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Biology Faculty Publications and Presentations

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Articles 181 - 210 of 662

Full-Text Articles in Biology

Complete Mitochondrial Genome Sequence Of The Gulf Coast Tick (Amblyomma Maculatum), Amanda E. Brenner, Rahul Raghavan Sep 2021

Complete Mitochondrial Genome Sequence Of The Gulf Coast Tick (Amblyomma Maculatum), Amanda E. Brenner, Rahul Raghavan

Biology Faculty Publications and Presentations

The complete circularized mitochondrial genome sequence of Amblyomma maculatum is 14,803 bp long. It encodes 13 protein coding genes, 2 rRNA genes, 22 tRNA genes, 2 tick box motifs, and 2 control regions. The gene arrangement and content are consistent with those of previously reported Metastriata tick mitochondrial genomes.


Dynamic Control Of Upper Limb Stretch Reflex In Wrestlers, Sho Ito, Kento Nakagawa, Tsuyoshi Nakajima, Misaki Iteya, Larry Crawshaw, Kazuyuki Kanosue Sep 2021

Dynamic Control Of Upper Limb Stretch Reflex In Wrestlers, Sho Ito, Kento Nakagawa, Tsuyoshi Nakajima, Misaki Iteya, Larry Crawshaw, Kazuyuki Kanosue

Biology Faculty Publications and Presentations

Purpose: The objective of this study was to clarify the characteristics of the upper limb stretch reflex in wrestlers.

Methods: Ten wrestlers and 11 control subjects participated in the study. The experiment was divided into two sessions. In the extension perturbation session, participants either relaxed or flexed the elbow when they felt a perturbation (abrupt elbow extension induced by a dynamometer). This was done 30 times by each subject for both sessions. In the flexion perturbation session, participants also relaxed or extended the elbow when they felt a perturbation (abrupt elbow flexion). During the tasks, the stretch reflex …


Health Reference Intervals And Values For Common Bottlenose Dolphins (Tursiops Truncatus), Indo-Pacific Bottlenose Dolphins (Tursiops Aduncus), Pacific White-Sided Dolphins (Lagenorhynchus Obliquidens), And Beluga Whales (Delphinapterus Leucas), Lisa K. Lauderdale, Michael T. Walsh, Kevin A. Mitchell, Douglas A. Granger, Jill D. Mellen, Lance J. Miller Aug 2021

Health Reference Intervals And Values For Common Bottlenose Dolphins (Tursiops Truncatus), Indo-Pacific Bottlenose Dolphins (Tursiops Aduncus), Pacific White-Sided Dolphins (Lagenorhynchus Obliquidens), And Beluga Whales (Delphinapterus Leucas), Lisa K. Lauderdale, Michael T. Walsh, Kevin A. Mitchell, Douglas A. Granger, Jill D. Mellen, Lance J. Miller

Biology Faculty Publications and Presentations

This study reports comprehensive clinical pathology data for hematology, serum, and plasma biochemistry reference intervals for 174 apparently healthy common bottlenose dolphins (Tursiops truncatus) and reference values for 27 Indo-Pacific bottlenose dolphins (Tursiops aduncus), 13 beluga whales (Delphinapterus leucas), and 6 Pacific white-sided dolphins (Lagenorhynchus obliquidens) in zoos and aquariums accredited by the Alliance for Marine Mammal Parks and Aquariums and the Association of Zoos & Aquariums. Blood samples were collected as part of a larger study titled “Towards understanding the welfare of cetaceans in zoos and aquariums” (colloquially called the Cetacean Welfare Study). Two blood samples were collected following …


Reference Intervals And Values For Fecal Cortisol, Aldosterone, And The Ratio Of Cortisol To Dehydroepiandrosterone Metabolites In Four Species Of Cetaceans, Lance J. Miller, Lisa K. Lauderdale, Michael T. Walsh, Jocelyn L. Bryant, Kevin A. Mitchell, Douglas A. Granger, Jill D. Mellen Aug 2021

Reference Intervals And Values For Fecal Cortisol, Aldosterone, And The Ratio Of Cortisol To Dehydroepiandrosterone Metabolites In Four Species Of Cetaceans, Lance J. Miller, Lisa K. Lauderdale, Michael T. Walsh, Jocelyn L. Bryant, Kevin A. Mitchell, Douglas A. Granger, Jill D. Mellen

Biology Faculty Publications and Presentations

The goal of the current study was to create reference intervals and values for several common and one potential novel physiological indicators of animal welfare for four species of cetaceans. The subjects included 189 bottlenose dolphins (Tursiops truncatus), 27 Indo-Pacific bottlenose dolphins (Tursiops aduncus), eight Pacific white-sided dolphins (Lagenorhynchus obliquidens), and 13 beluga whales (Delphinapterus leucas) at Alliance of Marine Mammal Parks and Aquariums and/or Association of Zoos and Aquariums accredited facilities. During two sampling time periods between July and November of 2018 and between January and April of 2019, fecal samples were collected weekly for five weeks from all …


Behavioral Diversity As A Potential Positive Indicator Of Animal Welfare In Bottlenose Dolphins, Lance J. Miller, Lisa K. Lauderdale, Jocelyn L. Bryant, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger Aug 2021

Behavioral Diversity As A Potential Positive Indicator Of Animal Welfare In Bottlenose Dolphins, Lance J. Miller, Lisa K. Lauderdale, Jocelyn L. Bryant, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger

Biology Faculty Publications and Presentations

Accredited zoological facilities are committed to fully understanding the behavioral, mental, and physical needs of each species to continuously improve the welfare of the animals under their professional care and detect when welfare has diminished. In order to accomplish this goal, internally consistent and externally valid indicators of animal welfare are necessary to advance our understanding of the current welfare status of individual animals. Historically, efforts have focused on monitoring visible or observable signs of poor health or problem behavior, but lack of signs or problems does not necessarily demonstrate that an individual animal is thriving. The current study examined …


Towards Understanding The Welfare Of Cetaceans In Accredited Zoos And Aquariums, Lisa K. Lauderdale, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger, Lance J. Miller Aug 2021

Towards Understanding The Welfare Of Cetaceans In Accredited Zoos And Aquariums, Lisa K. Lauderdale, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger, Lance J. Miller

Biology Faculty Publications and Presentations

Cetaceans are long-lived, social species that are valued as ambassadors inspiring the public to engage in conservation action. Under professional care, they are critical partners with the scientific community to understanding the biology, behavior, physiology, health, and welfare requirements of this taxonomic group. The Cetacean Welfare Study was a highly collaborative research effort among zoos and aquariums accredited by the Alliance for Marine Mammal Parks and Aquariums and/or the Association of Zoos & Aquariums that provided important empirical and comparative information on the care and management of cetaceans. The goal was to identify factors that were related to the welfare …


Habitat Characteristics And Animal Management Factors Associated With Habitat Use By Bottlenose Dolphins In Zoological Environments, Lisa K. Lauderdale, K. Alex Shorter, Ding Zhang, Joaquin Gabaldon, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger, Lance J. Miller Aug 2021

Habitat Characteristics And Animal Management Factors Associated With Habitat Use By Bottlenose Dolphins In Zoological Environments, Lisa K. Lauderdale, K. Alex Shorter, Ding Zhang, Joaquin Gabaldon, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger, Lance J. Miller

Biology Faculty Publications and Presentations

The way an animal uses its habitat can serve as an indicator of habitat appropriateness for the species and individuals. Bottlenose dolphins (Tursiops truncatus and Tursiops aduncus) in accredited zoos and aquariums experience a range of habitat types and management programs that provide opportunities for dolphins to engage in species-appropriate behaviors and potentially influence their individual and group welfare. Data in the present study were collected as part of a larger study titled “Towards understanding the welfare of cetaceans in zoos and aquariums” (colloquially called the Cetacean Welfare Study). Non-invasive bio-logging devices (Movement Tags) recorded the diving behavior and vertical …


Bottlenose Dolphin Habitat And Management Factors Related To Activity And Distance Traveled In Zoos And Aquariums, Lisa K. Lauderdale, K. Alex Shorter, Ding Zhang, Joaquin Gabaldon, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger, Lance J. Miller Aug 2021

Bottlenose Dolphin Habitat And Management Factors Related To Activity And Distance Traveled In Zoos And Aquariums, Lisa K. Lauderdale, K. Alex Shorter, Ding Zhang, Joaquin Gabaldon, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger, Lance J. Miller

Biology Faculty Publications and Presentations

High-resolution non-invasive cetacean tagging systems can be used to investigate the influence of habitat characteristics and management factors on behavior by quantifying activity levels and distance traveled by bottlenose dolphins (Tursiops truncatus and Tursiops aduncus) in accredited zoos and aquariums. Movement Tags (MTags), a bio-logging device, were used to record a suite of kinematic and environmental information outside of formal training sessions as part of a larger study titled “Towards understanding the welfare of cetaceans in zoos and aquariums” (colloquially called the Cetacean Welfare Study). The purpose of the present study was to explore if and how habitat characteristics, environmental …


Environmental Enrichment, Training, And Habitat Characteristics Of Common Bottlenose Dolphins (Tursiops Truncatus) And Indo-Pacific Bottlenose Dolphins (Tursiops Aduncus), Lisa K. Lauderdale, Michael T. Walsh, Jill D. Mellen, Douglas A. Granger, Lance J. Miller Aug 2021

Environmental Enrichment, Training, And Habitat Characteristics Of Common Bottlenose Dolphins (Tursiops Truncatus) And Indo-Pacific Bottlenose Dolphins (Tursiops Aduncus), Lisa K. Lauderdale, Michael T. Walsh, Jill D. Mellen, Douglas A. Granger, Lance J. Miller

Biology Faculty Publications and Presentations

In recent decades, animal welfare science has evolved to utilize a multidisciplinary approach to assess the welfare of animals in accredited zoos and aquariums. Science-based animal welfare assessments have become an essential component of management programs and widespread application is expected by animal care professionals. Management practices for bottlenose dolphins in accredited facilities incorporate several programs that potentially impact animal welfare including environmental enrichment and animal training. Additionally, habitat characteristics, such as the dimensions of the habitat, have been proposed to affect welfare. While accredited facilities are required to meet high standards of care, habitat characteristics and management practices are …


Assessment Of Animal Management And Habitat Characteristics Associated With Social Behavior In Bottlenose Dolphins Across Zoological Facilities, Lance J. Miller, Lisa K. Lauderdale, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger Aug 2021

Assessment Of Animal Management And Habitat Characteristics Associated With Social Behavior In Bottlenose Dolphins Across Zoological Facilities, Lance J. Miller, Lisa K. Lauderdale, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger

Biology Faculty Publications and Presentations

Bottlenose dolphins are a behaviorally complex, social species that display a variety of social behaviors. Because of this, it is important for zoological facilities to strive to ensure animals display species-appropriate levels of social behavior. The current study is part of the multi-institutional study entitled “Towards understanding the welfare of cetaceans in zoos and aquariums” commonly referred to as the Cetacean Welfare Study. All participating facilities were accredited by the Alliance of Marine Mammal Parks and Aquariums and/or the Association of Zoos and Aquariums. Behavioral data were collected on 47 bottlenose dolphins representing two subspecies, Tursiops truncatus and Tursiops aduncus, …


Relationships Between Animal Management And Habitat Characteristics With Two Potential Indicators Of Welfare For Bottlenose Dolphins Under Professional Care, Lance J. Miller, Lisa K. Lauderdale, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger Aug 2021

Relationships Between Animal Management And Habitat Characteristics With Two Potential Indicators Of Welfare For Bottlenose Dolphins Under Professional Care, Lance J. Miller, Lisa K. Lauderdale, Jill D. Mellen, Michael T. Walsh, Douglas A. Granger

Biology Faculty Publications and Presentations

Accredited zoos and aquariums continually strive to ensure high levels of animal welfare for the animals under their professional care. Best management practices include conducting research to better understand factors that lead to optimal welfare and then turning findings into practice. The current study is part of the larger Cetacean Welfare Study or more formally, “Towards understanding the welfare of cetaceans in zoos and aquariums.” Facilities participating in the study were accredited by the Alliance of Marine Mammal Parks and Aquariums and/or the Association of Zoos and Aquariums. Animal management factors and habitat characteristics were examined in relation to two …


Scaling Up Sagebrush Chemistry With Near-Infrared Spectroscopy And Uas-Acquired Hyperspectral Imagery, Peter J. Olsoy, Brecken C. Robb, Jennifer Sorenson Forbey, T. Trevor Caughlin, Chelsea Merriman, Jordan D. Nobler Aug 2021

Scaling Up Sagebrush Chemistry With Near-Infrared Spectroscopy And Uas-Acquired Hyperspectral Imagery, Peter J. Olsoy, Brecken C. Robb, Jennifer Sorenson Forbey, T. Trevor Caughlin, Chelsea Merriman, Jordan D. Nobler

Biology Faculty Publications and Presentations

Sagebrush ecosystems (Artemisia spp.) face many threats including large wildfires and conversion to invasive annuals, and thus are the focus of intense restoration efforts across the western United States. Specific attention has been given to restoration of sagebrush systems for threatened herbivores, such as Greater Sage-Grouse (Centrocercus urophasianus) and pygmy rabbits (Brachylagus idahoensis), reliant on sagebrush as forage. Despite this, plant chemistry (e.g., crude protein, monoterpenes and phenolics) is rarely considered during reseeding efforts or when deciding which areas to conserve. Near-infrared spectroscopy (NIRS) has proven effective in predicting plant chemistry under laboratory conditions in …


Trem2 Is Thyroid Hormone Regulated Making The Trem2 Pathway Druggable With Ligands For Thyroid Hormone Receptor., Skylar J. Ferrara, Priya Chaudhary, Margaret J. Debell, Gail Marracci, Hannah Miller, Evan Calkins, Edvinas Pocius, Brooke A. Napier, Ben Emery, Dennis Bourdette, Thomas S. Scanlan Aug 2021

Trem2 Is Thyroid Hormone Regulated Making The Trem2 Pathway Druggable With Ligands For Thyroid Hormone Receptor., Skylar J. Ferrara, Priya Chaudhary, Margaret J. Debell, Gail Marracci, Hannah Miller, Evan Calkins, Edvinas Pocius, Brooke A. Napier, Ben Emery, Dennis Bourdette, Thomas S. Scanlan

Biology Faculty Publications and Presentations

Triggering receptor expressed on myeloid cells-2 (TREM2) is a cell surface receptor on macrophages and microglia that senses and responds to disease-associated signals to regulate the phenotype of these innate immune cells. The TREM2 signaling pathway has been implicated in a variety of diseases ranging from neurodegeneration in the central nervous system to metabolic disease in the periphery. Here, we report that TREM2 is a thyroid hormone-regulated gene and its expression in macrophages and microglia is stimulated by thyroid hormone and synthetic thyroid hormone agonists (thyromimetics). Our findings report the endocrine regulation of TREM2 by thyroid hormone, and provide a …


Long-Term Crop Rotation Diversification Enhances Maize Drought Resistance Through Soil Organic Matter, Leah L.R. Renwick, William Deen, Lucas Silva, Matthew E. Gilbert, Toby Maxwell, Timothy M. Bowles, Amélie C.M. Gaudin Aug 2021

Long-Term Crop Rotation Diversification Enhances Maize Drought Resistance Through Soil Organic Matter, Leah L.R. Renwick, William Deen, Lucas Silva, Matthew E. Gilbert, Toby Maxwell, Timothy M. Bowles, Amélie C.M. Gaudin

Biology Faculty Publications and Presentations

Climate change adaptation requires building agricultural system resilience to warmer, drier climates. Increasing temporal plant diversity through crop rotation diversification increases yields of some crops under drought, but its potential to enhance crop drought resistance and the underlying mechanisms remain unclear. We conducted a drought manipulation experiment using rainout shelters embedded within a 36-year crop rotation diversity and no-till experiment in a temperate climate and measured a suite of soil and crop developmental and eco-physiological traits in the field and laboratory. We show that diversifying maize-soybean rotations with small grain cereals and cover crops mitigated maize water stress at the …


Exploring Microbiome Functional Dynamics Through Space And Time With Trait-Based Theory, Leonora S. Bittleston, Jessica R. Bernardin Aug 2021

Exploring Microbiome Functional Dynamics Through Space And Time With Trait-Based Theory, Leonora S. Bittleston, Jessica R. Bernardin

Biology Faculty Publications and Presentations

Microbiomes play essential roles in the health and function of animal and plant hosts and drive nutrient cycling across ecosystems. Integrating novel trait-based approaches with ecological theory can facilitate the prediction of microbial functional traits important for ecosystem functioning and health. In particular, the yield-acquisition-stress (Y-A-S) framework considers dominant microbial life history strategies across gradients of resource availability and stress. However, microbiomes are dynamic, and spatial and temporal shifts in taxonomic and trait composition can affect ecosystem functions. We posit that extending the Y-A-S framework to microbiomes during succession and across biogeographic gradients can lead to generalizable rules for how …


The Role Of Genome Duplication In Big Sagebrush Growth And Fecundity, Bryce A. Richardson, Matthew J. Germino, Marcus V. Warwell, Sven Buerki Aug 2021

The Role Of Genome Duplication In Big Sagebrush Growth And Fecundity, Bryce A. Richardson, Matthew J. Germino, Marcus V. Warwell, Sven Buerki

Biology Faculty Publications and Presentations

Premise: Adaptive traits can be dramatically altered by genome duplication. The study of interactions among traits, ploidy, and the environment are necessary to develop an understanding of how polyploidy affects niche differentiation and to develop restoration strategies for resilient native ecosystems.

Methods: Growth and fecundity were measured in common gardens for 39 populations of big sagebrush (Artemisia tridentata) containing two subspecies and two ploidy levels. General linear mixed-effect models assessed how much of the trait variation could be attributed to genetics (i.e., ploidy and climatic adaptation), environment, and gene–environment interactions.

Results: Growth and fecundity variation were explained well …


Resolving Species Boundaries In A Recent Radiation With The Angiosperms353 Probe Set: The Lomatium Packardiae/L. Anomalum Clade Of The L. Triternatum (Apiaceae) Complex, Michael V. Ottenlips, Sven Buerki, James F. Smith Jul 2021

Resolving Species Boundaries In A Recent Radiation With The Angiosperms353 Probe Set: The Lomatium Packardiae/L. Anomalum Clade Of The L. Triternatum (Apiaceae) Complex, Michael V. Ottenlips, Sven Buerki, James F. Smith

Biology Faculty Publications and Presentations

Premise: Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here.

Methods: The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species …


A Higher-Level Nuclear Phylogenomic Study Of The Carrot Family (Apiaceae), James F. Smith Jul 2021

A Higher-Level Nuclear Phylogenomic Study Of The Carrot Family (Apiaceae), James F. Smith

Biology Faculty Publications and Presentations

PREMISE: The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap.

METHODS: Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches.

RESULTS: We recovered hundreds of nuclear …


Using An Ultraviolet Light Test To Improve Sagebrush Identification And Predict Forage Quality For Wildlife, Roger Rosentreter, Brecken C. Robb, Jennifer S. Forbey Jul 2021

Using An Ultraviolet Light Test To Improve Sagebrush Identification And Predict Forage Quality For Wildlife, Roger Rosentreter, Brecken C. Robb, Jennifer S. Forbey

Biology Faculty Publications and Presentations

Sagebrush identification can be improved by using a relatively easy ultraviolet (UV) light test on specimens. Sagebrush produces a variety of water-soluble polyphenols called coumarins, which fluoresce a blue color under UV light and can help differentiate species, subspecies, and hybrids. We tested 16 different sagebrush taxa (including species and subspecies) from herbarium specimens and found 3 taxa (low sagebrush, Artemisia arbuscula; Wyoming sagebrush, A. tridentata wyomingensis; and basin sagebrush, A. t. tridentata) that were often misidentified. We show that the UV light test can greatly improve identification of these species. Moreover, given that the UV+ chemicals …


Data Management Tools To Measure The Impact Of Core Facilities, Diane B. Smith, Tracy L. Yarnell, Barbara J. Jibben, Linda E. Liou, Carolyn J. Hovde, Julia Thom Oxford Jul 2021

Data Management Tools To Measure The Impact Of Core Facilities, Diane B. Smith, Tracy L. Yarnell, Barbara J. Jibben, Linda E. Liou, Carolyn J. Hovde, Julia Thom Oxford

Biology Faculty Publications and Presentations

The Biomolecular Research Center at Boise State University is a research core facility that supports the study of biomolecules with an emphasis on protein structure and function, molecular interactions, and imaging. The mission of the core is to facilitate access to instrumentation that might otherwise be unavailable because of the cost, training for new users, and scientific staff with specialized skills to support early-stage investigators, as well as more established senior investigators. Data collection and management of users and their research output is essential to understand the impact of the center on the research environment and research productivity. However, challenges …


An Updated Infra-Familial Classification Of Sapindaceae Based On Targeted Enrichment Data, Sven Buerki Jul 2021

An Updated Infra-Familial Classification Of Sapindaceae Based On Targeted Enrichment Data, Sven Buerki

Biology Faculty Publications and Presentations

Premise: The economically important, cosmopolitan soapberry family (Sapindaceae) comprises ca. 1900 species in 144 genera. Since the seminal work of Radlkofer, several authors have attempted to overcome challenges presented by the family’s complex infra-familial classification. With the advent of molecular systematics, revisions of the various proposed groupings have provided significant momentum, but we still lack a formal classification system rooted in an evolutionary framework.

Methods: Nuclear DNA sequence data were generated for 123 genera (86%) of Sapindaceae using target sequence capture with the Angiosperms353 universal probe set. HybPiper was used to produce aligned DNA matrices. Phylogenetic inferences were obtained using …


Poor Vector Competence Of The Human Flea, Pulex Irritans, To Transmit Yersinia Pestis, Adélaïde Miarinjara, David M. Bland, James R. Belthoff, B. Joseph Hinnebusch Jun 2021

Poor Vector Competence Of The Human Flea, Pulex Irritans, To Transmit Yersinia Pestis, Adélaïde Miarinjara, David M. Bland, James R. Belthoff, B. Joseph Hinnebusch

Biology Faculty Publications and Presentations

Background: The human flea, Pulex irritans, is widespread globally and has a long association with humans, one of its principal hosts. Its role in plague transmission is still under discussion, although its high prevalence in plague-endemic regions and the presence of infected fleas of this species during plague outbreaks has led to proposals that it has been a significant vector in human-to-human transmission in some historical and present-day epidemiologic situations. However, based on a limited number of studies, P. irritans is considered to be a poor vector and receives very little attention from public health policymakers. In this study …


Decellularized Porcine Cartilage Scaffold: Validation Of Decellularization And Evaluation Of Biomarkers Of Chondrogenesis, Roxanne N. Stone, Stephanie M. Frahs, Makenna J. Hardy, Akina Fujimoto, Xinzhu Pu, Cynthia Keller-Peck, Julia Thom Oxford Jun 2021

Decellularized Porcine Cartilage Scaffold: Validation Of Decellularization And Evaluation Of Biomarkers Of Chondrogenesis, Roxanne N. Stone, Stephanie M. Frahs, Makenna J. Hardy, Akina Fujimoto, Xinzhu Pu, Cynthia Keller-Peck, Julia Thom Oxford

Biology Faculty Publications and Presentations

Osteoarthritis is a major concern in the United States and worldwide. Current non-surgical and surgical approaches alleviate pain but show little evidence of cartilage restoration. Cell-based treatments may hold promise for the regeneration of hyaline cartilage-like tissue at the site of injury or wear. Cell–cell and cell–matrix interactions have been shown to drive cell differentiation pathways. Biomaterials for clinically relevant applications can be generated from decellularized porcine auricular cartilage. This material may represent a suitable scaffold on which to seed and grow chondrocytes to create new cartilage. In this study, we used decellularization techniques to create an extracellular matrix scaffold …


Unifying Community Detection Across Scales From Genomes To Landscapes, Stephanie F. Hudon, Andrii Zaiats, Anna Roser, Anand Roopsind, Cristina Barber, Brecken Robb, Britt Pendleton, Merry M. Davidson, Jonas Frankel-Bricker, Marcella Fremgen-Tarantino, Jennifer Sorensen Forbey, Eric Hayden, Olivia K. Rodriguez, T. Trevor Caughlin Jun 2021

Unifying Community Detection Across Scales From Genomes To Landscapes, Stephanie F. Hudon, Andrii Zaiats, Anna Roser, Anand Roopsind, Cristina Barber, Brecken Robb, Britt Pendleton, Merry M. Davidson, Jonas Frankel-Bricker, Marcella Fremgen-Tarantino, Jennifer Sorensen Forbey, Eric Hayden, Olivia K. Rodriguez, T. Trevor Caughlin

Biology Faculty Publications and Presentations

Biodiversity science encompasses multiple disciplines and biological scales from molecules to landscapes. Nevertheless, biodiversity data are often analyzed separately with discipline-specific methodologies, constraining resulting inferences to a single scale. To overcome this, we present a topic modeling framework to analyze community composition in cross-disciplinary datasets, including those generated from metagenomics, metabolomics, field ecology and remote sensing. Using topic models, we demonstrate how community detection in different datasets can inform the conservation of interacting plants and herbivores. We show how topic models can identify members of molecular, organismal and landscape-level communities that relate to wildlife health, from gut microbes to forage …


Linking Behavioral States To Landscape Features For Improved Conservation Management, Maitreyi Sur, Jim R. Belthoff Jun 2021

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, …


Inter- And Intracontinental Migration By The Eastern Kingbird (Tyrannus Tyrannus), Daniel H. Kim, Lucas J. Redmond, James R. Fox, Michael T. Murphy Jun 2021

Inter- And Intracontinental Migration By The Eastern Kingbird (Tyrannus Tyrannus), Daniel H. Kim, Lucas J. Redmond, James R. Fox, Michael T. Murphy

Biology Faculty Publications and Presentations

We recovered 12 archival geolocators deployed on Eastern Kingbirds (Tyrannus tyrannus) breeding in New York (NY; n¼3, 2 with 2 years of data), Nebraska (NE; n¼6, 1 with 2 years of data), and Oregon (OR; n¼3) to describe migratory routes, timing and rates of migration, nonbreeding season distributions, and migratory connectedness. NY fall migrants migrated along the Atlantic coast to Florida, flew either nonstop across the Gulf of Mexico (GoM; 2 of 3 birds) or stopped once along the way (Cuba and Cayman Islands in different years) to land in Yucatan/Central America. Fall birds from NE and OR arrived at …


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 May 2021

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 …


Coxiella Burnetii And Related Tick Endosymbionts Evolved From Pathogenic Ancestors, Amanda E. Brenner, Sebastián Muñoz-Leal, Madhur Sachan, Marcelo B. Labruna, Rahul Raghavan May 2021

Coxiella Burnetii And Related Tick Endosymbionts Evolved From Pathogenic Ancestors, Amanda E. Brenner, Sebastián Muñoz-Leal, Madhur Sachan, Marcelo B. Labruna, Rahul Raghavan

Biology Faculty Publications and Presentations

Both symbiotic and pathogenic bacteria in the family Coxiellaceae cause morbidity and mortality in humans and animals. For instance, Coxiella-like endosymbionts (CLEs) improve the reproductive success of ticks—a major disease vector, while Coxiella burnetii causes human Q fever, and uncharacterized coxiellae infect both animals and humans. To better understand the evolution of pathogenesis and symbiosis in this group of intracellular bacteria, we sequenced the genome of a CLE present in the soft tick Ornithodoros amblus (CLEOA) and compared it to the genomes of other bacteria in the order Legionellales. Our analyses confirmed that CLEOA is more closely related to …


Evolution Of An Epidermal Differentiation Complex (Edc) Gene Family In Birds, Anthony Davis, Matthew J. Greenwold May 2021

Evolution Of An Epidermal Differentiation Complex (Edc) Gene Family In Birds, Anthony Davis, Matthew J. Greenwold

Biology Faculty Publications and Presentations

The transition of amniotes to a fully terrestrial lifestyle involved the adaptation of major molecular innovations to the epidermis, often in the form of epidermal appendages such as hair, scales and feathers. Feathers are diverse epidermal structures of birds, and their evolution has played a key role in the expansion of avian species to a wide range of lifestyles and habitats. As with other epidermal appendages, feather development is a complex process which involves many different genetic and protein elements. In mammals, many of the genetic elements involved in epidermal development are located at a specific genetic locus known as …


Nest Site Selection And Nesting Behavior Of The Mud Turtle Kinosternon Scorpiodes (Testudines, Kinosternidae) In Palo Verde National Park, Costa Rica: Implications For Management, José M. Mora, Franklin E. Castañeda May 2021

Nest Site Selection And Nesting Behavior Of The Mud Turtle Kinosternon Scorpiodes (Testudines, Kinosternidae) In Palo Verde National Park, Costa Rica: Implications For Management, José M. Mora, Franklin E. Castañeda

Biology Faculty Publications and Presentations

Habitat selection is the process whereby individuals preferentially use, or occupy, a non-random set of available habitats. At the same time, nest site selection is defined as the placement of eggs by females at sites differing from random sites within a delimited area. We located 59 nests of the mud turtle Kinosternon scorpioides in Palo Verde National Park (PVNP) in Northwestern Costa Rica. We compared eight microhabitat variables at nest sites against those at random sites. Females significantly placed their eggs at sites with more understory, leaf litter cover, and greater leaf litter depth than in random sites. Additionally, females …