Other Life Sciences Commons^™

Analyses Of The 2019 Nobel Prize In Physiology Or Medicine: Molecular Machinery For Cellular Oxygen Level Response, Neyda V. Gilman

Library Scholarship

Gregg L. Semenza, William G Kaelin, Jr, and Sir Peter J. Ratcliffe were awarded the 2019 Nobel Prize for Physiology or Medicine on October 7, 2019. Their work led to the understanding of how cells recognize and adapt to varying oxygen levels. Hypoxia-inducible nuclear factors play an essential role in this mechanism by turning on other genes that work towards increasing oxygen levels in hypoxic environments. Other vital pieces of the machinery include von Hippel-Lindau proteins and prolyl hydroxylation. Due to the necessity of oxygen in numerous human physiological systems, this discovery will likely have nearly immeasurable impacts on human …

Hydrods: Data Services In Support Of Physically Based, Distributed Hydrological Models, Tseganeh Zekiewos Gichamo, Nazmus S. Sazib, David G. Tarboton, Pabitra Dash

Publications

Physically based distributed hydrologic models require geospatial and time-series data that take considerable time and effort in processing them into model inputs. Tools that automate and speed up input processing facilitate the application of these models. In this study, we developed a set of web-based data services called HydroDS to provide hydrologic data processing ‘software as a service.’ HydroDS provides functions for processing watershed, terrain, canopy, climate, and soil data. The services are accessed through a Python client library that facilitates developing simple but effective data processing workflows with Python. Evaluations of HydroDS by setting up the Utah Energy Balance …

Faculty Spotlight—Dr. Robert Dores, Anit Tyagi, William Moody

DU Undergraduate Research Journal Archive

Robert Dores Interview

Edited by Will Moody

Land Use Influences Along Elevation Gradient On Macroinvertebrate Communities, Brittany Sprout

Electronic Theses and Dissertations

Land use activities have caused disturbances that affect the quality of freshwater ecosystems worldwide. How the influences of land use along an environmental gradient and the associated environmental variables that may influence stream diversity and function is unclear. We address these issues by studying biodiversity, abundance, and functional diversity of macroinvertebrates across different land types along a gradient in Colorado, USA. We also address how diversity may change along an elevation gradient by analyzing previously published macroinvertebrate research. We found evidence that land use and disturbance are stronger explanations of changes in macroinvertebrate communities, rather than elevation. Functional trait patterns …

Association Between Breastfeeding And Child Stunting In Mexico, Ana Paola Campos, Mireya Vilar-Compte, Summer Sherburne Hawkins

Department of Public Health Scholarship and Creative Works

Background: Globally, the prevalence of child stunting has been decreasing over the past decades. How-ever, in low-and middle-income countries such as Mexico, stunting is still the most prevalent form of undernutrition affecting a large number of children in the most vulnerable conditions. Breastfeeding has been identified as one of the key affordable and modifiable maternal health behaviors protecting against child stunting. Objective: To examine the association between breastfeeding (defined as never breastfed, any breast-feeding for <6 months, and any breastfeeding for ≥6 months) and other individual-, household-, and area-level factors with child stunting (defined as length/height-for-age-z-score for sex under –2 standard deviations of the World Health Organization child growth standards’ median) in Mexico. Methods: Secondary data analysis using the 2012 Mexican Health and Nutrition Survey, which allowed representativeness of rural and urban areas at national level and among 4 regions in Mexico. Our subset included data on 2,089 singleton Mexican children aged 6–35 months with information on previously identified risk and protective factors for stunting. We conducted fixed-and mixed-effects logistic regression models sequentially controlling for each level of factors. Findings: Overall, 12.3% of children were stunted and 71.1% were breastfed for ≥6 months. Any breast-feeding and being female were consistent protective factors against child stunting across all models. In contrast, child low birthweight, maternal short stature, higher number of children aged <5 years per household, and moderate to severe food insecurity were consistent risk factors for child stunting across all models. Conclusions: According to our findings, efforts to reduce child stunting in Mexico should include prenatal strategies aiming to prevent low birthweight offspring particularly among short-stature women, moderate to severe food insecure households, families with a higher number of children aged <5 years, and indigenous communities. Postnatal components should include multilevel strategies to support breastfeeding.

Characterizing The Requirements For The Matricellular Protein, Dccn, In Nervous System Function, Elizabeth L. Catudio Garrett

Graduate Student Theses, Dissertations, & Professional Papers

The brain is organized as a complex network of specialized neurons that communicate via a combination of electrical and chemical signals. Our brains function to generate movement, control organ function, or direct complex behaviors; all of which requires the ability to regulate the flow of communication between circuits and networks. Work in this thesis addresses two areas of neuron communication: first, how does the release of more than one neurotransmitter from a single neuron impact behavior, and second, are matricellular proteins (MCPs) key contributors to synaptic transmission and neuron function? The conserved CCN family of MCPs have a …

Application Of Optical Trapping To Obtain Single-Source Str Profiles From Forensically Relevant Body Fluid Mixtures With Modified Dna Analysis Workflow, Benjamin J. O'Brien

Master of Science in Forensic Science Directed Research Projects

Current methods of mixture separation in forensic DNA laboratories typically deconvolute the mixture after analysis using statistical analysis or probabilistic genotyping. To save time and effort of labs already backlogged, a method to separate mixtures on a cellular level before analysis needs to be developed. Optical trapping is a method that uses a focused 1064 nm laser to manipulate cells. Previous research has shown that approximately 50 spermatozoa or 15 leukocytes from a liquid sample are required to produce a full STR DNA profile. It was found that the number of spermatozoa required remains constant when the method of sample …

Dna Analysis And The Postmortem Submersion Interval From The Microbiome Of Waterlogged Sus Scrofa Skeletal Remains, Claire Cartozzo

Theses and Dissertations

Following water-related deaths, soft tissue on victims’ remains may be entirely absent after a temperature dependent period of time. Due to their physical and chemical components, which protect them from environmental deterioration and biological attack, bones preserve DNA for longer periods of time. Therefore, the ability to both identify an individual and estimate the postmortem submersion interval (PMSI) may depend on DNA obtained from skeletal remains. The goals of the dissertation were to examine differences in both the degradation of skeletal DNA and the microbiome inhabiting bone in freshwater aquatic environments (e.g., Henley Lake and the James River). At each …

Interactions With Humans Shape Coyote Responses To Hazing, Julie K. Young, Edd Hammill, Stewart W. Breck

Wildland Resources Faculty Publications

Medium and large carnivores coexist with people in urban areas globally, occasionally resulting in negative interactions that prompt questions about how to reduce human-wildlife conflict. Hazing, i.e., scaring wildlife, is frequently promoted as an important non-lethal means for urbanites to reduce conflict but there is limited scientific evidence for its efficacy. We used a population of captive coyotes (Canis latrans) to simulate urban human-coyote interactions and subsequent effects of hazing on coyote behavior. Past experiences with humans significantly affected the number of times a coyote approached a human to necessitate hazing. Coyotes that had been hand fed by …

Potential Distribution Of Six North American Higher-Attine Fungus-Farming Ant (Hymenoptera: Formicidae) Species, Sarah F. Senula, Joseph T. Scavetta, Joshua A. Banta, Ulrich G. Mueller, Jon N. Seal, Katrin Kellner

Biology Faculty Publications and Presentations

Ants are among the most successful insects in Earth’s evolutionary history. However, there is a lack of knowledge regarding range-limiting factors that may influence their distribution. The goal of this study was to describe the environmental factors (climate and soil types) that likely impact the ranges of five out of the eight most abundant Trachymyrmex species and the most abundant Mycetomoellerius species in the United States. Important environmental factors may allow us to better understand each species’ evolutionary history. We generated habitat suitability maps using MaxEnt for each species and identified associated most important environmental variables. We quantified niche overlap …

Sage‐Grouse Breeding And Late Brood‐Rearing Habitat Guidelines In Utah, David K. Dahlgren, Terry A. Messmer, Benjamin A. Crabb, Michel T. Kohl, Shandra Nicole Frey, Eric T. Thacker, Randy T. Larsen, Rick J. Baxter

Wildland Resources Faculty Publications

Delineation, protection, and restoration of habitats provide the basis for endangered and threatened species recovery plans. Species recovery plans typically contain guidelines that provide managers with a scientific basis to designate and manage critical habitats. As such, habitat guidelines are best developed using data that capture the full diversity of ecological and environmental conditions that provide habitat across the species’ range. However, when baseline information, which fails to capture habitat diversity, is used to develop guidelines, inconsistencies and problems arise when applying those guidelines to habitats within an ecologically diverse landscape. Greater sage‐grouse (Centrocercus urophasianus; sage‐ grouse) populations …

Improving Lake Mixing Process Simulations In The Community Land Model By Using K Profile Parameterization, Qunhui Zhang, Jiming Jin, Xiaochun Wang, Phaedra E. Budy, Nick Barrett, Sarah E. Null

Watershed Sciences Faculty Publications

We improved lake mixing process simulations by applying a vertical mixing scheme, K profile parameterization (KPP), in the Community Land Model (CLM) version 4.5, developed by the National Center for Atmospheric Research. Vertical mixing of the lake water column can significantly affect heat transfer and vertical temperature profiles. However, the current vertical mixing scheme in CLM requires an arbitrarily enlarged eddy diffusivity to enhance water mixing. The coupled CLM-KPP considers a boundary layer for eddy development, and in the lake interior water mixing is associated with internal wave activity and shear instability. We chose a lake in Arctic Alaska and …

The Next Frontier: Making Research More Reproducible, David E. Rosenberg, Yves Fillion, Rebecca L. Teasley, Samuel Sandoval-Solis, Jory S. Hecht, Jakobus E. Van Zyl, George F. Mcmahon, Jeffery S. Horsburgh, Joseph R. Kasprzyk, David G. Tarboton

Publications

Science and engineering rest on the concept of reproducibility. An important question for any study is: are the results reproducible? Can the results be recreated independently by other researchers or professionals? Research results need to be independently reproduced and validated before they are accepted as fact or theory. Across numerous fields like psychology, computer systems, and water resources there are problems to reproduce research results (Aarts et al. 2015; Collberg et al. 2014; Hutton et al. 2016; Stagge et al. 2019; Stodden et al. 2018). This editorial examines the challenges to reproduce research results and suggests community practices to overcome …

Soil Net Nitrogen Mineralisation Across Global Grasslands, A. C. Risch, S. Zimmermann, R. Ochoa-Hueso, M. Schütz, B. Frey, J. L. Firn, P. A. Fay, F. Hagedorn, E. T. Borer, E. W. Seabloom, W. S. Harpole, J. M. H. Knops, R. L. Mcculley, A. A. D. Broadbent, C. J. Stevens, M. L. Silveira, Peter B. Adler, Et Al.

Wildland Resources Faculty Publications

Soil nitrogen mineralisation (N_min), the conversion of organic into inorganic N, is important for productivity and nutrient cycling. The balance between mineralisation and immobilisation (net N_min) varies with soil properties and climate. However, because most global-scale assessments of net N_min are laboratory-based, its regulation under field-conditions and implications for real-world soil functioning remain uncertain. Here, we explore the drivers of realised (field) and potential (laboratory) soil net N_min across 30 grasslands worldwide. We find that realised N_min is largely explained by temperature of the wettest quarter, microbial biomass, clay content and bulk density. …

Estimating Total And Bioavailable Nutrient Loading To Utah Lake From The Atmosphere, Janice Brahney

Watershed Sciences Faculty Publications

Anthropogenic activities have led to increases in the emission, atmospheric transport, and deposition of key nutrients. In addition, climate change along with anthropogenic soil disturbance has led to recent increases in the mobilization and transport of soils and other particles through the atmosphere, collectively described here as dust. These increased emissions have led to growing interest and concern over the composition of atmospheric deposition and total loading of nutrients to aquatic systems. In the last several decades, much effort has been directed towards the measurement and modeling of nitrogen deposition through wet and aerosol deposition. Less is known about the …

Green Club After School Program Curriculum, Megan Willburn

Honors Program: Expanded Learning Clubs

Green Club is an after school program which encourages students to develop environmental empathy, passions for environmental sustainability, and knowledge about the workings of environmental systems.

Timing Of Invasion By Africanized Bees Coincides With Local Extinction Of A Specialized Pollinator Of A Rare Poppy In Utah, Usa, Amber D. Tripodi, Vincent J. Tepedino, Zachary M. Portman

All PIRU Publications

The introduction of exotic species can have profound impacts on mutualisms between native species in invaded areas. However, determining whether a new invader has impacted native species depends on accurately reconstructing the invasion timing. The arrival of Africanized honey bees (AHB) in southern Utah at some point between 1994 and 2011 has recently been implicated in the local extinction of Perdita meconis, a native specialist pollinator of an endangered poppy, Arctomecon humilis. Although AHBs were purportedly first detected in southern Utah in 2008, their presence in nearby Nevada, Arizona, and New Mexico by 1998–2001 suggests that they may …

Investigating The Knowledge Surrounding Folate And Folic Acid In A Cohort Of Vegetarians, Michael Dolan, Katherine Younger, Lucy Brennan, Jessica Roche

SURE Journal: Science Undergraduate Research Experience Journal

Background
The aim is to identify any gaps in the knowledge of folate and folic acid in vegetarians, which is of interest given the increasing adoption of vegetarian type diets.

Methods
In this convenience sample, 106 people answered an online questionnaire regarding folate intake and awareness among vegetarians. This was created using Google Forms and was shared via Facebook, including on various national and college vegetarian group pages. There were 44 questions. Twenty-four participants were excluded, because they reported eating fish, chicken or other meat. Final data analysis included 82 subjects. The majority of these vegetarians were females over the …

Effects Of Severe Water Stress On Maize Growth Processes In The Field, Libing Song, Jiming Jin, Jianqiang He

Watershed Sciences Faculty Publications

In this study, we investigated the effects of water stress on the growth and yield of summer maize (Zea mays L.) over four phenological stages: Seedling, jointing, heading, and grain-filling. Water stress treatments were applied during each of these four stages in a water-controlled field in the Guanzhong Plain, China between 2013 and 2016. We found that severe water stress during the seedling stage had a greater effect on the growth and development of maize than stress applied during the other three stages. Water stress led to lower leaf area index (LAI) and biomass owing to reduced intercepted photosynthetically active …

Effects Of Land-Use Change And Prey Abundance On The Body Condition Of An Obligate Carnivore At The Wildland-Urban Interface, Courtney A. C. Coon, Bradley C. Nichols, Zara Mcdonald, David C. Stoner

Wildland Resources Faculty Publications

Land-use change represents a primary driver of carnivore population declines, yet some large carnivore species have acclimated and persist within anthropogenically altered landscapes. Previous attention has been focused on the genetic and behavioral implications of land-use changes, but few studies have investigated how human development impacts animal physiology and health. Here we examined how body condition scores of a widely distributed North American carnivore, the puma (Puma concolor), are affected by anthropogenic habitat modification. For this study we collected 252 puma camera trap events across a land-use gradient in the San Francisco Bay Area. We found that pumas …

A Case For Eustress In Grazing Animals, Juan J. Villalba, Xavier Manteca

Wildland Resources Faculty Publications

Herbivores grazing in extensive systems are exposed to a series of challenges, rooted in the inherent spatial and temporal variability of their environment that potentially constrain their health, nutrition, and welfare. Nevertheless, in this review, we argue that challenges induced by some biotic (e.g., vegetation) and abiotic (e.g., terrain) factors may also be viewed as “positive” sources of stress or eustress, since they present complex problems, that when solved successfully elicit a greater degree of behavioral plasticity and adaptability in grazing animals. Chemically and structurally diverse landscapes require animals to display complex behaviors and exhibit adaptive capabilities, like building a …

Use Of Low-Cost Ambient Particulate Sensors In Nablus, Palestine With Application To The Assessment Of Regional Dust Storms, Abdelhaleem Khader, Randal S. Martin

Publications

Few air pollutant studies within the Palestinian territories have been reported in the literature. In March–April and May–June of 2018, three low-cost, locally calibrated particulate monitors (AirU’s) were deployed at different elevations and source areas throughout the city of Nablus in Northern West Bank, Palestine. During each of the three-week periods, high but site-to-site similar particulate matter less than 2.5 µm in aerodynamic diameter (PM_2.5) and less than 10 µm (PM₁₀) concentrations were observed. The PM_2.5 concentrations at the three sampling locations and during both sampling periods averaged 38.2 ± 3.6 µg/m³, well …

Climate Change Accelerates Recovery Of The Tatra Mountain Lakes From Acidification And Increases Their Nutrient And Chlorophyll A Concentrations, Jiří Kopáček, Jiří Kaňa, Svetlana Bičárová, Janice Brahney, Tomáš Navrátil, Stephen A. Norton, Petr Porcal, Evžen Stuchlik

Watershed Sciences Faculty Publications

We evaluated changes in the concentration of cations, anions, nutrients (dissolved organic carbon, DOC; phosphorus, P; and nitrogen forms including nitrate, NO₃⁻ and total organic nitrogen, TON), and chlorophyll a (Chl-a) in 31 Tatra Mountain lakes in Slovakia and Poland during their recovery from acidic deposition (1992–2018). Typical effects of decreasing acidic deposition on the lakes’ water composition, such as decreasing base cation concentrations, were confounded by climate change and catchment characteristics, including areal proportions of well-developed soils and scree. A climate-related increase in physical erosion provided freshly exposed unweathered granodiorite (the dominant bedrock) to chemical …

The Future Of Blue Carbon Science, Peter I. Macreadie, Andrea Anton, John A. Raven, Nicola Beaumont, Rod M. Connolly, Daniel A. Friess, Jeffrey J. Kelleway, Hilary Kennedy, Tomohiro Kuwae, Paul S. Lavery, Catherine E. Lovelock, Dan A. Smale, Eugenia T. Apostolaki, Trisha Brooke Atwood, Jeff Baldock, Thomas S. Bianchi, Gail L. Chmura, Bradley D. Eyre, James W. Fourqurean, Jason M. Hall-Spencer, Mark Huxham, Iris E. Hendriks, Dorte Krause-Jensen, Dan Laffoley, Tiziana Luisetti, Núria Marbà, Pere Masque, Karen J. Mcglathery, J. Patrick Megonigal, Daniel Murdiyarso, Bayden D. Russell, Rui Santos, Oscar Serrano, Brian R. Silliman, Kenta Watanabe, Carlos M. Duarte

Watershed Sciences Faculty Publications

The term Blue Carbon (BC) was first coined a decade ago to describe the disproportionately large contribution of coastal vegetated ecosystems to global carbon sequestration. The role of BC in climate change mitigation and adaptation has now reached international prominence. To help prioritise future research, we assembled leading experts in the field to agree upon the top-ten pending questions in BC science. Understanding how climate change affects carbon accumulation in mature BC ecosystems and during their restoration was a high priority. Controversial questions included the role of carbonate and macroalgae in BC cycling, and the degree to which greenhouse gases …

Tannin-Containing Legumes And Forage Diversity Influence Foraging Behavior, Diet Digestibility, And Nitrogen Excretion By Lambs, Sebastian Lagrange, Juan J. Villalba

Wildland Resources Faculty Publications

Diverse combinations of forages with different nutrient profiles and plant secondary compounds may improve intake and nutrient utilization by ruminants. We tested the influence of diverse dietary combinations of tannin- (sainfoin-Onobrichis viciifolia; birdsfoot trefoil-Lotus corniculatus) and non-tannin- (alfalfa-Medicago sativa L.) containing legumes on intake and diet digestibility in lambs. Freshly cut birdsfoot trefoil, alfalfa, and sainfoin were offered in ad libitum amounts to 42 lambs in individual pens assigned to 7 treatments (6 animals/treatment): 1) single forage species (sainfoin [SF], birdsfoot trefoil [BFT], and alfalfa [ALF]), 2) all possible …

A Review And Updated Classification Of Pollen Gathering Behavior In Bees (Hymenoptera, Apoidea), Zachary M. Portman, Michael C. Orr, Terry Griswold

All PIRU Publications

Pollen is the primary protein and nutrient source for bees and they employ many different behaviors to gather it. Numerous terms have been coined to describe pollen gathering behaviors, creating confusion as many are not clearly-defined or overlap with existing terms. There is a need for a clear yet flexible classification that enables accurate, succinct descriptions of pollen gathering behaviors to enable meaningful discussion and comparison. Here, we classify the different pollen gathering behaviors into two main classes: active and incidental pollen collection. Active pollen collection is subdivided into six behaviors: scraping with the extremities, buzzing, rubbing with the body …

Controls And Adaptive Management Of Nitrification In Agricultural Soils, Jeanette M. Norton, Yang Ouyang

Plants, Soils, and Climate Faculty Publications

Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, …

On-The-Road Testing Of The Effects Of Driver’S Experience, Gender, Speed, And Road Grade On Car Emissions, Abdelhaleem I. Khader, Randy S. Martin

Publications

On-road vehicles have become a dominant source of air pollution and energy consumption in many parts of the world. As a result, estimating the amount of pollution from these vehicles and analyzing the factors affecting their emission is necessary to understand and manage ambient air quality. Traditionally, automobile emissions have been measured with dynamometer tests using representative driving cycles. A review of the related literature shows that there is a lack of real life, on-the-road testing of automobile emissions. Moreover, a few previous studies have directly discussed the impact of driver variability on emissions from the vehicles. This research analyzes …

Environmental Differences Between Migratory And Resident Ungulates—Predicting Movement Strategies In Rocky Mountain Mule Deer (Odocoileus Hemionus) With Remotely Sensed Plant Phenology, Snow, And Land Cover, Benjamin Robb, Qiongyu Huang, Joseph O. Sexton, David C. Stoner, Peter Leimgruber

Wildland Resources Faculty Publications

Migration is a valuable life history strategy for many species because it enables individuals to exploit spatially and temporally variable resources. Globally, the prevalence of species’ migratory behavior is decreasing as individuals forgo migration to remain resident year-round, an effect hypothesized to result from anthropogenic changes to landscape dynamics. Efforts to conserve and restore migrations require an understanding of the ecological characteristics driving the behavioral tradeoff between migration and residence. We identified migratory and resident behaviors of 42 mule deer (Odocoileus hemionus) based on GPS locations and correlated their locations to remotely sensed indicators of forage quality, land cover, snow …

The Differences Between Rewilding And Restoring An Ecologically Degraded Landscape, Johan T. Du Toit, Nathalie Pettorelli

Wildland Resources Faculty Publications

1. Rewilding is a developing concept in ecosystem stewardship that involves reorganizing and regenerating wildness in an ecologically degraded landscape, with present and future ecosystem function being of higher consideration than historical benchmark conditions. This approach differs from ecosystem restoration but the two concepts are often conflated because (a) they both rely on similar management actions (at least initially) and (b) it can be erroneously assumed that they both aim for similar states of wildness.
2. Rewilding and restoring both influence biodiversity, and common management actions such as species reintroductions (e.g. beavers or wolves) can be integral to a rewilding project. However, …