Physical Sciences and Mathematics Commons^™

Power In Pairs: Assessing The Statistical Value Of Paired Samples In Tests For Differential Expression, John R. Stevens, Jennifer S. Herrick, Roger K. Wolff, Martha L. Slattery

Mathematics and Statistics Faculty Publications

Background: When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and researchers can plan for a certain proportion of subjects to have paired samples. We consider the effect of this paired samples proportion on the statistical power of the study, using characteristics of both count (RNA-Seq) and continuous (microarray) expression data from a colorectal cancer study.

Results: We demonstrate that a higher proportion of subjects with paired samples yields higher statistical power, for various total numbers of samples, and for various strengths of …

Carbene Triel Bonds Between Trr3 (Tr=B, Al) And N-Heterocyclic Carbenes, Zongqing Chi, Wenbo Dong, Qingzhong Li, Xin Yang, Steve Scheiner, Shufeng Liu

Chemistry and Biochemistry Faculty Publications

The carbene triel bond is predicted and characterized by theoretical calculations. The C lone pair of N‐heterocyclic carbenes (NHCs) is allowed to interact with the central triel atom of TrR₃ (Tr = B and Al; R = H, F, Cl, and Br). The ensuing bond is very strong, with an interaction energy of nearly 90 kcal/mol. Replacement of the C lone pair by that of either N or Si weakens the binding. The bond is strengthened by electron‐withdrawing substituents on the triel atom, and the reverse occurs with substitution on the NHC. However, these effects do not strictly follow …

Parental Habituation To Human Disturbance Over Time Reduces Fear Of Humans In Coyote Offspring, Christopher J. Schell, Julie K. Young, Elizabeth V. Lonsdorf, Rachel M. Santymire, Jill M. Mateo

Wildland Resources Faculty Publications

A fundamental tenet of maternal effects assumes that maternal variance over time should have discordant consequences for offspring traits across litters. Yet, seldom are parents observed across multiple reproductive bouts, with few studies consider‐ ing anthropogenic disturbances as an ecological driver of maternal effects. We ob‐ served captive coyote (Canis latrans) pairs over two successive litters to determine whether among‐litter differences in behavior (i.e., risk‐taking) and hormones (i.e., cortisol and testosterone) corresponded with parental plasticity in habituation. Thus, we explicitly test the hypothesis that accumulating experiences of anthropogenic disturbance reduces parental fear across reproductive bouts, which should have disparate phenotypic …

Assessment Of The Effects Of Climate Change On Evapotranspiration With An Improved Elasticity Method In A Nonhumid Area, Lei Tian, Jiming Jin, Pute Wu, Guo-Yue Niu

Watershed Sciences Faculty Publications

Climatic elasticity is a crucial metric to assess the hydrological influence of climate change. Based on the Budyko equation, this study performed an analytical derivation of the climatic elasticity of evapotranspiration (ET). With this derived elasticity, it is possible to quantitatively separate the impacts of precipitation, air temperature, net radiation, relative humidity, and wind speed on ET in a watershed. This method was applied in the Wuding River Watershed (WRW), located in the center of the Yellow River Watershed of China. The estimated rate of change in ET caused by climatic variables is −10.69 mm/decade, which is close to the …

Quantifying The Impact Of Climate Change And Human Activities On Streamflow In A Semi-Arid Watershed With The Budyko Equation Incorporating Dynamic Vegetation Information, Lei Tian, Jiming Jin, Pute Wu, Guo-Yue Niu

Watershed Sciences Faculty Publications

Understanding hydrological responses to climate change and land use and land cover change (LULCC) is important for water resource planning and management, especially for water-limited areas. The annual streamflow of the Wuding River Watershed (WRW), the largest sediment source of the Yellow River in China, has decreased significantly over the past 50 years at a rate of 5.2 mm/decade. Using the Budyko equation, this study investigated this decrease with the contributions from climate change and LULCC caused by human activities, which have intensified since 1999 due to China’s Grain for Green Project (GFGP). The Budyko parameter that represents watershed characteristics …

Ncer Assistance Agreement Annual Progress Report For Grant #83582401 - Assessment Of Stormwater Harvesting Via Manage Aquifer Recharge (Mar) To Develop New Water Supplies In The Arid West: The Salt Lake Valley Example, Ryan Dupont, Joan E. Mclean, Richard C. Peralta, Sarah E. Null, Douglas B. Jackson-Smith

Civil and Environmental Engineering Faculty Publications

The goals of the original proposed project remain the same, that is, to test the hypothesis that Managed Aquifer Recharge (MAR) for stormwater harvesting is a technically feasible, socially and environmentally acceptable, economically viable, and legally feasible option for developing new water supplies for arid Western urban ecosystems experiencing increasing population, and climate change pressures on existing water resources. The project is being carried out via three distinct but integrated components that include: 1) Monitoring of existing distributed MAR harvesting schemes involving a growing number of demonstration Green Infrastructure (GI) test sites; 2) Integrated stormwater/vadose zone/groundwater/ ecosystem services modeling; and …

Crystallographic And Computational Characterization Of Methyl Tetrel Bonding In S-Adenosylmethionine-Dependent Methyltransferases, Raymond C. Trievel, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in S_N2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the S_N2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered …

Wild Bees Of Grand Staircase-Escalante National Monument: Richness, Abundance, And Spatio-Temporal Beta-Diversity, Olivia Messinger Carril, Terry Griswold, James Haefner, Joseph S. Wilson

All PIRU Publications

Interest in bees has grown dramatically in recent years in light of several studies that have reported widespread declines in bees and other pollinators. Investigating declines in wild bees can be difficult, however, due to the lack of faunal surveys that provide baseline data of bee richness and diversity. Protected lands such as national monuments and national parks can provide unique opportunities to learn about and monitor bee populations dynamics in a natural setting because the opportunity for large-scale changes to the landscape are reduced compared to unprotected lands. Here we report on a 4-year study of bees in Grand …

Developmental Parameters Of A Southern Mountain Pine Beetle (Coleoptera: Curculionidae) Population Reveal Potential Source Of Latitudinal Differences In Generation Time, Anne E. Mcmanis, James A. Powell, Barbara J. Bentz

Mathematics and Statistics Faculty Publications

Mountain pine beetle (Dendroctonus ponderosae, Hopkins) is a major disturbance agent in pine ecosystems of western North America. Adaptation to local climates has resulted in primarily univoltine generation time across a thermally diverse latitudinal gradient. We hypothesized that voltinism patterns have been shaped by selection for slower developmental rates in southern populations inhabiting warmer climates. To investigate traits responsible for latitudinal differences we measured lifestage-specific development of southern mountain pine beetle eggs, larvae and pupae across a range of temperatures. Developmental rate curves were fit using maximum posterior likelihood estimation with a Bayesian prior to improve fit stability. …

Dependence Of Nmr Chemical Shifts Upon Ch Bond Lengths Of A Methyl Group Involved In A Tetrel Bond, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Four different Lewis acids that might participate in a tetrel bond with a nucleophile (SEt₂Me⁺, NMe₄⁺, SMe₂, NMe₃) are examined. The NMR chemical shifts of the methyl C and H atoms are calculated as the CH bond lengths are systematically stretched and contracted, in the absence of a base. The C shielding diminishes by roughly 2 ppm for a stretch of 0.01 Å, while that of H drops by only 0.3 ppm. The deshieldings caused purely by the bond length changes are far too small to account for the …

Genome-Wide Association Study For Variants That Modulate Relationships Between Cerebrospinal Fluid Amyloid-Beta 42, Tau, And P-Tau Levels, Taylor J. Maxwell, Chris Corcoran, Jorge L. Del-Aguila, John P. Budde, Yuetiva Deming, Carlos Cruchaga, Alison M. Goate, John S. K. Kauwe, Alzheimer's Disease Neuroimaging Initiative

Mathematics and Statistics Faculty Publications

Background: A relationship quantitative trait locus exists when the correlation between multiple traits varies by genotype for that locus. Relationship quantitative trait loci (rQTL) are often involved in gene-by-gene (G×G) interactions or gene-by-environmental interactions, making them a powerful tool for detecting G×G.

Methods: We performed genome-wide association studies to identify rQTL between tau and Aβ42 and ptau and Aβ42 with over 3000 individuals using age, gender, series, APOE ε2, APOE ε4, and two principal components for population structure as covariates. Each significant rQTL was separately screened for interactions with other loci for each trait in the rQTL model. Parametric bootstrapping …

El Niño-Southern Oscillation Complexity, Axel Timmermann, Soon-Il An, Jong-Seong Kug, Fei-Fei Jin, Wenju Cai, Antonietta Capotondi, Kim Cobb, Matthieu Lengaigne, Michal J. Mcphaden, Malte F. Stuecker, Karl Stein, Andrew T. Wittenberg, Kyung-Sook Yun, Tobias Bayr, Han-Ching Chen, Yoshimitsu Chikamoto, Et Al.

Plants, Soils, and Climate Faculty Publications

El Niño events are characterized by surface warming of the tropical Pacific Ocean and weakening of equatorial trade winds that occur every few years. Such conditions are accompanied by changes in atmospheric and oceanic circulation, affecting global climate, marine and terrestrial ecosystems, fisheries and human activities. The alternation of warm El Niño and cold La Niña conditions, referred to as the El Niño–Southern Oscillation (ENSO), represents the strongest year-to-year fluctuation of the global climate system. Here we provide a synopsis of our current understanding of the spatio-temporal complexity of this important climate mode and its influence on the Earth system.

Comparison Between Tetrel Bonded Complexes Stabilized By Σ And Π Hole Interactions, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The σ-hole tetrel bonds formed by a tetravalent molecule are compared with those involving a π-hole above the tetrel atom in a trivalent bonding situation. The former are modeled by TH4, TH3F, and TH2F2 (T = Si, Ge, Sn) and the latter by TH2=CH2, THF=CH2, and TF2=CH2, all paired with NH3 as Lewis base. The latter π-bonded complexes are considerably more strongly bound, despite the near equivalence of the σ and π-hole intensities. The larger binding energies of the π-dimers are attributed to greater electrostatic attraction and orbital interaction. Each progressive replacement of H by F increases the strength of …

Feasibility Of Predicting Vietnam’S Autumn Rainfall Regime Based On The Tree-Ring Record And Decadal Variability, Yan Sun, Shih-Yu (Simon) Wang, Rong Li, Brendan M. Buckley, Robert R. Gilies, Kyle G. Hansen

Mathematics and Statistics Faculty Publications

We investigate the feasibility of developing decadal prediction models for autumn rainfall ( R_A ) over Central Vietnam by utilizing a published tree-ring reconstruction of October–November (ON) rainfall derived from the earlywood width measurements from a type of Douglas-fir (Pseudotsuga sinensis). Autumn rainfall for this region accounts for a large percentage of the annual total, and is often the source of extreme flooding. Central Vietnam’s R_A along with its notable autocorrelation and significant cross-correlation with basin-wide Pacific sea surface temperature (SST) variability, to develop four discrete time-series models. The sparse autoregressive model, with Pacific SST as …

Organic Compound Emissions From A Landfarm Used For Oil And Gas Solid Waste Disposal, Seth N. Lyman, Marc L. Mansfield

Chemistry and Biochemistry Faculty Publications

Solid or sludgy hydrocarbon waste is a byproduct of oil and gas exploration and production. One commonly-used method of disposing of this waste is landfarming. Landfarming involves spreading hydrocarbon waste on soils, tilling it into the soil, and allowing it to biodegrade. We used a dynamic flux chamber to measure fluxes of methane, a suite of 54 non-methane hydrocarbons, and light alcohols from an active and a remediated landfarm in eastern Utah, U.S.A. Fluxes from the remediated landfarm were not different from a PTFE sheet or from undisturbed soils in the region. Fluxes of methane, total non-methane hydrocarbons, and alcohols …

Structure Of Frequency-Interacting Rna Helicase From Neurospora Crassa Reveals High Flexibility In A Domain Critical For Circadian Rhythm And Rna Surveillance, Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean J. Johnson

Chemistry and Biochemistry Faculty Publications

The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH …

Low Offspring Survival In Mountain Pine Beetle Infesting The Resistant Great Basin Bristlecone Pine Supports The Preference-Performance Hypothesis, Erika L. Eidson, Karen E. Mock, Barbara J. Bentz

Wildland Resources Faculty Publications

The preference-performance hypothesis states that ovipositing phytophagous insects will select host plants that are well-suited for their offspring and avoid host plants that do not support offspring performance (survival, development and fitness). The mountain pine beetle (Dendroctonus ponderosae), a native insect herbivore in western North America, can successfully attack and reproduce in most species of Pinus throughout its native range. However, mountain pine beetles avoid attacking Great Basin bristlecone pine (Pinus longaeva), despite recent climate-driven increases in mountain pine beetle populations at the high elevations where Great Basin bristlecone pine grows. Low preference for a potential …

The Relationship Between Measures Of Annual Livestock Disturbance In Western Riparian Areas And Stream Conditions Important To Trout, Salmon, And Char, Lindsey M. Goss, Brett B. Roper

Watershed Sciences Faculty Publications

Managing livestock disturbance in riparian zones in a manner that provides economic returns to ranchers while protecting streams is an important aspect of rangeland management on public lands in the western United States. Attempts to balance economic and ecologic outcomes have been made more difficult due to the presence of several salmonid species that are protected under the Endangered Species Act. One approach to proper management of livestock use near streams has been to define the allowable limits of disturbance using 2 metrics, streambank alteration and stubble height. We evaluated 153 stream reaches within the Interior Columbia Basin to determine …

Gymnosperms On The Edge, Félix Forest, Justin Moat, Elisabeth Baloch, Neil A. Brummitt, Steve P. Bachman, Steffi Ickert-Bond, Peter M. Hollingsworth, Aaron Liston, Damon P. Little, Sarah Mathews, Hardeep Rai, Catarina Rydin, Dennis W. Stevenson, Philip Thomas, Sven Buerki

Wildland Resources Faculty Publications

Driven by limited resources and a sense of urgency, the prioritization of species for conservation has been a persistent concern in conservation science. Gymnosperms (comprising ginkgo, conifers, cycads, and gnetophytes) are one of the most threatened groups of living organisms, with 40% of the species at high risk of extinction, about twice as many as the most recent estimates for all plants (i.e. 21.4%). This high proportion of species facing extinction highlights the urgent action required to secure their future through an objective prioritization approach. The Evolutionary Distinct and Globally Endangered (EDGE) method rapidly ranks species based on their evolutionary …

Genetic Variation Determines Which Feedbacks Drive And Alter Predator–Prey Eco-Evolutionary Cycles, Michael H. Cortez

Mathematics and Statistics Faculty Publications

Evolution can alter the ecological dynamics of communities, but the effects depend on the magnitudes of standing genetic variation in the evolving species. Using an eco‐coevolutionary predator–prey model, I identify how the magnitudes of prey and predator standing genetic variation determine when ecological, evolutionary, and eco‐evolutionary feedbacks influence system stability and the phase lags in predator–prey cycles. Here, feedbacks are defined by subsystems, i.e., the dynamics of a subset of the components of the whole system when the other components are held fixed; ecological (evolutionary) feedbacks involve the direct and indirect effects between population densities (species traits) and eco‐evolutionary feedbacks …

Magnetic Properties Of Acenes And Their O-Quinone Derivatives: Computer Simulation, A. A. Starikova, A. G. Starikov, R. M. Minyaev, Alexander I. Boldyrev, V. I. Minkin

Chemistry and Biochemistry Faculty Publications

Quantum chemical study (DFT UB3LYP/6-311++G(d,p)) of the structure and properties of acenes functionalized with two o-benzoquinone groups and their complexes with sodium cations has been performed. An increase in the number of fused rings has been shown to result in the stabilization of biradicaloid state of acenes and the switching of the character of exchange interactions between redox-active moieties from antiferromagnetic to ferromagnetic. The obtained results allow one to consider o-quinone acene derivatives as a basis for designing magnetoactive compounds.

Mxin Differentially Regulates Monomeric And Oligomeric Species Of The Shigella Type Three Secretion System Atpase Spa47, Heather B. Case, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

Shigella rely entirely on the action of a single type three secretion system (T3SS) to support cellular invasion of colonic epithelial cells and to circumvent host immune responses. The ATPase Spa47 resides at the base of the Shigella needle-like type three secretion apparatus (T3SA), supporting protein secretion through the apparatus and providing a likely means for native virulence regulation by Shigella and a much needed target for non-antibiotic therapeutics to treat Shigella infections. Here, we show that MxiN is a differential regulator of Spa47 and that its regulatory impact is determined by the oligomeric state of the Spa47 ATPase, with …

Alluvial Substrate Mapping By Automated Texture Segmentation Of Recreational-Grade Side Scan Sonar Imagery, Daniel Hamill, Daniel Buscombe, Joseph Michael Wheaton

Watershed Sciences Faculty Publications

Side scan sonar in low-cost ‘fishfinder’ systems has become popular in aquatic ecology and sedimentology for imaging submerged riverbed sediment at coverages and resolutions sufficient to relate bed texture to grain-size. Traditional methods to map bed texture (i.e. physical samples) are relatively high-cost and low spatial coverage compared to sonar, which can continuously image several kilometers of channel in a few hours. Towards a goal of automating the classification of bed habitat features, we investigate relationships between substrates and statistical descriptors of bed textures in side scan sonar echograms of alluvial deposits. We develop a method for automated segmentation of …

Benthic Meiofaunal Community Response To The Cascading Effects Of Herbivory Within An Algal Halo System Of The Great Barrier Reef, Quinn R. Ollivier, Edward Hammill, David J. Booth, Elizabeth M.P. Madin, Charles Hinchliffe, Alastair R. Harborne, Catherine E. Lovelock, Peter I. Macreadie, Trisha Brooke Atwood

Watershed Sciences Faculty Publications

Benthic fauna play a crucial role in organic matter decomposition and nutrient cycling at the sediment-water boundary in aquatic ecosystems. In terrestrial systems, grazing herbivores have been shown to influence below-ground communities through alterations to plant distribution and composition, however whether similar cascading effects occur in aquatic systems is unknown. Here, we assess the relationship between benthic invertebrates and above-ground fish grazing across the ‘grazing halos’ of Heron Island lagoon, Australia. Grazing halos, which occur around patch reefs globally, are caused by removal of seagrass or benthic macroalgae by herbivorous fish that results in distinct bands of unvegetated sediments surrounding …

Electron Transfer To Nitrogenase In Different Genomic And Metabolic Backgrounds, Saroj Poudel, Daniel R. Colman, Kathryn R. Fixen, Rhesa N. Ledbetter, Yanning Zheng, Natasha Pence, Lance C. Seefeldt, John W. Peters, Caroline S. Harwood, Eric S. Boyd

Chemistry and Biochemistry Faculty Publications

Nitrogenase catalyzes the reduction of dinitrogen (N₂) using low-potential electrons from ferredoxin (Fd) or flavodoxin (Fld) through an ATP-dependent process. Since its emergence in an anaerobic chemoautotroph, this oxygen (O₂)-sensitive enzyme complex has evolved to operate in a variety of genomic and metabolic backgrounds, including those of aerobes, anaerobes, chemotrophs, and phototrophs. However, whether pathways of electron delivery to nitrogenase are influenced by these different metabolic backgrounds is not well understood. Here, we report the distribution of homologs of Fds, Flds, and Fd-/Fld-reducing enzymes in 359 genomes of putative N₂ fixers (diazotrophs). Six distinct lineages …

Implications Of Monomer Deformation For Tetrel And Pnicogen Bonds, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A series of TF₄ and ZF₅ molecules (T = Si, Ge, Sn and Z = P, As, Sb) were allowed to engage in tetrel and pnicogen bonds, respectively, with NH₃, pyrazine, and HCN. The interaction energies are quite large, approaching 50 kcal mol^-1 in some cases. The formation of each complex is accompanied by substantial geometrical deformation of the Lewis acid to accommodate the approaching base. The energy associated with this monomer rearrangement is the largest for the smaller central atoms Si and P, where it exceeds 20 kcal mol^-1. The total reaction …

Biodiverse Cities: The Nursery Industry, Homeowners, And Neighborhood Differences Drive Urban Tree Composition, Meghan L. Avolio, Diane E. Pataki, Tara L. E. Trammell, Joanna Endter-Wada

Environment and Society Faculty Publications

In arid and semiarid regions, where few if any trees are native, city trees are largely human planted. Societal factors such as resident preferences for tree traits, nursery offerings, and neighborhood characteristics are potentially key drivers of urban tree community composition and diversity, however, they remain critically understudied. We investigated patterns of urban tree structure in residential neighborhoods of the Salt Lake Valley, Utah, combining biological variables, such as neighborhood and plant nursery tree species and trait composition, and sociological data comprised of resident surveys and U.S. Census data. We sampled nine neighborhoods that varied in household income and age …

Pi Tetrel Bonds, And Their Influence On Hydrogen Bonds And Proton Transfers, Yuanxin Wei, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The positive region that lies above the plane of F2TO (T=C and Si) interacts with malondialdehyde (MDA), which contains an intramolecular H‐bond. The T atom of F2TO can lie either in the MDA molecular plane, forming a T⋅⋅⋅O tetrel bond, or F2TO can stack directly above MDA in a parallel arrangement. The former structure is more stable than the latter, and in either case, F2SiO engages in a much stronger interaction than does F2CO, reaching nearly 200 kJ mol−1. The π‐tetrel bond strengthens/weakens the MDA H‐bond when the bond is formed to the hydroxyl/carbonyl group of MDA, and causes an …

Survival Rates Indicate That Correlations Between Community-Weighted Mean Traits And Environments Can Be Unreliable Estimates Of The Adaptive Value Of Traits, Daniel C. Laughlin, Robert T. Strahan, Peter B. Adler, Margaret M. Moore

Wildland Resources Faculty Publications

Correlations between community-weighted mean (CWM) traits and environmental gradients are often assumed to quantify the adaptive value of traits. We tested this assumption by comparing these correlations with models of survival probability using 46 perennial species from long-term permanent plots in pine forests of Arizona. Survival was modeled as a function of trait-by-environment interactions, plant size, climatic variation, and neighborhood competition. The effect of traits on survival depended on the environmental conditions, but the two statistical approaches were inconsistent. For example, CWM specific leaf area (SLA) and soil fertility were uncorrelated. However, survival was highest for species with low SLA …

Transplanting A Bacterial Immune System: Determining The Function Of A Novel Crispr System, Riannon Smith, Melena Garrett

Research on Capitol Hill

CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats) loci and cas (CRISPR-associated) genes provide adaptive immunity (see panel below) in bacteria and have recently been repurposed for genome editing.

Systems are structurally and functionally diverse.

• 2 classes, 6 types, 33 subtypes
• Very few have been studied experimentally
• None of the Type IV systems have been characterized