Biology Commons^™

Low Intensity Vibrations Augment Mesenchymal Stem Cell Proliferation And Differentiation Capacity During In Vitro Expansion, Guniz Bas, Stacie Loisate, Stephanie F. Hudon, Kali Woods, Eric J. Hayden, Xinzhu Pu, Richard Beard, Julia T. Oxford, Gunes Uzer

Biology Faculty Publications and Presentations

A primary component of exercise, mechanical signals, when applied in the form of low intensity vibration (LIV), increases mesenchymal stem cell (MSC) osteogenesis and proliferation. While it is generally accepted that exercise effectively combats the deleterious effects of aging in the musculoskeletal system, how long-term exercise affects stem cell aging, which is typified by reduced proliferative and differentiative capacity, is not well explored. As a first step in understanding the effect of long-term application of mechanical signals on stem cell function, we investigated the effect of LIV during in vitro expansion of MSCs. Primary MSCs were subjected to either a …

Quantifying The Relative Importance Of Variation In Predation And The Environment For Species Coexistence, Lauren G. Shoemaker, Allison K. Barner, Leonora S. Bittleston, Ashley I. Teufel

Biology Faculty Publications and Presentations

Coexistence and food web theory are two cornerstones of the long‐standing effort to understand how species coexist. Although competition and predation are known to act simultaneously in communities, theory and empirical study of these processes continue to be developed largely independently. Here, we integrate modern coexistence theory and food web theory to simultaneously quantify the relative importance of predation and environmental fluctuations for species coexistence. We first examine coexistence in a theoretical, multitrophic model, adding complexity to the food web using machine learning approaches. We then apply our framework to a stochastic model of the rocky intertidal food web, partitioning …

Effects Of Management For Productivity On Adult Survival Of Snowy Plovers, Eleanor P. Gaines, Stephen J. Dinsmore, Michael T. Murphy

Biology Faculty Publications and Presentations

Understanding the factors contributing to variation in demographic parameters and their influences on population growth is fundamental to effective conservation of small populations, but this information is often not available. Among shorebirds, population growth is generally most sensitive to changes in adult survival so understanding the factors affecting this vital rate is important. We used a long‐term mark–resight dataset and Program MARK to examine the effect of management actions, initiated to improve nesting productivity, on adult survival in a threatened population of Snowy Plovers (Charadrius nivosus ) in Oregon, USA. Apparent adult survival averaged 0.71 ± 0.01 (SE), but …

Clinical Trials In Alzheimer’S Disease: A Hurdle In The Path Of Remedy, Alexandra E. Oxford, Erica S. Stewart, Troy T. Rohn

Biology Faculty Publications and Presentations

Human clinical trials seek to ameliorate the disease states and symptomatic progression of illnesses that, as of yet, are largely untreatable according to clinical standards. Ideally, clinical trials test “disease-modifying drugs,” i.e., therapeutic agents that specifically modify pathological features or molecular bases of the disease and would presumably have a large impact on disease progression. In the case of Alzheimer’s disease (AD), however, this approach appears to have stalled progress in the successful development of clinically useful therapies. For the last 25 years, clinical trials involving AD have centered on beta-amyloid (Aβ) and the Aβ hypothesis of …

Relevance Of Individual And Environmental Drivers Of Movement Of Golden Eagles, Maitreyi Sur

Biology Faculty Publications and Presentations

An animal’s movement is expected to be governed by an interplay between goals determined by its internal state and energetic costs associated with navigating through the external environment. Understanding this ecological process is challenging when an animal moves in two dimensions and even more difficult for birds that move in a third dimension. To understand the dynamic interaction between the internal state of an animal and the variable external environment, we evaluated hypotheses explaining association of different covariates of movement and the trade-offs birds face as they make behavioural decisions in a fluctuating landscape. We used ~870 000 GPS telemetry …

Context-Dependent Dynamics Lead To The Assembly Of Functionally Distinct Microbial Communities, Leonora S. Bittleston, Matti Gralka, Gabriel E. Levanthal, Itzhak Mizrahi, Otto X. Cordero

Biology Faculty Publications and Presentations

Niche construction through interspecific interactions can condition future community states on past ones. However, the extent to which such history dependency can steer communities towards functionally different states remains a subject of active debate. Using bacterial communities collected from wild pitchers of the carnivorous pitcher plant, Sarracenia purpurea, we test the effects of history on composition and function across communities assembled in synthetic pitcher plant microcosms. We find that the diversity of assembled communities is determined by the diversity of the system at early, pre-assembly stages. Species composition is also contingent on early community states, not only because of …

Tropical Pitcher Plants (Nepenthes) Act As Ecological Filters By Altering Properties Of Their Fluid Microenvironments, Kadeem J. Gilbert, Leonora S. Bittleston, Wenfei Tong, Naomi E. Pierce

Biology Faculty Publications and Presentations

Characteristics of host species can alter how other, interacting species assemble into communities by acting as ecological filters. Pitchers of tropical pitcher plants (Nepenthes) host diverse communities of aquatic arthropods and microbes in nature. This plant genus exhibits considerable interspecific diversity in morphology and physiology; for example, different species can actively control the pH of their pitcher fluids and some species produce viscoelastic fluids. Our study investigated the extent to which Nepenthes species differentially regulate pitcher fluid traits under common garden conditions, and the effects that these trait differences had on their associated communities. Sixteen species of Nepenthes …

Operational Large-Area Land-Cover Mapping: An Ethiopia Case Study, Trevor Caughlin

Biology Faculty Publications and Presentations

Knowledge of land cover and land use nationally is a prerequisite of many studies on drivers of land change, impacts on climate, carbon storage and other ecosystem services, and allows for sufficient planning and management. Despite this, many regions globally do not have accurate and consistent coverage at the national scale. This is certainly true for Ethiopia. Large-area land-cover characterization (LALCC), at a national scale is thus an essential first step in many studies of land-cover change, and yet is itself problematic. Such LALCC based on remote-sensing image classification is associated with a spectrum of technical challenges such as data …

Patterns And Mechanisms Of Heterogeneous Breeding Distribution Shifts Of North American Migratory Birds, Hanna M. Mccaslin, Julie A. Heath

Biology Faculty Publications and Presentations

There is widespread evidence that species distributions are shifting in response to climate change. Warming temperatures and climate niche constraints are hypothesized drivers of northward shifts in temperate migratory bird breeding distributions, but heterogeneity in the direction of distribution shifts suggests that the climate niche hypothesis does not explain all changes in distributions. We propose that: 1) changes in migration costs and benefits related to dampened seasonal differences between breeding and winter areas, 2) sensitivity to supplemental cues that affect duration of migration and onset of reproduction, 3) a latitudinal mismatch-driven fitness gradient, or a combination of these drivers may …

Do Foliar Endophytes Matter In Litter Decomposition?, Emily R. Wolfe, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

Litter decomposition rates are affected by a variety of abiotic and biotic factors, including the presence of fungal endophytes in host plant tissues. This review broadly analyzes the findings of 67 studies on the roles of foliar endophytes in litter decomposition, and their effects on decomposition rates. From 29 studies and 1 review, we compiled a comprehensive table of 710 leaf-associated fungal taxa, including the type of tissue these taxa were associated with and isolated from, whether they were reported as endo- or epiphytic, and whether they had reported saprophytic abilities. Aquatic (i.e., in-stream) decomposition studies of endophyte-affected litter were …

Evaluation Of The Efficacy Of A Cholera Toxin-Based Staphylococcus Aureus Vaccine Against Bovine Intramammary Challenge, Hussain A. Alabdullah, Elise Overgaard, Danielle Scarbrough, Janet E. Williams, Omid Mohammad Mousa, Gary Dunn, Laura Bond, Mark A. Mcguire, Juliette K. Tinker

Biology Faculty Publications and Presentations

Staphylococcus aureus (S. aureus) is a primary agent of bovine mastitis and a source of significant economic loss for the dairy industry. We previously reported antigen-specific immune induction in the milk and serum of dairy cows following vaccination with a cholera toxin A₂ and B subunit (CTA₂/B) based vaccine containing the iron-regulated surface determinant A (IsdA) and clumping factor A (ClfA) antigens of S. aureus (IsdA + ClfA-CTA₂/B). The goal of the current study was to assess the efficacy of this vaccine to protect against S. aureus infection after intramammary challenge. Six mid-lactation …

Pedigree Validation Using Genetic Markers In An Intensively-Managed Taonga Species, The Critically Endangered Kakī (Himantopus Novaezelandiae), Ashley Overbeek, Stephanie Galla, Liz Brown, Simon Cleland, Cody Thyne, Richard Maloney, Tammy Steeves

Biology Faculty Publications and Presentations

Many species recovery programmes use pedigrees to understand the genetic ancestry of individuals to inform conservation management. However, incorrect parentage assignment may limit the accuracy of these pedigrees and subsequent management decisions. This is especially relevant for pedigrees that include wild individuals, where misassignment may not only be attributed to human error, but also promiscuity (i.e. extra-pair parentage) or egg-dumping (i.e. brood parasitism). Here, we evaluate pedigree accuracy in the socially monogamous and critically endangered kakī (black stilt, Himantopus novaezelandiae) using microsatellite allele-exclusion analyses for 56 wild family groups across three breeding seasons (2014–2016, n= 340). We identified …

Gateway Scholarships In Biological Sciences: Year 3 Annual Report, Vicki Stieha, Julia Oxford, Amy Ulappa, Brittnee Earl, Jennifer Forbey, Laura Bond, Kevin Feris, Jocelyn Cullers

Biology Faculty Publications and Presentations

This report summarizes grant activities, progress toward goals, and broader impacts of the Gateway Scholars Program in the Boise State Department of Biological Sciences during the 2019-20 academic year.

Development, Characterization, And Cross-Amplification Of Polymorphic Microsatellite Markers For North American Trachymyrmex And Mycetomoellerius Ants, Alix E. Matthews, Chase Rowan, Colby Stone, Katrin Kellner, Jon Seal

Biology Faculty Publications and Presentations

Objective: The objective of this study is to develop and identify polymorphic microsatellite markers for fungus-gardening (attine) ants in the genus Trachymyrmex sensu lato. These ants are important ecosystem engineers and have been a model group for understanding complex symbiotic systems, but very little is understood about the intraspecific genetic patterns across most North American attine species. These microsatellite markers will help to better study intraspecific population genetic structure, gene flow, mating habits, and phylogeographic patterns in these species and potentially other congeners. Results: Using next-generation sequencing techniques, we identified 17 and 12 polymorphic microsatellite markers from T. septentrionalis and …

Fatty Acid Composition Analyses Of Commercially Important Fish Species From The Pearl River Estuary, China, Xiyang Zhang, Xi Ning, Xiaoxiao He, Xian Sun, Xinjian Yu, Yuanxiong Cheng, Riqing Yu, Yuping Wu

Biology Faculty Publications and Presentations

Evaluation of fish nutritional content information could provide essential guidance for seafood consumption and human health protection. This study investigated the lipid contents, fatty acid compositions, and nutritional qualities of 22 commercially important marine fish species from the Pearl River Estuary (PRE), South China Sea. All the analyzed species had a low to moderate lipid content (0.51–7.35% fat), with no significant differences in fatty acid profiles among fishes from different lipid categories (p > 0.05). Compared with previous studies from other regions, the examined fish species exhibited higher proportions of saturated fatty acids (SFAs, 39.1 ± 4.00%) and lower contents of …

Mitochondrial Dna Variation And Selfish Propagation Following Experimental Bottlenecking In Two Distantly Related Caenorhabditis Briggsae Isolates, Josiah Tad Wagner, Dana K. Howe, Suzanne Estes, Dee R. Denver

Biology Faculty Publications and Presentations

Understanding mitochondrial DNA (mtDNA) evolution and inheritance has broad implications for animal speciation and human disease models. However, few natural models exist that can simultaneously represent mtDNA transmission bias, mutation, and copy number variation. Certain isolates of the nematode Caenorhabditis briggsae harbor large, naturally-occurring mtDNA deletions of several hundred base pairs affecting the NADH dehydrogenase subunit 5 (nduo-5) gene that can be functionally detrimental. These deletion variants can behave as selfish DNA elements under genetic drift conditions, but whether all of these large deletion variants are transmitted in the same preferential manner remains unclear. In addition, the degree to which …

A Basic Ddradseq Two‐Enzyme Protocol Performs Well With Herbarium And Silica‐Dried Tissues Across Four Genera, Ingrid E. Jordon‐Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nick Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels

Biology Faculty Publications and Presentations

PREMISE: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double-digest restriction site–associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica-dried and herbarium tissue.

METHODS: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a ddRADseq protocol. The effects of DNA degradation, taxon, and specimen age were assessed. RESULTS: Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were …

First Report Of Molecular Characterization And Phylogeny Of Trichuris Fossor Hall, 1916 (Nematoda: Trichuridae), Malorri R. Hughes, Deborah A. Duffield, Dana K. Howe, Dee Denver

Biology Faculty Publications and Presentations

Because species of Trichuris are morphologically similar and ranges of host preference are variable, using molecular data to evaluate species delineations is essential for properly quantifying biodiversity of and relationships within Trichuridae. Trichuris fossor has been reported from Thomomys spp. (Rodentia: Geomyidae, ‘pocket gophers’) hosts based on morphological features alone. Partial 18S rRNA sequences for specimens identified as T. fossor based on morphology, along with sequences from 26 additional taxa, were used for a phylogenetic analysis. Evolutionary histories were constructed using maximum likelihood and Bayesian inference. In both analyses, the specimens fell within the Trichuris clade with 100% support and …

Crossing Boundaries: Steps Toward Measuring Undergraduates' Interdisciplinary Science Understanding, Brie Tripp, Sophia A. Voronoff, Erin Shortlidge

Biology Faculty Publications and Presentations

A desired outcome of education reform efforts is for undergraduates to effectively integrate knowledge across disciplines in order to evaluate and address real-world issues. Yet there are few assessments designed to measure if and how students think interdisciplinarily. Here, a sample of science faculty were surveyed to understand how they currently assess students’ interdisciplinary science understanding. Results indicate that individual writing-intensive activities are the most frequently used assessment type (69%). To understand how writing assignments can accurately assess students’ ability to think interdisciplinarily, we used a preexisting rubric, designed to measure social science students’ interdisciplinary understanding, to assess writing assignments …

Genotypic Diversity And Host-Specificity Of Frankia Bacteria Associated With Sympatric Populations Of Alnus Rubra And Alnus Rhombifolia In Oregon, Mehmet Ali Balkan, Nathan U. Stewart, Emily S. Kauffman, Emily R. Wolfe, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

Biological nitrogen fixation is one of the most critical processes contributing to ecosystem productivity and stability on a global scale. In temperate climates of the northern hemisphere, plant-root associated bacteria of the genus Frankia are the major nitrogen fixers in forest environments. Trees belonging to the genus Alnus are the most widespread hosts of Frankia in the Pacific Northwest, and a myriad of biotic and abiotic factors can influence the robustness of this symbiosis. Host identity and bacterial strain are important features that can impact Alnus-Frankia association, but little is known about the interplay of intrageneric hosts that co-occur in …

Roadmap For Naming Uncultivated Archaea And Bacteria, Alison Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T. Konstantinidis, Christopher E. Lane, R. Thane Papke, Anna-Louise Reysenbach, Multiple Additional Authors

Biology Faculty Publications and Presentations

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code …

Integrating Oceanographic Research Into High School Curricula: Achieving Broader Impacts Through Systems Education Experiences Modules, Monica V. Orellana, Claudia Ludwig, Anne W. Thompson, Nitin S. Baliga

Biology Faculty Publications and Presentations

We describe a framework for incorporating cross-disciplinary oceanographic research into high school curriculum modules and discuss how this framework could be adopted broadly by ocean scientists to build cohesive broader impacts programs nested within individual oceanographic research programs.

Reemergence Of Guadalupe Fur Seals In The U.S. Pacific Northwest: The Epidemiology Of Tranding Events During 2005–2016, Erin D'Agnese, Dyanna M. Lambourn, James Rice, Debbie Duffield, Jessica L. Huggins, Terry Spraker, Stephen A. Raverty, Tetiana Kuzmina, Micheal E. Grigg, Kristin Wilkinson, Multiple Additional Authors

Biology Faculty Publications and Presentations

Guadalupe fur seals (GFS), Arctocephalus philippii townsendi, an U.S. Endangered Species Act threatened pinniped, have recently reappeared in their historic range along the western seaboard of the continental United States. Starting 2005 through 2016, 169 GFSs stranded in Washington and Oregon, involving two designated unusual mortality events. The circumstances surrounding GFS strandings, mortality, and their increased presence in Oregon and Washington were analyzed during this study. Detailed necropsies, histopathology (n = 93), and epidemiological analysis found three main causes of death (COD): emaciation (44%), trauma (29%), and infectious disease (19%) and the factors associated with overall strandings and …

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 …

Human-Carnivore Relations: Conflicts, Tolerance And Coexistence In The American West, Juan M. Requena-Mullor

Biology Faculty Publications and Presentations

Carnivore and humans live in proximity due to carnivore recovery efforts and ongoing human encroachment into carnivore habitats globally. The American West is a region that uniquely exemplifies these human-carnivore dynamics, however, it is unclear how the research community here integrates social and ecological factors to examine human-carnivore relations. Therefore, strategies promoting human-carnivore coexistence are urgently needed. We conducted a systematic review on human-carnivore relations in the American West covering studies between 2000 and 2018. We first characterized human-carnivore relations across states of the American West. Second, we analyzed similarities and dissimilarities across states in terms of coexistence, tolerance, number …

Integrating Anthropogenic Factors Into Regional-Scale Species Distribution Models: A Novel Application In The Imperiled Sagebrush Biome, Juan M. Requena-Mullor, Kaitlin C. Maguire, Douglas J. Shinneman, Timothy Trevor Caughlin

Biology Faculty Publications and Presentations

Species distribution models (SDM) that rely on regional-scale environmental variables will play a key role in forecasting species occurrence in the face of climate change. However, in the Anthropocene, a number of local-scale anthropogenic variables, including wildfire history, land-use change, invasive species, and ecological restoration practices can override regional-scale variables to drive patterns of species distribution. Incorporating these human-induced factors into SDMs remains a major research challenge, in part because spatial variability in these factors occurs at fine scales, rendering prediction over regional extents problematic. Here, we used big sagebrush (Artemisia tridentata Nutt.) as a model species to …

Species-Specific Effects Of Passive Warming In An Antarctic Moss System, Hannah M. Prather, Angélica Casanova-Katny, Andrew F. Clements, Matthew Chmielewski, Mehmet Ali Balkan, Erin Shortlidge, Todd Rosenstiel, Sarah Eppley

Biology Faculty Publications and Presentations

Polar systems are experiencing rapid climate change and the high sensitivity of these Arctic and Antarctic ecosystems make them especially vulnerable to accelerated ecological transformation. In Antarctica, warming results in a mosaic of ice-free terrestrial habitats dominated by a diverse assemblage of cryptogamic plants (i.e. mosses and lichens). Although these plants provide key habitat for a wide array of microorganisms and invertebrates, we have little understanding of the interaction between trophic levels in this terrestrial ecosystem and whether there are functional effects of plant species on higher trophic levels that may alter with warming. Here, we used open top chambers …

Cul3 Regulates Cyclin E1 Protein Abundance Via A Degron Located Within The N-Terminal Region Of Cyclin E, Brittney Marie Davidge, Katia De Oliveira Rebola, Larry N. Agbor, Curt D. Sigmund, Jeffrey D. Singer

Biology Faculty Publications and Presentations

mammalian cells. Increased levels of cyclin E are found in some cancers. Additionally, proteolytic removal of the cyclin E N-terminus occurs in some cancers and is associated with increased cyclin E–Cdk2 activity and poor clinical prognosis. Cyclin E levels are tightly regulated and controlled in part through ubiquitin-mediated degradation initiated by one of two E3 ligases, Cul1 and Cul3. Cul1 ubiquitylates phosphorylated cyclin E, but the mechanism through which Cul3 ubiquitylates cyclin E is poorly understood. In experiments to ascertain how Cul3 mediates cyclin E destruction, we identified a degron on cyclin E that Cul3 targets for ubiquitylation. Recognition of …

Where To Forage When Afraid: Does Perceived Risk Impair Use Of The Foodscape?, Samantha P.H. Dwinnell, Hall Sawyer, Jill E. Randall, Jeffery L. Beck, Jennifer S. Forbey, Gary L. Fralick, Kevin L. Monteith

Biology Faculty Publications and Presentations

The availability and quality of forage on the landscape constitute the foodscape within which animals make behavioral decisions to acquire food. Novel changes to the foodscape, such as human disturbance, can alter behavioral decisions that favor avoidance of perceived risk over food acquisition. Although behavioral changes and population declines often coincide with the introduction of human disturbance, the link(s) between behavior and population trajectory are difficult to elucidate. To identify a pathway by which human disturbance may affect ungulate populations, we tested the Behaviorally Mediated Forage‐Loss Hypothesis, wherein behavioral avoidance is predicted to reduce use of available forage adjacent to …

Phylogenomics Resolves Major Relationships And Reveals Significant Diversification Rate Shifts In The Evolution Of Silk Moths And Relatives, J. R. Barber

Biology Faculty Publications and Presentations

Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections.

Results: …