Biology Commons^™

Linking Behavioral States To Landscape Features For Improved Conservation Management, Maitreyi Sur, Jim R. Belthoff

Biology Faculty Publications and Presentations

1. A central theme for conservation is understanding how animals differentially use, and are affected by change in, the landscapes they inhabit. However, it has been challenging to develop conservation schemes for habitat-specific behaviors.
2. Here we use behavioral change point analysis to identify behavioral states of golden eagles (Aquila chrysaetos) in the Sonoran and Mojave Deserts of the southwestern United States, and we identify, for each behavioral state, conservation-relevant habitat associations.
3. We modeled behavior using 186,859 GPS points from 48 eagles and identified 2,851 distinct segments comprising four behavioral states. Altitude above ground level (AGL) best differentiated behavioral states, …

Phantom Rivers Filter Birds And Bats By Acoustic Niche, D. G. E. Gomes, C. A. Toth, H. J. Cole, C. D. Francis, J. R. Barber

Biology Faculty Publications and Presentations

Natural sensory environments, despite strong potential for structuring systems, have been neglected in ecological theory. Here, we test the hypothesis that intense natural acoustic environments shape animal distributions and behavior by broadcasting whitewater river noise in montane riparian zones for two summers. Additionally, we use spectrally-altered river noise to explicitly test the effects of masking as a mechanism driving patterns. Using data from abundance and activity surveys across 60 locations, over two full breeding seasons, we find that both birds and bats avoid areas with high sound levels, while birds avoid frequencies that overlap with birdsong, and bats avoid higher …

Sodah: The Soils Data Harmonization Database, An Open-Source Synthesis Of Soil Data From Research Networks, Version 1.0, Marie-Anne De Graaff

Biology Faculty Publications and Presentations

Data collected from research networks present opportunities to test theories and develop models about factors responsible for the long-term persistence and vulnerability of soil organic matter (SOM). Synthesizing datasets collected by different research networks presents opportunities to expand the ecological gradients and scientific breadth of information 55 available for inquiry. Synthesizing these data, are challenging, especially considering the legacy of soils data that has already been collected and an expansion of new network science initiatives. To facilitate this effort, here we present the SOils DAta Harmonization database (SoDaH; https://lter.github.io/som-website, last accessed 15 July 2020), a flexible database designed to harmonize …

New Applications For The Kinetic Exclusion Assay (Kinexa), Mark Harrison Smith

Boise State University Theses and Dissertations

This dissertation examines the fundamental principles and applicability of the kinetic exclusion assay (KinExA), developed and marketed by Sapidyne Instruments of Boise, Idaho, since 1995. Chapter One reviews and consolidates the manufacturer’s guidance and many early papers that delineate the practical and theoretical aspects of the technology. In brief, KinExA is a two stage analytical system. In stage one, a number of solutions are prepared, whereby one of the partners is kept constant (the constant binding partner, or CBP), while the other (the titrant) is varied, usually in serial dilution. As the titrant is increased, the free CBP decreases, and …

Natural Noise Can Influence Bird Foraging And Vigilance Behavior, Kate Antonia Sweet

Boise State University Theses and Dissertations

Natural sounds are an often overlooked, yet important component of an animal’s habitat. The acoustic environment may be especially significant during foraging, because a noisy world can limit auditory surveillance. Here, we investigated how natural noise structures the foraging vigilance trade-off to understand how intense acoustic environments may have shaped antipredator behavior across the evolutionary past, and better inform conservation efforts in the present.

First, in Chapter 1, I directly compared the foraging and vigilance behaviors of captive song sparrows (Melospiza melodia) in anthropogenic and natural noise. We recorded foraging trials in 4 playback conditions (roadway traffic, whitewater …

The American Kestrel (Falco Sparverius) Genoscape: Implications For Monitoring, Management, And Subspecies Boundaries, Michaela Brinkmeyer, Julie A. Heath

Biology Faculty Publications and Presentations

Identifying population genetic structure is useful for inferring evolutionary process and comparing the resulting structure with subspecies boundaries can aid in species management. The American Kestrel (Falco sparverius) is a widespread and highly diverse species with 17 total subspecies, only 2 of which are found north of U.S./Mexico border (F. s. paulus is restricted to southeastern United States, while F. s. sparverius breeds across the remainder of the U.S. and Canadian distribution). In many parts of their U.S. and Canadian range, American Kestrels have been declining, but it has been difficult to interpret demographic trends without a …

Otto Warburg And His Contributions To The Screw Pine Family (Pandanaceae), Martin W. Callmander, Robert Vogt, Anna Donatelli, Sven Buerki, Chiara Nepi

Biology Faculty Publications and Presentations

Otto Warburg (1859–1938) had a great interest in tropical botany. He travelled in South-East Asia and the South Pacific between 1885 and 1889 and brought back a considerable collection of plant specimens from this expedition later donated to the Royal Botanical Museum in Berlin. Warburg published the first comprehensive monograph on the family Pandanaceae in 1900 in the third issue of Das Pflanzenreich established and edited by Adolf Engler (1844–1930). The aim of this article is to clarify the taxonomy, nomenclature and typification of Warburg's contributions to the Pandanaceae. Considerable parts of Warburg's original material was destroyed in Berlin …

Weather Affects Post-Fire Recovery Of Sagebrush-Steppe Communities And Model Transferability Among Sites, Cara Applestein, T. Trevor Caughlin, Matthew J. Germino

Biology Faculty Publications and Presentations

Altered climate, including weather extremes, can cause major shifts in vegetative recovery after disturbances. Predictive models that can identify the separate and combined temporal effects of disturbance and weather on plant communities and that are transferable among sites are needed to guide vulnerability assessments and management interventions. We asked how functional group abundance responded to time since fire and antecedent weather, if long-term vegetation trajectories were better explained by initial post-fire weather conditions or by general five-year antecedent weather, and if weather effects helped predict post-fire vegetation abundances at a new site. We parameterized models using a 30- yr vegetation …

Low Activities Of Digestive Enzymes In The Guts Of Herbivorous Grouse (Aves: Tetraoninae), Jennifer Sorensen Forbey

Biology Faculty Publications and Presentations

Avian herbivores face the exceptional challenge of digesting recalcitrant plant material while under the selective pressure to reduce gut mass as an adaptation for fight. One mechanism by which avian herbivores may overcome this challenge is to maintain high activities of intestinal enzymes that facilitate the digestion and absorption of nutrients. However, previous studies in herbivorous animals provide equivocal evidence as to how activities of digestive enzymes may be adapted to herbivorous diets. For example, “rate-maximizing” herbivores generally exhibit rapid digesta transit times and high activities of digestive enzymes. Conversely, “yield-maximizing” herbivores utilize long gut retention times and express lower …

A Multiplexed, Automated Evolution Pipeline Enables Scalable Discovery And Characterization Of Biosensors, Brent Townshend, Joy S. Xiang, Gabriel Manzanarez, Eric J. Hayden, Christina D. Smolke

Biology Faculty Publications and Presentations

Biosensors are key components in engineered biological systems, providing a means of measuring and acting upon the large biochemical space in living cells. However, generating small molecule sensing elements and integrating them into in vivo biosensors have been challenging. Here, using aptamer-coupled ribozyme libraries and a ribozyme regeneration method, de novo rapid in vitro evolution of RNA biosensors (DRIVER) enables multiplexed discovery of biosensors. With DRIVER and high-throughput characterization (CleaveSeq) fully automated on liquid-handling systems, we identify and validate biosensors against six small molecules, including five for which no aptamers were previously found. DRIVER-evolved biosensors are applied directly to regulate …

Macrophages Expedite Cell Proliferation Of Prostate Intraepithelial Neoplasia Through Their Downstream Target Erk, Mikalah U. Thomas, Justin K. Messex, Tu Dang, Sarki A. Abdulkadir, Cheryl L. Jorcyk, Geou-Yarh Liou

Biology Faculty Publications and Presentations

The risk factors for prostate cancer include a high-fat diet and obesity, both of which are associated with an altered cell environment including increased inflammation. It has been shown that chronic inflammation due to a high-fat diet or bacterial infection has the potential to accelerate prostate cancer as well as its precursor, prostatic intraepithelial neoplasia (PIN), development. However, the underlying mechanism of how chronic inflammation promotes prostate cancer development, especially PIN, remains unclear. In this study, we showed that more macrophages were present in PIN areas as compared to the normal areas of human prostate. When co-culturing PIN cells with …

Noise Distracts Foraging Bats, Louise C. Allen, Nickolay I. Hristov, Juliette J. Rubin, Joseph T. Lightsey, Jesse R. Barber

Biology Faculty Publications and Presentations

Predators frequently must detect and localize their prey in challenging environments. Noisy environments have been prevalent across the evolutionary history of predator–prey relationships, but now with increasing anthropogenic activities noise is becoming a more prominent feature of many landscapes. Here, we use the gleaning pallid bat, Antrozous pallidus, to investigate the mechanism by which noise disrupts hunting behaviour. Noise can primarily function to mask—obscure by spectrally overlapping a cue of interest, or distract—occupy an animal's attentional or other cognitive resources. Using band-limited white noise treatments that either overlapped the frequencies of a prey cue or did not …

G2pminer: A Genome To Phenome Literature Review Approach, John M.A. Wojahn, Stephanie J. Galla, Anthony E. Melton, Sven Buerki

Biology Faculty Publications and Presentations

There is a gap in the conceptual framework linking genes to phenotypes (G2P) for non-model organisms, as most non-model organisms do not yet have genomic resources readily available. To address this, researchers often perform literature reviews to understand G2P linkages by curating a list of likely gene candidates, hinging upon other studies already conducted in closely related systems. Sifting through hundreds to thousands of articles is a cumbersome task that slows down the scientific process and may introduce bias into a study. To fill this gap, we created G2PMineR, a free and open source literature mining tool developed specifically for …

Artificial Nightlight Alters The Predator–Prey Dynamics Of An Apex Carnivore, Jesse R. Barber

Biology Faculty Publications and Presentations

Artificial nightlight is increasingly recognized as an important environmental disturbance that influences the habitats and fitness of numerous species. However, its effects on wide‐ranging vertebrates and their interactions remain unclear. Light pollution has the potential to amplify land‐use change, and as such, answering the question of how this sensory stimulant affects behavior and habitat use of species valued for their ecological roles and economic impacts is critical for conservation and land‐use planning. Here, we combined satellite‐derived estimates of light pollution, with GPS‐data from cougars Puma concolor (n = 56), mule deer Odocoileus hemionus (n = 263) and locations of cougar‐killed …

A Record Of Vapour Pressure Deficit Preserved In Wood And Soil Across Biomes, Adrian Broz, Gregory J. Retallack, Toby M. Maxwell, Lucas C.R. Silva

Biology Faculty Publications and Presentations

The drying power of air, or vapour pressure deficit (VPD), is an important measurement of potential plant stress and productivity. Estimates of VPD values of the past are integral for understanding the link between rising modern atmospheric carbon dioxide (pCO₂) and global water balance. A geological record of VPD is needed for paleoclimate studies of past greenhouse spikes which attempt to constrain future climate, but at present there are few quantitative atmospheric moisture proxies that can be applied to fossil material. Here we show that VPD leaves a permanent record in the slope (S) of least-squares …

Gateway Scholarships In Biological Sciences: Year 4 Annual Report, Vicki Stieha, Julia Oxford, Amy Ulappa, Brittnee Earl, Jennifer Forbey, Laura Bond, Kevin Feris, Jocelyn Cullers, Caleb Hartman

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 2020-21 academic year.

Does Experimentally Quieting Traffic Noise Benefit People And Birds?, Mitchell J. Levenhagen, Christopher J.W. Mcclure, Jesse R. Barber

Biology Faculty Publications and Presentations

Protected natural areas are not free from noise, especially noise generated by traffic within park boundaries. Natural soundscapes are important for maintaining community structure, providing positive visitor experiences, and increasing visitor support for management actions that reduce impacts on natural resources. To test experimental quieting as a strategy to increase both wildlife habitat quality and visitor experience, we enforced decreased speed limits and presented educational signage to reduce sound levels along a road system in an alternating, on–off block design within Grand Teton National Park, Wyoming, USA. We continuously recorded background sound levels while conducting bird space use assessments and …

A Repeated Triple Lysine Motif Anchors Complexes Containing Bone Sialoprotein And The Type Xi Collagen A1 Chain Involved In Bone Mineralization, Jeff P. Gorski, Nichole T. Franz, Daniel Pernoud, Andrew Keightley, David R. Eyre, Julia Thom Oxford

Biology Faculty Publications and Presentations

While details remain unclear, initiation of woven bone mineralization is believed to be mediated by collagen and potentially nucleated by bone sialoprotein (BSP). Interestingly, our recent publication showed that BSP and type XI collagen form complexes in mineralizing osteoblastic cultures. To learn more, we examined the protein composition of extracellular sites of de novo hydroxyapatite deposition which were enriched in BSP and Col11a1 containing an alternatively spliced “6b” exonal sequence. An alternate splice variant “6a” sequence was not similarly co-localized. BSP and Col11a1 co-purify upon ion-exchange chromatography or immunoprecipitation. Binding of the Col11a1 “6b” exonal sequence to bone sialoprotein was …

Monitoring Tropical Forest Succession At Landscape Scales Despite Uncertainty In Landsat Time Series, T. Trevor Caughlin, Cristina Barber, Gregory P. Asner, Nancy F. Glenn, Stephanie A. Bohlaman, Chris H. Wilson

Biology Faculty Publications and Presentations

Forecasting rates of forest succession at landscape scales will aid global efforts to restore tree cover to millions of hectares of degraded land. While optical satellite remote sensing can detect regional land cover change, quantifying forest structural change is challenging. We developed a state-space modeling framework that applies Landsat satellite data to estimate variability in rates of natural regeneration between sites in a tropical landscape. Our models work by disentangling measurement error in Landsat-derived spectral reflectance from process error related to successional variability.We applied our modeling framework to rank rates of forest succession between 10 naturally regenerating sites in Southwestern …

Climatic Drivers Of Verticillium Dahliae Occurrence In Mediterranean Olive-Growing Areas Of Southern Spain, Juan M. Requena-Mullor, Jose Manuel García-Garrido, Pedro Antonio García, Estefanía Rodríguez

Biology Faculty Publications and Presentations

Verticillium wilt, caused by the soil-borne fungus Verticillium dahliae, is one of the most harmful diseases in Mediterranean olive-growing areas. Although, the effects of both soil temperature and moisture on V. dahliae are well known, there is scant knowledge about what climatic drivers affect the occurrence of the pathogen on a large scale. Here, we investigate what climatic drivers determine V. dahliae occurrence in olive-growing areas in southern Spain. In order to bridge this gap in knowledge, a large-scale field survey was carried out to collect data on the occurrence of V. dahliae in 779 olive groves in Granada …

Biodiversity And Ecology Of Lichens Of Kenai Fjords National Park, Alaska, Roger Rosentreter

Biology Faculty Publications and Presentations

We inventoried lichens in Kenai Fjords National Park in Alaska, USA We assembled the known information on occurrence and ecology of lichens in this park by combining field, herbarium, and literature studies. Our results provide baseline data on lichen occurrence that may be used in resource condition assessments, vulnerability assessments, long-term ecological monitoring, and resource management. We report a total of 616 taxa of lichenized fungi from the Park, plus an additional five subspecies and three varieties, all of which are new additions to the National Park Service database for this park unit. An additional five species of nonlichenized lichenicolous …

Harvester Ants Reduce Seed Survivorship In Slickspot Peppergrass, A Rare Mustard Endemic To Idaho, Jennifer A. Brown, Ian C. Robertson

Biology Faculty Publications and Presentations

Seed predation can significantly reduce the reproductive success of individual plants and their populations. The consequences of seed predation often are most pronounced for rare plant species, in which loss of seeds can have a disproportionate effect on populations. The present study examined the effects of seed predation by Owyhee harvester ants (Pogonomyrmex salinus) on seed survivorship in slickspot peppergrass (Lepidium papilliferum), a rare mustard endemic to sagebrush-steppe habitat in southwestern Idaho. Within sagebrush-steppe, L. papilliferum is restricted to microsites known as “slick spots”—shallow depressions of soil characterized by distinct clay layers and surface water retention …

Soil Response To Fire Frequency In The Northern Columbia Basin Sagebrush Steppe, Leslie C. Nichols

Boise State University Theses and Dissertations

Fire is one of the most significant disturbances in an ecosystem, as it is capable of altering the physical, chemical, and biological properties of soil, and the fire frequency in semi-arid ecosystems is increasing. These changes can potentially alter plant-soil feedbacks that may affect post-fire recovery of the native plant and soil communities and lead to an ecosystem state change. However, there is much uncertainty about the magnitude of change as soils are exposed to more fires, because soil recovery and changes in fire severity following a first fire mediate the impact of successive fires on soil properties. To improve …

Notch Family Members Follow Stringent Requirements For Intracellular Domain Dimerization At Sequence-Paired Sites, Jacob J. Crow, Allan R. Albig

Biology Faculty Publications and Presentations

Notch signaling is essential for multicellular life, regulating core functions such as cellular identity, differentiation, and fate. These processes require highly sensitive systems to avoid going awry, and one such regulatory mechanism is through Notch intracellular domain dimerization. Select Notch target genes contain sequence-paired sites (SPS); motifs in which two Notch transcriptional activation complexes can bind and interact through Notch’s ankyrin domain, resulting in enhanced transcriptional activation. This mechanism has been mostly studied through Notch1, and to date, the abilities of the other Notch family members have been left unexplored. Through the utilization of minimalized, SPS-driven luciferase assays, we were …

Endothelial Cell Contributions To Covid-19, Alexandra E. Oxford, Fabio Halla, Evan B. Robertson, Brad E. Morrison

Biology Faculty Publications and Presentations

Understanding of the clinical, histological and molecular features of the novel coronavirus 2019 (Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)) has remained elusive. Coronavirus disease 2019 (COVID-19) caused by this virus has unusual clinical presentation with regard to other related coronaviruses. Recent reports suggest that SARS-CoV-2, unlike other related viruses, infects and replicates within endothelial cells, which may explain a significant portion of the observed clinical pathology. Likewise, mounting evidence associates vascular and endothelial cell dysfunction with increased mortality. This review focuses on understanding how endothelial cell pathology is caused by SARS-CoV-2 at the molecular and cellular levels and how …

Signaling And Other Functions Of Lipids In Autophagy: A Review, Alejandro Soto-Avellaneda, Brad E. Morrison

Biology Faculty Publications and Presentations

The process of autophagy is integral to cellular function. In this process, proteins, organelles, and metabolites are engulfed in a lipid vesicle and trafficked to a lysosome for degradation. Its central role in protein and organelle homeostasis has piqued interest for autophagy dysfunction as a driver of pathology for a number of diseases including cancer, muscular disorders, neurological disorders, and non-alcoholic fatty liver disease. For much of its history, the study of autophagy has centered around proteins, however, due to advances in mass spectrometry and refined methodologies, the role of lipids in this essential cellular process has become more apparent. …

Evolutionary Origins Of Three Rare Alpine-Endemic Species Of Lomatium (Apiaceae) In The Wallowa And Elkhorn Mountains Of Northeastern Oregon, Michael V. Ottenlips, Mary Ann E. Feist, Donald H. Mansfield, Gregory M. Plunkett, Sven Buerki, James F. Smith

Biology Faculty Publications and Presentations

Premise of research. Shared ancestry and convergent/parallel evolution are the two primary causes of morphologically similar species occurring in similar climatic niches. Alpine habitats harbor a unique biodiversity that is often characterized by many convergences in life-forms, such as cushion and rosulate habits. Three species of Lomatium (L. greenmanii, L. erythrocarpum, and L. oreganum) are high-alpine specialists endemic to the Wallowa and Elkhorn Mountains of northeastern Oregon. Earlier studies suggested that two of these species might be sister taxa, but because of the prevalence of convergence in alpine habitats and recent studies that have highlighted …

Long‐Distance Natal Dispersal Is Relatively Frequent And Correlated With Environmental Factors In A Widespread Raptor, Hanna M. Mccaslin, T. Trevor Caughlin, Julie A. Heath

Biology Faculty Publications and Presentations

1. Dispersal is a critical process influencing population dynamics and responses to global change. Long‐distance dispersal (LDD) can be especially important for gene flow and adaptability, although little is known about the factors influencing LDD because studying large‐scale movements is challenging and LDD tends to be observed less frequently than shorter‐distance dispersal (SDD).
2. We sought to understand patterns of natal dispersal at a large scale, specifically aiming to understand the relative frequency of LDD compared to SDD and correlates of dispersal distances.
3. We used bird banding and encounter data for American kestrels (Falco sparverius) to investigate the effects of …

Enhanced Hyaluronan Signaling And Autophagy Dysfunction By Vps35 D620n, Abir A. Rahman, Alejandro Soto-Avellaneda, Iva Stojkovska, Nathan K. Lai, Joshua E. Albright, Abby R. Webb, Emily Oe, Jacob P. Valarde, Alexandra E. Oxford, Paige E. Urquhart, Brandon Wager, Connor Brown, Isabella Amado, Peyton Vasquez, Nicholas Lehning, Xinzhu Pu, Brad E. Morrison

Biology Faculty Publications and Presentations

The motor features of Parkinson’s disease (PD) result from the loss of dopaminergic (DA) neurons in the substantia nigra with autophagy dysfunction being closely linked to this disease. A PD-causing familial mutation in VPS35 (D620N) has been reported to inhibit autophagy. In order to identify signaling pathways responsible for this autophagy defect, we performed an unbiased screen using RNA sequencing (RNA-Seq) of wild-type or VPS35 D620N-expressing retinoic acid-differentiated SH-SY5Y cells. We report that VPS35 D620N-expressing cells exhibit transcriptome changes indicative of alterations in extracellular matrix (ECM)-receptor interaction as well as PI3K-AKT signaling, a pathway known to regulate autophagy. Hyaluronan (HA) …

Colony Dynamics And Plant Community Associations Of The Harvester Ant, Pogonomyrmex Salinus (Hymenoptera: Formicidae) In Sagebrush-Steppe Habitat, Ian C. Robertson, Wilma G. Robertson

Biology Faculty Publications and Presentations

We present the results of a 5-yr field study on colony dynamics and plant community associations of Owyhee harvester ants, Pogonomyrmex salinus (Olsen), in sagebrush-steppe habitat in southwestern Idaho. Over a 5-yr period, the total number of ant colonies across 16 sites increased from 843 to 878 (4.15%) as a result of 315 colony deaths and 350 colony initiations. Up to 7.1% of colony initiations may have been instances of nest relocation. Colonies had a higher rate of failure in their first year than in subsequent years (12.4 vs 4.6–8.4% over the next 3 yr). Of the 11 sites analyzed …