-branched C₁₅, C₁₇ and C₁₉ fatty acids that are diagnostic for Thermus/Meiothermus, and some Firmicutes as well as into universally common C_16:0 and C_18:0 fatty acids. ¹³C-glucose showed a similar, but a 10–30 times lower uptake across most fatty acids. ¹³C-bicarbonate uptake, signifying the presence of autotrophic communities was only significant at “Bison Pool” and was observed predominantly in non-specific saturated C₁₆, C₁₈, C₂₀, and C₂₂ fatty acids. Incorporation of ¹³C-formate occurred only at very low rates at “Bison Pool” and was almost undetectable at Octopus Spring, suggesting that formate is not an important carbon source for SBC. ¹³C-uptake into archaeal lipids occurred predominantly with ¹³C-acetate, suggesting also that archaeal communities at both springs have primarily heterotrophic carbon assimilation pathways. We hypothesize that these communities are energy-limited and predominantly nurtured by input of exogenous organic material, with only a small fraction being sustained by autotrophic growth.

Explosive extrusion of cold material from the interior of icy bodies, or cryovolcanism, has been observed on Enceladus and, perhaps, Europa, Triton, and Ceres. It may explain the observed evidence for a young surface on Charon (Pluto’s surface is masked by frosts). Here, we evaluate prerequisites for cryovolcanism on dwarf planet-class Kuiper belt objects (KBOs). We first review the likely spatial and temporal extent of subsurface liquid, proposed mechanisms to overcome the negative buoyancy of liquid water in ice, and the volatile inventory of KBOs. We then present a new geochemical equilibrium model for volatile exsolution and its ability to drive upward crack propagation. This novel approach bridges geophysics and geochemistry, and extends geochemical modeling to the seldom-explored realm of liquid water at subzero temperatures. We show that carbon monoxide (CO) is a key volatile for gas-driven fluid ascent; whereas CO₂ and sulfur gases only play a minor role. N₂, CH₄, and H₂ exsolution may also drive explosive cryovolcanism if hydrothermal activity produces these species in large amounts (a few percent with respect to water). Another important control on crack propagation is the internal structure: a hydrated core makes explosive cryovolcanism easier, but an undifferentiated crust does not. We briefly discuss other controls on ascent such as fluid freezing on crack walls, and outline theoretical advances necessary to better understand cryovolcanic processes. Finally, we make testable predictions for the 2015 New Horizons flyby of the Pluto-Charon system.