Life Sciences Commons^™

Proteomic Dataset For Decellularization Of Porcine Auricular Cartilage, Roxanne N. Stone, Xinzhu Pu, Julia Thom Oxford

Biology Faculty Publications and Presentations

Objectives Osteoarthritis (OA) is a major concern in the United States and worldwide. Development and validation of robust decellularization techniques is critical in generating suitable bioscaffolds for future OA treatment options.

Data descriptions In the present study, proteins from porcine auricular cartilage before and after decellularization were extracted, digested, and identified using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The data represents protein profiles of both non-decellularized and decellularized porcine auricular cartilage. This data is intended to be useful to scientists who are interesting in generating biomaterials for potential relevant clinical applications using decellularized cartilage tissue.

9s1r Nullomer Peptide Induces Mitochondrial Pathology, Metabolic Suppression, And Enhanced Immune Cell Infiltration, In Triple-Negative Breast Cancer Mouse Model, Nilufar Ali, Cody Wolf, Swarna Kanchan, Shivakumar R. Veerabhadraiah, Laura Bond, Matthew W. Turner, Cheryl L. Jorcyk, Greg Hampikian

Biology Faculty Publications and Presentations

Nullomers are the shortest strings of absent amino acid (aa) sequences in a species or group of species. Primes are those nullomers that have not been detected in the genome of any species. 9S1R is a 5-aa peptide prime sequence attached to 5-arginine aa, used to treat triple negative breast cancer (TNBC) in an in vivo mouse model. This unique peptide, administered with a trehalose carrier (9S1R-NulloPT), offers enhanced solubility and exhibits distinct anti-cancer effects against TNBC. In our study, we investigated the effect of 9S1R-NulloPT on tumor growth, metabolism, metastatic burden, tumor immune-microenvironment (TME), and transcriptome of aggressive mouse …

Genomic Surveillance Of Sars-Cov-2 Sequence Variants At Universities In Southwest Idaho, Jennifer R. Chase, Laura Bond, Daniel J. Vail, Milan Sengthep, Adriana Rodriguez, Joe Christianson, Stephanie F. Hudon, Julia Thom Oxford

Biology Faculty Publications and Presentations

Although the impact of the SARS-CoV-2 pandemic on major metropolitan areas is broadly reported and readily available, regions with lower populations and more remote areas in the United States are understudied. The objective of this study is to determine the progression of SARS-CoV-2 sequence variants in a frontier and remote intermountain west state among university-associated communities. This study was conducted at two intermountain west universities from 2020 to 2022. Positive SARS-CoV-2 samples were confirmed by quantitative real-time reverse transcription-polymerase chain reaction and variants were identified by the next-generation sequencing of viral genomes. Positive results were obtained for 5355 samples, representing …

Doxorubicin-Induced Modulation Of Tgf-Β Signaling Cascade In Mouse Fibroblasts: Insights Into Cardiotoxicity Mechanisms, Conner Patricelli, Parker Lehmann, Julia Thom Oxford, Xinzhu Pu

Biology Faculty Publications and Presentations

Doxorubicin (DOX)-induced cardiotoxicity has been widely observed, yet the specific impact on cardiac fibroblasts is not fully understood. Additionally, the modulation of the transforming growth factor beta (TGF-β) signaling pathway by DOX remains to be fully elucidated. This study investigated DOX’s ability to modulate the expression of genes and proteins involved in the TGF-β signaling cascade in mouse fibroblasts from two sources by assessing the impact of DOX treatment on TGF-β inducible expression of pivotal genes and proteins within fibroblasts. Mouse embryonic fibroblasts (NIH3T3) and mouse primary cardiac fibroblasts (CFs) were treated with DOX in the presence of TGF-β1 to …

Advances In Cartilage Tissue Engineering Using Bioinks With Decellularized Cartilage And Three-Dimensional Printing, Roxanne N. Stone, Jonathon C. Reeck, Julia Thom Oxford

Biology Faculty Publications and Presentations

Osteoarthritis, a chronic, debilitating, and painful disease, is one of the leading causes of disability and socioeconomic burden, with an estimated 250 million people affected worldwide. Currently, there is no cure for osteoarthritis and treatments for joint disease require improvements. To address the challenge of improving cartilage repair and regeneration, three-dimensional (3D) printing for tissue engineering purposes has been developed. In this review, emerging technologies are presented with an overview of bioprinting, cartilage structure, current treatment options, decellularization, bioinks, and recent progress in the field of decellularized extracellular matrix (dECM)–bioink composites is discussed. The optimization of tissue engineering approaches using …

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 …

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 …

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 …

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.

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 …

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. …

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) …

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 …

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 …

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.

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 …

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 …

Correcting Forensic Dna Errors, Greg Hampikian

Biology Faculty Publications and Presentations

DNA mixture interpretation can produce opposing conclusions by qualified forensic analysts, even within the same laboratory. The long-delayed publication of the National Institutes of Standards and Technology (NIST) study of 109 North American crime laboratories in this journal demonstrates this most clearly. This latest study supports earlier work that shows common methods such as the Combined Probability of Inclusion (CPI) have wrongly included innocent people as contributors to DNA mixtures.The 2016 President’s Council of Advisors on Science and Technology report concluded,“In summary, the interpretation of complex DNA mixtures with the CPI statistic has been an inadequately specified—and thus inappropriately subjective—method. …

Conservation Genomics In The Sagebrush Sea: Population Divergence, Demographic History, And Local Adaptation In Sage-Grouse (Centrocercus Spp.), Kevin P. Oh, Cameron L. Aldridge, Jennifer S. Forbey, Carolyn Y. Dadabay, Sara J. Oyler-Mccance

Biology Faculty Publications and Presentations

Sage-grouse are two closely related iconic species of the North American West, with historically broad distributions across sagebrush-steppe habitat. Both species are dietary specialists on sagebrush during winter, with presumed adaptations to tolerate the high concentrations of toxic secondary metabolites that function as plant chemical defenses. Marked range contraction and declining population sizes since European settlement have motivated efforts to identify distinct population genetic variation, particularly that which might be associated with local genetic adaptation and dietary specialization of sage-grouse. We assembled a reference genome and performed whole-genome sequencing across sage-grouse from six populations, encompassing both species and including several …

Trophic Interactions And Abiotic Factors Drive Functional And Phylogenetic Structure Of Vertebrate Herbivore Communities Across The Arctic Tundra Biome, Jennifer Forbey

Biology Faculty Publications and Presentations

Communities are assembled from species that evolve or colonise a given geographic region, and persist in the face of abiotic conditions and interactions with other species. The evolutionary and colonisation histories of communities are characterised by phylogenetic diversity, while functional diversity is indicative of abiotic and biotic conditions. The relationship between functional and phylogenetic diversity infers whether species functional traits are divergent (differing between related species) or convergent (similar among distantly related species). Biotic interactions and abiotic conditions are known to influence macroecological patterns in species richness, but how functional and phylogenetic diversity of guilds vary with biotic factors, and …

Contributions Of Vps35 Mutations To Parkinson’S Disease, Abir A. Rahman, Brad E. Morrison

Biology Faculty Publications and Presentations

Parkinson’s Disease (PD) is a multi-system neurodegenerative disease where approximately 90% of cases are idiopathic. The remaining 10% of the cases can be traced to a genetic origin and research has largely focused on these associated genes to gain a better understanding of the molecular and cellular pathogenesis for PD. The gene encoding vacuolar protein sorting protein 35 (VPS35) has been definitively linked to late onset familial PD following the identification of a point mutation (D620N) as the causal agent in a Swiss family. Since its discovery, numerous studies have been undertaken to characterize the role of VPS35 in cellular …

Co-Expression Of Vegf And Il-6 Family Cytokines Is Associated With Decreased Survival In Her2 Negative Breast Cancer Patients: Subtype-Specific Il-6 Family Cytokine-Mediated Vegf Secretion, Ken Tawara, Hannah Scott, Jacqueline Emathinger, Alex Ide, Ryan Fox, Daniel Greiner, Dollie Lajoie, Danielle Hedeen, Madhuri Nandakumar, Andrew J. Oler, Ryan Holzer, Cheryl Jorcyk

Biology Faculty Publications and Presentations

Breast cancer cell-response to inflammatory cytokines such as interleukin-6 (IL-6) and oncostatin M (OSM) may affect the course of clinical disease in a cancer subtype-dependent manner. Furthermore, vascular endothelial growth factor A (VEGF) secretion induced by IL-6 and OSM may also be subtype-dependent. Utilizing datasets from Oncomine, we show that poor survival of invasive ductal carcinoma (IDC) breast cancer patients is correlated with both high VEGF expression and high cytokine or cytokine receptor expression in tumors. Importantly, epidermal growth factor receptor-negative (HER2-), but not HER2-positive (HER2+), patient survival is significantly lower with high tumor co-expression of VEGF and OSM, OSMRβ, …

Preferences Of Specialist And Generalist Mammalian Herbivores For Mixtures Versus Individual Plant Secondary Metabolites, Jordan D. Nobler, Jennifer S. Forbey

Biology Faculty Publications and Presentations

Herbivores that forage on chemically defended plants consume complex mixtures of plant secondary metabolites (PSMs). However, the mechanisms by which herbivores tolerate mixtures of PSMs are relatively poorly understood. As such, it remains difficult to predict how PSMs, singly or as complex mixtures, influence diet selection by herbivores. Although relative rates of detoxification of PSMs have been used to explain tolerance of PSMs by dietary specialist herbivores, few studies have used the rate of detoxification of individual PSMs to understand dietary preferences of individual herbivores for individual versus mixtures of PSMs. We coupled in vivo experiments using captive feeding trials …

A Fragment Of Apolipoprotein E4 Leads To The Downregulation Of A Cxorf56 Homologue, A Novel Er-Associated Protein, And Activation Of Bv2 Microglial Cells, Tanner B. Pollock, Jacob M. Mack, Noail F. Isho, Raquel J. Brown, Alexandra E. Oxford, Brad E. Morrison, Eric J. Hayden, Troy T. Rohn

Biology Faculty Publications and Presentations

Despite the fact that harboring the apolipoprotein E4 (APOE4) allele represents the single greatest risk factor for late-onset Alzheimer’s disease (AD), the exact mechanism by which apoE4 contributes to disease progression remains unknown. Recently, we demonstrated that a 151 amino-terminal fragment of apoE4 (nApoE4_1-151) localizes within the nucleus of microglia in the human AD brain, suggesting a potential role in gene expression. In the present study, we investigated this possibility utilizing BV2 microglia cells treated exogenously with nApoE4_1-151. The results indicated that nApoE4_1-151 leads to morphological activation of microglia cells through, at least in part, …

Review: Using Physiologically Based Models To Predict Population Responses To Phytochemicals By Wild Vertebrate Herbivores, J. S. Forbey, T. T. Caughlin

Biology Faculty Publications and Presentations

To understand how foraging decisions impact individual fitness of herbivores, nutritional ecologists must consider the complex in vivo dynamics of nutrient–nutrient interactions and nutrient–toxin interactions associated with foraging. Mathematical modeling has long been used to make foraging predictions (e.g. optimal foraging theory) but has largely been restricted to a single currency (e.g. energy) or using simple indices of nutrition (e.g. fecal nitrogen) without full consideration of physiologically based interactions among numerous co-ingested phytochemicals. Here, we describe a physiologically based model (PBM) that provides a mechanistic link between foraging decisions and demographic consequences. Including physiological mechanisms of absorption, digestion and metabolism …

Genetic Testing: Should I Get Tested For Alzheimer’S Risk?, Troy Rohn

Biology Faculty Publications and Presentations

Genetic testing is available to people who want to know if they carry a variant of a gene that confers susceptibility for Alzheimer’s. But knowing whether to get tested is hard.

Effects Of Mowing And Tebuthiuron On The Nutritional Quality Of Wyoming Big Sagebrush, Kurt T. Smith, Jennifer S. Forbey, Jeffrey L. Black

Biology Faculty Publications and Presentations

Wyoming big sagebrush (Artemisia tridentata Nutt. ssp. wyomingensis Beetle & Young) is the most abundant and widely distributed subspecies of big sagebrush and has been treated through chemical application, mechanical treatments, and prescribed burning in efforts thought to improve habitat conditions for species such as greater sage-grouse (Centrocercus urophasianus) and mule deer (Odocoileus hemionus). Although the response of structural attributes of sagebrush communities to treatments is well understood, there is a need to identify how treatments influence the quality of sagebrush as winter food for wildlife. Our purpose was to identify how mowing and tebuthiuron …

Osm Potentiates Preintravasation Events, Increases Ctc Counts, And Promotes Breast Cancer Metastasis To The Lung, Ken Tawara, Celeste Bolin, Jordan Koncinsky, Sujatha Kadaba, Hunter Covert, Caleb Sutherland, Laura Bond, Cheryl L. Jorcyk

Biology Faculty Publications and Presentations

Background: Systemic and chronic inflammatory conditions in patients with breast cancer have been associated with reduced patient survival and increased breast cancer aggressiveness. This paper characterizes the role of an inflammatory cytokine, oncostatin M (OSM), in the preintravasation aspects of breast cancer metastasis.

Methods: OSM expression levels in human breast cancer tissue samples were assessed using tissue microarrays, and expression patterns based on clinical stage were assessed. To determine the in vivo role of OSM in breast cancer metastasis to the lung, we used three orthotopic breast cancer mouse models, including a syngeneic 4T1.2 mouse mammary cancer model, the MDA-MB-231 …

Dietary Partitioning Of Toxic Leaves And Fibrous Stems Differs Between Sympatric Specialist And Generalist Mammalian Herbivores, M. M. Crowell, L. A. Shipley, J. S. Forbey, J. L. Rachlow, R. G. Kelsey

Biology Faculty Publications and Presentations

Dietary specialists often reside in habitats that provide a high and predictable abundance of their primary food, which is usually difficult for other herbivores to consume because of high levels of plant toxins or structural impediments. Therefore, sympatric specialist and generalist herbivores may partition food resources within and among plants. We compared how a dietary specialist (pygmy rabbit, Brachylagus idahoensis) and generalist (mountain cottontail, Sylvilagus nuttallii) used sagebrush as a food resource during winter across 3 field sites in Idaho, USA, and in controlled feeding trials with captive rabbits. The proportion of sagebrush consumed by both rabbit species …