Biology Commons^™

Importance Of Local Weather And Environmental Gradients On Demography Of A Broadly Distributed Temperate Frog, Hallie Lingo, James C. Munger

Biology Faculty Publications and Presentations

Amphibian populations are sensitive to environmental temperatures and moisture, which vary with local weather conditions and may reach new norms and extremes as contemporary climate change progresses. Using long-term (11–16 years) mark-recapture data from 10 populations of the Columbia spotted frog (Rana luteiventris) from across its U.S. range, we addressed hypotheses about how demographic relationships to weather depend upon a population’s position along climate gradients. We estimated the effect of seasonal weather on annual survival probability and recruitment rates both within populations and across the species’ range from subalpine forests to semi-arid deserts. We calculated population-specific weather variables …

Mitonuclear Mismatch Is Associated With Increased Male Frequency, Outcrossing, And Male Sperm Size In Experimentally-Evolved C. Elegans, Brent W. Bever, Zachary P. Dietz, Jennifer Anne Sullins, Ariana M. Montoya, Ulfar Bergthorsson, Vaishali Katju, Suzanne Estes

Biology Faculty Publications and Presentations

We provide a partial test of themitonuclear sex hypothesiswith the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. Among facultatively outcrossing lines, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested—nuclear isp-1, mitochondrial cox-1 and ctb-1, and an isp-1 IV; ctb-1M mitonuclear double mutant—and confirmed for …

Genome-Wide Identification Of Novel Srnas In Streptococcus Mutans, Madeline Claire Krieger, Justin Merritt, Rahul Raghavan

Biology Faculty Publications and Presentations

Streptococcus mutans is a major pathobiont involved in the development of dental caries. Its ability to utilize numerous sugars and to effectively respond to environmental stress promotes S. mutans proliferation in oral biofilms. Because of their quick action and low energetic cost, non-coding small RNAs (sRNAs) represent an ideal mode of gene regulation in stress response networks, yet their roles in oral pathogens have remained largely unexplored. We identified 15 novel sRNAs in S. mutans and show that they respond to four stress-inducing conditions commonly encountered by the pathogen in human mouth: sugar-phosphate stress, hydrogen peroxide exposure, high temperature, and …

Recombination Mediator Proteins: Misnomers That Are Key To Understanding The Genomic Instabilities In Cancer, Justin Courcelle, Travis K. Worley, Charmain Courcelle

Biology Faculty Publications and Presentations

Recombination mediator proteins have come into focus as promising targets for cancer therapy, with synthetic lethal approaches now clinically validated by the efficacy of PARP inhibitors in treating BRCA2 cancers and RECQ inhibitors in treating cancers with microsatellite instabilities. Thus, understanding the cellular role of recombination mediators is critically important, both to improve current therapies and develop new ones that target these pathways. Our mechanistic understanding of BRCA2 and RECQ began in . Here, we review the cellular roles of RecF and RecQ, often considered functional homologs of these proteins in bacteria. Although these proteins were originally isolated as genes …

Diversity, Biology, And History Of Psilocybin-Containing Fungi: Suggestions For Research And Technological Development, R. C. Van Court, K. W. Meyer, M. S. Wiseman, Daniel J. Ballhorn, K. R. Amses, J. C. Slot, B.T. M. Dentinger, R. Garibay-Orijel, J. K. Uehling

Biology Faculty Publications and Presentations

Therapeutic use of psilocybin has become a focus of recent international research, with preliminary data showing promise to address a range of treatment-resistant mental health conditions. However, use of psilocybin as a healing entheogen has a long history through traditional consumption of mushrooms from the genus Psilocybe. The forthcoming adoption of new psilocybin-assisted therapeutic practices necessitates identification of preferred sources of psilocybin; consequently, comprehensive understanding of psilocybin-containing fungi is fundamental to consumer safety. Here we examine psilocybin producing fungi, discuss their biology, diversity, and ethnomycological uses. We also review recent work focused on elucidation of psilocybin biosynthetic production pathways, especially …

Interactions Between Strains Govern The Eco-Evolutionary Dynamics Of Microbial Communities, Akshit Goyal, Leonora S. Bittleston, Gabriel E. Leventhal, Lu Lu, Otto X. Cordero

Biology Faculty Publications and Presentations

Genomic data has revealed that genotypic variants of the same species, that is, strains, coexist and are abundant in natural microbial communities. However, it is not clear if strains are ecologically equivalent, and at what characteristic genetic distance they might exhibit distinct interactions and dynamics. Here, we address this problem by tracking 10 taxonomically diverse microbial communities from the pitcher plant Sarracenia purpurea in the laboratory for more than 300 generations. Using metagenomic sequencing, we reconstruct their dynamics over time and across scales, from distant phyla to closely related genotypes. We find that most strains are not ecologically equivalent and …

New Opportunities And Untapped Scientific Potential In The Abyssal Ocean, Jeffrey J. Marlowe, Rika E. Anderson, Anna-Louise Reysenbach, Jeffrey S. Seewald, Timothy M. Shank, Andreas P. Teske, V. Dorsey Wanless, S. Adam Soule

Biology Faculty Publications and Presentations

The abyssal ocean covers more than half of the Earth’s surface, yet remains understudied and underappreciated. In this Perspectives article, we mark the occasion of the Deep Submergence Vehicle Alvin’s increased depth range (from 4500 to 6500 m) to highlight the scientific potential of the abyssal seafloor. From a geologic perspective, ultra-slow spreading mid-ocean ridges, Petit Spot volcanism, transform faults, and subduction zones put the full life cycle of oceanic crust on display in the abyss, revealing constructive and destructive forces over wide ranges in time and space. Geochemically, the abyssal pressure regime influences the solubility of constituents such as …

Mule Deer Do More With Less: Comparing Their Nutritional Requirements And Tolerances With White-Tailed Deer, Anna R. Staudenmaier, Lisa A. Shipley, Meghan J. Camp, Jennifer S. Forbey, Ann E. Hagerman, Abigail E. Brandt, Daniel H. Thornton

Biology Faculty Publications and Presentations

Congeneric species often share ecological niche space resulting in competitive interactions that either limit co-occurrence or lead to niche partitioning. Differences in fundamental nutritional niches mediated through character displacement or isolation during evolution are potential mechanisms that could explain overlapping distribution patterns of congenerics. We directly compared nutritional requirements and tolerances that influence the fundamental niche of mule (Odocoileus hemionus) and white-tailed deer (O. virginianus), which occur in allopatry and sympatry in similar realized ecological niches across their ranges in North America. Digestible energy and protein requirements and tolerances for plant fiber and plant secondary …

Culturable Fungal Endophyte Communities Of Primary Successional Plants On Mount St. Helens, Wa, Usa, Emily R. Wolfe, Robyn Dove, Cassandra Webster, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

Background: While a considerable amount of research has explored plant community composition in primary successional systems, little is known about the microbial communities inhabiting these pioneer plant species. Fungal endophytes are ubiquitous within plants, and may play major roles in early successional ecosystems. Specifically, endophytes have been shown to affect successional processes, as well as alter host stress tolerance and litter decomposition dynamics—both of which are important components in harsh environments where soil organic matter is still scarce.

Results: To determine possible contributions of fungal endophytes to plant colonization patterns, we surveyed six of the most common woody …

The Nutritional Condition Of Moose Co-Varies With Climate, But Not With Density, Predation Risk, Or Diet Composition, Jennifer S. Forbey, Daniel P. Melody

Biology Faculty Publications and Presentations

A fundamental question about the ecology of herbivore populations pertains to the relative influence of biotic and abiotic processes on nutritional condition. Nutritional condition is influenced in important, yet poorly understood, ways by plant secondary metabolites (PSMs) which can adversely affect a herbivore’s physiology and energetics. Here we assess the relative influence of various abiotic (weather) and biotic (intraspecific competition, predation risk and diet composition) factors on indicators of nutritional condition and the energetic costs of detoxifying PSMs for the moose population in Isle Royale National Park (U.S.A.). Specifically, we observed interannual variation in the ratio of urea nitrogen to …

The Relevance Of Pedigrees In The Conservation Genomics Era, Stephanie J. Galla, Julie A. Heath

Biology Faculty Publications and Presentations

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long-standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome-wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic …

Species-Specific Interactions In Avian–Bryophyte Dispersal Networks, Matthew Chmielewski, Sarah Eppley

Biology Faculty Publications and Presentations

Studies from seed plants have shown that animal dispersal fundamentally alters the success of plant dispersal, shaping community composition through time. Our understanding of this phenomenon in spore plants is comparatively limited. Though little is known about species-specific dispersal relationships between passerine birds and bryophytes, birds are particularly attractive as a potential bryophyte dispersal vector given their highly vagile nature as well as their association with bryophytes when foraging and building nests. We captured birds in Gifford Pinchot National Forest to sample their legs and tails for bryophyte propagules. We found 24 bryophyte species across 34 bird species. We examined …

Phylogenetics And Genetic Variation Of Heligmosomoides Thomomyos In Western Pocket Gophers (Thomomys Spp.), Malorri R. Hughes, Alexandra A. Gibson, Emily R. Wolfe, Cecily D. Bronson, Deborah A. Duffield

Biology Faculty Publications and Presentations

The host specificities and systematics of North American Heligmosomoides species remain particularly uncertain. The primary aim of this study was to verify that a species described previously based only on morphology, H. thomomyos, from pocket gopher (Rodentia: Geomyidae) hosts in Oregon represented a monophyletic lineage. In order to address this aspect, as well as to further understand relationships and geographic patterns, we carried out phylogenetic, genetic diversity, and population dynamic analyses using partial 18S rRNA and COI mtDNA sequences of Heligmosomoides specimens. Phylogenetic analyses suggested that there are likely multiple Heligmosomoides species present in these hosts. This was supported by …

Commentary: The Past, Present, And Future Of The Global Raptor Impact Network, James R. Belthoff, Julie A. Heath

Biology Faculty Publications and Presentations

Most raptor populations are declining and nearly a fifth are threatened with extinction; thus there is a need to increase collaboration to ensure efficient and effective research, management, and conservation. Here, we introduce the Global Raptor Impact Network (GRIN; www.globalraptors.org), a tool to enhance collaboration and conservation impact of the raptor research community. We provide an overview of the history and current state of GRIN, including plans for expansion. Predecessors to GRIN include The African Raptor DataBank, which was launched in 2012 to ascertain the conservation status of raptors across Africa; and the Global Raptor Information Network, which was launched …

Expanding The Conservation Genomics Toolbox: Incorporating Structural Variants To Enhance Genomic Studies For Species Of Conservation Concern, Stephanie J. Galla

Biology Faculty Publications and Presentations

Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics …

Coevolutionary Methods Enable Robust Design Of Modular Repressors By Reestablishing Intra-Protein Interactions, Xian-Li Jiang, Rey P. Dimas, Clement T.Y. Chan, Faruck Morcos

Biology Faculty Publications and Presentations

enetic sensors with unique combinations of DNA recognition and allosteric response can be created by hybridizing DNA-binding modules (DBMs) and ligand-binding modules (LBMs) from distinct transcriptional repressors. This module swapping approach is limited by incompatibility between DBMs and LBMs from different proteins, due to the loss of critical module-module interactions after hybridization. We determine a design strategy for restoring key interactions between DBMs and LBMs by using a computational model informed by coevolutionary traits in the LacI family. This model predicts the influence of proposed mutations on protein structure and function, quantifying the feasibility of each mutation for rescuing hybrid …

Applying Behavioral And Physiological Measures To Assess The Relative Impact Of The Prolonged Covid-19 Pandemic Closure On Two Mammal Species At The Oregon Zoo: Cheetah (A. Jubatus) And Giraffe (G. C. Reticulata And G. C. Tippelskirchii), Laurel Fink, Candace D. Scarlata, Becca Vanbeek, Todd Bodner, Nadja C. Wielebnowski

Biology Faculty Publications and Presentations

The effect of visitor presence on zoo animals has been explored in numerous studies over the past two decades. However, the opportunities for observations without visitors have been very limited at most institutions. In 2020, the Oregon Zoo was closed, in response to the global SARSCoV-2 (COVID-19) pandemic, from 15 March 2020 to 12 July 2020, resulting in approximately four consecutive months without visitor presence. This study aimed to quantify potential behavioral and hormonal changes expressed during two transition periods in zoo visitor attendance: the initial time period before and after closure in March 2020 and time before and after …

A Resource For Understanding And Evaluating Outcomes Of Undergraduate Field Experiences, Erin E. Shortlidge, Alison Jolley, Stephanie Shaulskiy, Emily Geraghty Ward, Christopher N. Lorentz, Kari O'Connell

Biology Faculty Publications and Presentations

Undergraduate field experiences (UFEs) are a prominent element of science education across many disciplines; however, empirical data regarding the outcomes are often limited. UFEs are unique in that they typically take place in a field setting, are often interdisciplinary, and include diverse students. UFEs range from courses, to field trips, to residential research experiences, and thereby have the potential to yield a plethora of outcomes for undergraduate participants. The UFE community has expressed interest in better understanding how to assess the outcomes of UFEs. In response, we developed a guide for practitioners to use when assessing their UFE that promotes …

Pelagic Tunicate Grazing On Marine Microbes Revealed By Integrative Approaches, Kelly R. Sutherland, Anne W. Thompson

Biology Faculty Publications and Presentations

Marine microorganisms comprise a large fraction of ocean carbon and are central players in global biogeochemical cycling. Significant gaps remain, however, in our understanding of processes that determine the fate, distribution, and community structure of microbial communities. Protists and viruses are accepted as being part of the microbial loop and a source of microbial mortality. However, pelagic tunicates (salps, doliolods, pyrosomes, and appendicularians), which are abundant in oceanic and coastal environments and consume microorganisms with higher individual grazing rates than other common grazers, remain underappreciated in their role controlling microbial communities, distributions, and flux through ecosystems. In spite of sampling …

Bio-Acoustic Tracking And Localization Using Heterogeneous, Scalable Microphone Arrays, Erik Verreycken, Ralph Simon, Brandt Quirk-Royal, Walter Daems, Jesse Barber, Jan Steckel

Biology Faculty Publications and Presentations

Microphone arrays are an essential tool in the field of bioacoustics as they provide a non-intrusive way to study animal vocalizations and monitor their movement and behavior. Microphone arrays can be used for passive localization and tracking of sound sources while analyzing beamforming or spatial filtering of the emitted sound. Studying free roaming animals usually requires setting up equipment over large areas and attaching a tracking device to the animal which may alter their behavior. However, monitoring vocalizing animals through arrays of microphones, spatially distributed over their habitat has the advantage that unrestricted/unmanipulated animals can be observed. Important insights have …

Intraspecific Variation Mediates Density Dependence In A Genetically Diverse Plant Species, Andrii Zaiats, Matthew J. Germino, Marcelo D. Serpe, Bryce Richardson, T. Trevor Caughlin

Biology Faculty Publications and Presentations

Interactions between neighboring plants are critical for biodiversity maintenance in plant populations and communities. Intraspecific trait variation and genome duplication are common in plant species and can drive eco-evolutionary dynamics through genotype-mediated plant-plant interactions. However, few studies have examined how species-wide intraspecific variation may alter interactions between neighboring plants. We investigate how subspecies and ploidy variation in a genetically diverse species, big sagebrush (Artemisia tridentata), can alter the demographic outcomes of plant interactions. Using a replicated, long-term common garden experiment that represents range-wide diversity of A. tridentata, we ask how intraspecific variation, environment, and stand age mediate …

Golden Eagle Dietary Shifts Following Wildfire And Shrub Loss Have Negative Consequences For Nestling Survivorship, Julie A. Heath, Michael N. Kochert, Karen Steenhof

Biology Faculty Publications and Presentations

Wildfires and invasive species have caused widespread changes in western North America’s shrub-steppe landscapes. The bottom–up consequences of degraded shrublands on predator ecology and demography remain poorly understood. We used a before–after paired design to study whether Golden Eagle (Aquila chrysaetos) diet and nestling survivorship changed following wildfires in southwestern Idaho, USA. We assessed burn extents from 1981 to 2013 and vegetation changes between 1979 (pre-burn) and 2014 (post-burn) within 3 km of Golden Eagle nesting centroids. We measured the frequency and biomass of individual prey, calculated diet diversity indexes, and monitored nestling survivorship at 15 territories in …

A Draft Genome Provides Hypotheses On Drought Tolerance In A Keystone Plant Species In Western North America Threatened By Climate Change, Anthony E. Melton, James Beck, Stephanie J. Galla, Marcelo Serpe, Stephen Novak, Sven Buerki

Biology Faculty Publications and Presentations

Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome-to-phenome research, a draft genome was assembled for a diploid individual of Artemisia tridentata subsp. tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin …

Intra-Specific Variation In Migration Phenology Of American Kestrels (Falco Sparverius) In Response To Spring Temperatures, Breanna F. Powers, Jason M. Winiarski, Juan M. Requena-Mullor, Julie A. Heath

Biology Faculty Publications and Presentations

In migratory birds, among- and within-species heterogeneity in response to climate change may be attributed to differences in migration distance and environmental cues that affect timing of arrival at breeding grounds. We used eBird observations and a within-species comparative approach to examine whether migration distance (with latitude as a proxy) and weather predictors can explain spring arrival dates at the breeding site in a raptor species with a widespread distribution and diverse migration strategies, the American Kestrel Falco sparverius. We found an interactive effect between latitude and spring minimum temperatures on arrival dates, whereby at lower latitudes (short-distance migrants) …

A Small Rna Is Functional In Escherichia Fergusonii Despite Containing A Large Insertion., Austin P. Wright, H. Auguste Dutcher, Brianna Butler, Timothy J. Nice, Rahul Raghavan

Biology Faculty Publications and Presentations

Bacterial small RNAs (sRNAs) are important regulators of gene expression; however, the impact of natural mutations on sRNA functions has not been studied extensively. Here we show that the sRNA MgrR contains a unique 53 bp insertion in Escherichia fergusonii, a close relative of Escherichia coli and Salmonella enterica. The insertion is a repetitive extragenic palindromic (REP) sequence that could block transcription, but full-length MgrR is produced in E. fergusonii, showing that the insertion has not affected sRNA production. Additionally, despite containing the large insertion, the sRNA appears to be functional because deletion of mgrR made E. fergusonii …

Weak Coupling Among Barrier Loci And Waves Of Neutral And Adaptive Introgression Across An Expanding Hybrid Zone, Mitchell Cruzan, Pamela G. Thompson, Nicolas Alexander Diaz, Elizabeth C. Hendrickson, Katie R. Gerloff, Katie A. Kline, Hannah M. Machiorlete, Jessica Persinger

Biology Faculty Publications and Presentations

Hybridization can serve as an evolutionary stimulus, but we have little understanding of introgression at early stages of hybrid zone formation. We analyze reproductive isolation and introgression between a range-limited and a widespread species. Reproductive barriers are estimated based on differences in flowering time, ecogeographic distributions, and seed set from crosses. We find an asymmetrical mating barrier due to cytonuclear incompatibility that is consistent with observed clusters of coincident and concordant tension zone clines (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of concordant clines are spread across the hybrid zone, resulting in weak coupling among barrier loci …

Authentication Of A Novel Antibody To Zebrafish Collagen Type Xi Alpha 1 Chain (Col11a1a), Jonathon C. Reeck, Makenna J. Hardy, Xinzhu Pu, Cynthia Keller-Peck, Julia Thom Oxford

Biology Faculty Publications and Presentations

Objective: Extracellular matrix proteins play important roles in embryonic development and antibodies that specifically detect these proteins are essential to understanding their function. The zebrafish embryo is a popular model for vertebrate development but suffers from a dearth of authenticated antibody reagents for research. Here, we describe a novel antibody designed to detect the minor fibrillar collagen chain Col11a1a in zebrafish (AB strain).

Results: The Col11a1a antibody was raised in rabbit against a peptide comprising a unique sequence within the zebrafish Col11a1a gene product. The antibody was affinity-purified and characterized by ELISA. The antibody is effective for immunoblot and immunohistochemistry …

Cellular Activity Of Salmonella Typhimurium Artab Toxin And Its Receptor-Binding Subunit, Elise Overgaard, Brad Morris, Omid Mohammad Mousa, Adriana Rodriguez, Leyla Cufurovic, Richard S. Beard, Juliette K. Tinker

Biology Faculty Publications and Presentations

Salmonellosis is among the most reported foodborne illnesses in the United States. The Salmonella enterica Typhimurium DT104 phage type, which is associated with multidrug-resistant disease in humans and animals, possesses an ADP-ribosylating toxin called ArtAB. Full-length artAB has been found on a number of broad-host-range non-typhoidal Salmonella species and serovars. ArtAB is also homologous to many AB₅ toxins from diverse Gram-negative pathogens, including cholera toxin (CT) and pertussis toxin (PT), and may be involved in Salmonella pathogenesis, however, in vitro cellular toxicity of ArtAB has not been characterized. artAB was cloned into E. coli and initially isolated …

Artificial Night Light And Anthropogenic Noise Interact To Influence Bird Abundance Over A Continental Scale, Ashley A. Wilson, Mark A. Ditmer, Jesse R. Barber, Neil H. Carter, Eliot T. Miller, Luke P. Tyrell, Clinton D. Francis

Biology Faculty Publications and Presentations

The extent of artificial night light and anthropogenic noise (i.e., “light” and “noise”) impacts is global and has the capacity to threaten species across diverse ecosystems. Existing research involving impacts of light or noise has primarily focused on noise or light alone and single species; however, these stimuli often co-occur and little is known about how co-exposure influences wildlife and if and why species may vary in their responses. Here, we had three aims: (1) to investigate species-specific responses to light, noise, and the interaction between the two using a spatially explicit approach to model changes in abundance of 140 …

Biological Soil Crusts Of The Great Plains: A Review, Steven D. Warren, Roger Rosentreter, Nicole Pietrasiak

Biology Faculty Publications and Presentations

Biological soil crusts (BSCs), or biocrusts, are composed of fungi, bacteria, algae, and bryophytes (mosses, etc.) that occupy bare soil, entwining soil particles with filaments or rootlike structures and/or gluing them together with polysaccharide exudates to form a consolidated surface crust that stabilizes the soil against erosion. BSCs are common in arid and semiarid regions where vascular plant cover is naturally sparse, maximizing the exposure of surface-dwelling organisms to direct sunlight. Although less prominent and less studied there, BSC organisms are also present in more mesic areas such as the Great Plains where they can be found in shortgrass and …