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Full-Text Articles in Life Sciences

Nest Success By A Female Black-Chinned Hummingbird (Archilochus Alexandri) With Male-Like Plumage, Cooper M. Farr, John Middleton Jun 2023

Nest Success By A Female Black-Chinned Hummingbird (Archilochus Alexandri) With Male-Like Plumage, Cooper M. Farr, John Middleton

Western North American Naturalist

Female-limited polymorphism, a phenomenon in which female animals can exhibit male-like coloration, is known to occur in approximately 25% of hummingbird species, but it has not previously been recognized in Black-chinned Hummingbirds (Archilochus alexandri). Between May and July 2021, we documented a Black-chinned Humming­bird with male plumage features that built a nest, incubated eggs, and successfully fledged 2 chicks in Salt Lake City, Utah. The bird’s gorget feathers, including the chin and upper throat, were predominantly dark with a small number of white feathers interspersed. Because the bird participated in nest building, presumed egg production, and incubation—behaviors not …

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Ebi2, Rodney Till, Dr. Brian Poole Jun 2023

Ebi2, Rodney Till, Dr. Brian Poole

Journal of Undergraduate Research

My project this year was a great learning experience and helped me to better understand the complexity of lab work, as well as, the tools used in troubleshooting problems; including collaboration with lab researchers and professors. I learned about flow cytometry and how to analyze migration data. I also learned how to do transfections with HEK cells and how to separate B cells from a fresh sample of blood. I was thankful that I could spend time doing lab work because it’s the best teaching environment I know of in academia. I came across genuine problems and studied topics with …

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Examination Of The Role Of The Lana Protein In Persistence Of Kaposi’S Sarcoma-Associated Herpesvirus Infections, Marshall Sheide, Dr. Bradford Berges Jun 2023

Examination Of The Role Of The Lana Protein In Persistence Of Kaposi’S Sarcoma-Associated Herpesvirus Infections, Marshall Sheide, Dr. Bradford Berges

Journal of Undergraduate Research

Kaposi’s sarcoma herpes virus (KSHV) is one of seven known cancer causing viruses which have the capacity to persist in the host for many years. This particular virus can undergo a long latent infection which ensures that the virus can hide by not expressing its genes. Last year, we proposed an experiment that would show the importance of a particular gene in the viral genome, LANA, in establishing a latent infection. The experiment required us to create stocks of a mutant virus that did not have the LANA gene inside (bac36deltaLANA) and then infect humanized mice with it. After infection, …

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Search For Mitochondrial Dna Mutation In A Family With Myopathies And Lactic Acidosis, Mary Rennick, Dr. Brent Nielsen Jun 2023

Search For Mitochondrial Dna Mutation In A Family With Myopathies And Lactic Acidosis, Mary Rennick, Dr. Brent Nielsen

Journal of Undergraduate Research

This research focused on the search for the probable mitochondrial DNA (mtDNA) mutation in one family affected with fibromyalgia and lactic acidosis. The hypothesis was that there is mixture of normal and mutated mtDNA, called heteroplasmy. I first obtained the four patients’ consent to participate in the study. The four patients were between the age of 19 and 25 years-­‐two males and two females. They donated urine samples to be used for DNA analysis. I isolated DNA using a Qiagen DNA extraction kit and obtained concentration measurements of 8-­‐ 10 nanograms per microliter using the nanodrop spectrophotometer in the RIC …

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Antibody Production And Diversification In Humanized Mice, Stanton Nielsen, Dr. Brad Berges Jun 2023

Antibody Production And Diversification In Humanized Mice, Stanton Nielsen, Dr. Brad Berges

Journal of Undergraduate Research

Many scientists are skeptical of using humanized mice to study the human adaptive immune response. The reasoning behind this skepticism stems from discrepancies in various studies seen previously. A study conducted by Traggiai et al. showed that humanized mice elicited a human adaptive immune response when challenged with the tetanus toxin (Traggiai). In addition, good antibody responses have been shown in humanized mice when challenged with Dengue virus (Kuruvilla). However, others have found only rare antibody responses to HIV when humanized mice were challenged (Baenziger). As mentioned earlier, a study conducted by Becker et al. showed the production of human …

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Vitamin D3 As An Adjuvant To Produce Localized Immunity, Kaitlyn Vance, Dr. Eric Wilson Jun 2023

Vitamin D3 As An Adjuvant To Produce Localized Immunity, Kaitlyn Vance, Dr. Eric Wilson

Journal of Undergraduate Research

The aim of our research was to help elucidate the degree of specificity employed by antibody secreting cells (lymphocytes) through a study of the role of CCR10 in the differential homing of these cells to mucosal issues. We used vitamin D3, known to upregulate expression of CCR10 on activated lymphocytes, as an adjuvant in our vaccines and tracked cell homing to mucosal tissues that express the CCR10 ligand CCL28 by detecting antigen specific antibody accumulation. Since mucosal tissues are ideal locations for vaccinations, the long-term aim was to develop a method for targeting antigen specific lymphocytes, and thus robust immune …

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Raw Diffraction Data For 1tel-Aa-Vwa (Sumo), Wwpdb Id: 7n1o, Moriah H. Mathis, Braydan D. Bezzant, Diana T. Ramírez, Supeshala D. Nawarathnage, Tzanko I. Doukov, James Moody Jun 2023

Raw Diffraction Data For 1tel-Aa-Vwa (Sumo), Wwpdb Id: 7n1o, Moriah H. Mathis, Braydan D. Bezzant, Diana T. Ramírez, Supeshala D. Nawarathnage, Tzanko I. Doukov, James Moody

ScholarsArchive Data

This X-ray diffraction dataset was collected on October 21Oct2020 at SSRL Beamline BL9-2. The crystal was of Batch 1 1TEL-AA-vWa (SUMO) The solved structure used frames 1-999 and has been deposited in the wwPDB under the PDB ID 7N1O. This data can be readily processed using XDS, AutoProc, CCP4, HKL2000/3000, or other crystallographic X-ray diffraction data processing software. The files have a human-readable header but are otherwise binary.

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Raw Diffraction Data For 3tel-Hlx-Darpin (Sumo), Wwpdb Id: 7n2b, Supeshala D. Nawarathnage, Parag Laljibhai Gajjar, Derick R. Bunn, Cameron Stewart, Tzanko I. Doukov, James Moody Jun 2023

Raw Diffraction Data For 3tel-Hlx-Darpin (Sumo), Wwpdb Id: 7n2b, Supeshala D. Nawarathnage, Parag Laljibhai Gajjar, Derick R. Bunn, Cameron Stewart, Tzanko I. Doukov, James Moody

ScholarsArchive Data

This X-ray diffraction dataset was collected on October 21Oct2020 at SSRL Beamline BL9-2. The crystal was of 3TEL-hlx-DARPin (SUMO) The solved structure used frames 1-1799 and has been deposited in the wwPDB under the PDB ID 7N2B. This data can be readily processed using XDS, AutoProc, CCP4, HKL2000/3000, or other crystallographic X-ray diffraction data processing software. The files have a human-readable header but are otherwise binary.

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Characterizing Proteins That Interact With Pas Kinase, Jordan Mackay, Dr. Julianne Grose Jun 2023

Characterizing Proteins That Interact With Pas Kinase, Jordan Mackay, Dr. Julianne Grose

Journal of Undergraduate Research

Characterizing the interacting protein partners of Per-Arnt-Sim (PAS) kinase has proven to be a formidable task. Since the beginning of 2012, I have been working hard with graduate student Desi DeMille on confirming the putative interactors uncovered by genetic screening done the previous year. This endeavor has yielded both successes and failures.

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How ‘Bout Them Apples?: A Study On Antioxidants, Kylie Measom, Dr. Kim O'Neill Jun 2023

How ‘Bout Them Apples?: A Study On Antioxidants, Kylie Measom, Dr. Kim O'Neill

Journal of Undergraduate Research

They say “an apple a day keeps the doctor away.” Apples are laden with antioxidants which have been shown to prevent against cancer and other illnesses.1 Antioxidants are molecules that prevent cancer by collecting excess free radicals in the body. Free radicals are highly reactive molecules. They may interfere with DNA and other biomolecules leading to DNA damage and mutations. Antioxidants prevent this by scavenging for free radicals before they can interact with other important biomolecules.2 Apples, particularly the skins, have high phenolic content. Phenols are antioxidants that protect against oxidative damage caused by free radicals.3 Different …

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Ebi2 Knockdown And Effects On B-Cell Migration, Jordan Mabey, Dr. Brian Poole Jun 2023

Ebi2 Knockdown And Effects On B-Cell Migration, Jordan Mabey, Dr. Brian Poole

Journal of Undergraduate Research

B cells are specialized cells which participate in the normal immune response to an infection. As B cells encounter antigens in the body, they become activated and travel to what is known as a B cell follicle within a lymph node. At the outer follicle B cells combine with T cells and move to the inner follicle to become specialized immunity participating cells. Normally upon reaching the outer follicle, the B cell up-regulates Epstein-Barr virus induced molecule-2 (EBI2) which causes it to pause until the cell can complex with the proper T cell. Once this connection between the two cells …

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Assessing The Effects Of The Irf5 Exon 1b On Translation, Jared Lambert, Dr. Brian Poole Jun 2023

Assessing The Effects Of The Irf5 Exon 1b On Translation, Jared Lambert, Dr. Brian Poole

Journal of Undergraduate Research

With our lab’s previous finding revealing a hairpin folding structure in exon 1B (IRF5 risk allele), not found in the other first exons, this project was focused towards more fully understanding the role of IRF5 exon 1B’s hairpin structure and its effect on the translation of downstream proteins. The data acquired through this project will provide much needed information regarding the mechanism through which the risk allele of IRF5 affects the development of Systemic Lupus Erythmatosus (SLE).

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Determining The Role Of Kaposi’S Sarcoma-Associated Herpesvirus Lana Protein In The Development Of Persistent Infection, Jamie Gardiner, Dr. Brad Berges Jun 2023

Determining The Role Of Kaposi’S Sarcoma-Associated Herpesvirus Lana Protein In The Development Of Persistent Infection, Jamie Gardiner, Dr. Brad Berges

Journal of Undergraduate Research

Kaposi’s Sarcoma-associated Herpesvirus (KSHV) is a human cancer virus that causes Kaposis’ sarcoma, the most common cancer found in AIDS patients. Our lab is working to develop humanized mice as a novel animal model to study KSHV infection and related diseases, since there has previously been no animal model established. The purpose of my project was to determine the role of the viral protein LANA (latencyassociated nuclear antigen) in establishing a latent KSHV infection in humanized mice. My project included two major aims:

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Understanding The Molecular Targets Of Antimicrobial Chemokines, Brittany Kartchner, Dr. Eric Wilson Jun 2023

Understanding The Molecular Targets Of Antimicrobial Chemokines, Brittany Kartchner, Dr. Eric Wilson

Journal of Undergraduate Research

For this project, I hypothesized that the amino acid composition of the C terminus of chemokine proteins allows some chemokines to bind to different sites on the bacterial cell wall and that the chemokines with a strong positive charge (CCL25 and CCL28) will bind to the same target, while CCL27, which has no positively charged C terminus region, will have a different binding site. In order to study the binding properties of each chemokine, I began by performing binding assays. In these assays, approximately 105 colony-forming units of exponentially growing bacteria were incubated on ice with the appropriate chemokine. This …

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Identifying Proteins That Interact With Human Pas Kinase, Tacie Hall, Dr. Julianne Grose Jun 2023

Identifying Proteins That Interact With Human Pas Kinase, Tacie Hall, Dr. Julianne Grose

Journal of Undergraduate Research

When PAS kinase is knocked out in mice placed on high-fat diets, these mice show such symptoms as decreased weight gain, hypermetabolic phenotype, decreased liver triglyceride accumulation, and retained insulin sensitivity when compared with their wild type littermates.1 These symptoms are highly associated with chronic diseases commonly seen in humans today, such as diabetes, obesity, and heart disease. PAS kinase is a highly conserved protein from yeast to man which allows for the use of yeast as model organism to help discover the molecular mechanisms behind PAS kinase function. Since little is known about how PAS kinase functions, it …

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Accumulation Of Attached Chemokines On Gram-Negative Bacterial Membranes, Peter Janzen, Dr. Eric Wilson Jun 2023

Accumulation Of Attached Chemokines On Gram-Negative Bacterial Membranes, Peter Janzen, Dr. Eric Wilson

Journal of Undergraduate Research

The purpose of this project was to see if a genetic alteration to gram-negative bacteria would affect the phenotypic ability to resist the attachment of chemokines. In other words, we were trying to see if we could change the structure of a bacterium by altering the DNA. As a result of that alteration, would our immune systems fight the infection more easily with a chemokines response.

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Casting For A Putative Dna Binding Sequence For Nbmp2, Brian Earley, Dr. Laura Bridgewater Jun 2023

Casting For A Putative Dna Binding Sequence For Nbmp2, Brian Earley, Dr. Laura Bridgewater

Journal of Undergraduate Research

Bmp2 is a secretory mammalian protein that plays important roles in bone development and adult pathology. Recently, a nuclear variant (nBmp2) was discovered with an unknown function for this typically secretory protein in the nucleus (Felin et al., 2010). The purpose of this project is to find an in vitro DNA binding sequence for nBmp2. This discovery would lead to further research for how nBmp2 could affect transcription in vivo. However, since the conception of this CASTing project 16 months ago, I have faced challenges in plasmid construction, cell culture, and concessions with a fused nBmp2:GFP plasmid. While the plasmid …

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Ex Vivo Infection And Re‐Isolation Of Human Herpesvirus 6, Stephanie Carlson, Dr. Bradford Berges Jun 2023

Ex Vivo Infection And Re‐Isolation Of Human Herpesvirus 6, Stephanie Carlson, Dr. Bradford Berges

Journal of Undergraduate Research

Science rarely cooperates as anticipated, but that can often lead to unexpected insight and solution. I ran into that this semester with a certain aspect of our project. We are continuing to collect data for the American Society for Virology in late July and a future publication. We will need more replicates for a publication, but we have optimized our approach and protocol.

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Genomic And Proteomic Analysis Of An Erwinia Amylovora Phage, Alicia Brighton, Dr. Julianne Grose Jun 2023

Genomic And Proteomic Analysis Of An Erwinia Amylovora Phage, Alicia Brighton, Dr. Julianne Grose

Journal of Undergraduate Research

Fireblight is a disease, caused by the bacteria Erwinia amylovora, that can infect some fruit trees, including apple and pear trees. When an infection occurs, the effects can be devastating—any infected part of the tree must be removed and destroyed, sometimes resulting in loss of the entire tree. Furthermore, in the warm and moist conditions typical of springtime, the spread of fireblight can be nearly impossible to control with current management methods.1

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Use Of Highway Infrastructure By Bats: A Literature Review And Survey Of The Trans-Pecos Region Of Texas, Holly G. Wilson, Stirling J. Robertson, Richard D. Stevens Jun 2023

Use Of Highway Infrastructure By Bats: A Literature Review And Survey Of The Trans-Pecos Region Of Texas, Holly G. Wilson, Stirling J. Robertson, Richard D. Stevens

Western North American Naturalist

Bats are important components of nature and provide both monetary and nonmonetary benefits to mankind. While anthropogenic effects on wildlife and their habitats are typically viewed as negative, highway infrastructure might benefit numerous species of plants and animals, bats in particular. Cracks, crevices, and grooves within structures provide places for bats to roost. Here we review the literature on this topic as well as describe results of our own survey of bridges and culverts in the Trans-Pecos of Texas. We surveyed 204 bridges and 768 culverts between 2018 and 2019. We observed 7 species of bats using bridges or culverts …

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Improving Restoration Success Of Winterfat: Influences Of Hydrophobic Seed Coatings And Planting Depth On Seedling Emergence, Kyle Andrew Cook Jun 2023

Improving Restoration Success Of Winterfat: Influences Of Hydrophobic Seed Coatings And Planting Depth On Seedling Emergence, Kyle Andrew Cook

Theses and Dissertations

In western North America, winterfat (Krascheninnikovia lanata (Pursh) A. Meeuse & Smit) is a valuable protein-rich subshrub whose restoration has been limited by poor seed flowability and low rates of seedling establishment. Seed flowability can be limited by a dense covering of hairs on winterfat fruits that can cause them to clog in mechanized equipment. Seedling establishment can be limited by premature germination of fall-sown seeds that can cause over-winter seedling mortality from freezing, pathogen attack, and winter drought. Seed coatings may provide a way to overcome both of these barriers to winterfat restoration. Coatings can compress hairs against the …

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Adapting The Auxin Inducible Degron (Aid) System To Danio Rerio, Benjamin Stubblefield Jun 2023

Adapting The Auxin Inducible Degron (Aid) System To Danio Rerio, Benjamin Stubblefield

Undergraduate Honors Theses

The Auxin-Inducible Degron (AID) system is a protein degradation system naturally occurring in plants. In the presence of the hormone auxin, plant proteins conjugated with the AID degron (a short amino acid sequence which signals for the protein’s degradation) are recruited via an interaction with the protein TIR1, into an E3 ubiquitin ligase protein complex. Following this interaction, AID-tagged proteins are ubiquitinated and sent for degradation. When auxin is metabolized or transported out of the cell through efflux transporters, the transcript of the protein of interest is translated without being degraded, allowing the concentration of the targeted protein to return …

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Semantic Memory And Decision-Making: An Fmri Study Regarding Covid-19 Vaccine Misinformation, Morgan Chase Jun 2023

Semantic Memory And Decision-Making: An Fmri Study Regarding Covid-19 Vaccine Misinformation, Morgan Chase

Undergraduate Honors Theses

With the continued use and prevalence of social media, misinformation is likewise becoming more prevalent. Information about the COVID-19 pandemic was an example of the way misinformation spreads and presents challenges to society through polarization and discord. As people made decisions regarding whether to receive the COVID-19 vaccine, misinformation may have impacted their decision making. The goal of this study was to understand how misinformation and corrections to misinformation differentially activate the brain, in contrast to how correct information activates the brain, and how misinformation impacts decision making.

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Copus Profiles Paper Data, Jamie Jensen, Rebecca L. Sansom, Jennifer B. Nielson, Richard E. West, Geoffrey Wright, Bryn St. Clair May 2023

Copus Profiles Paper Data, Jamie Jensen, Rebecca L. Sansom, Jennifer B. Nielson, Richard E. West, Geoffrey Wright, Bryn St. Clair

ScholarsArchive Data

COPUS profile data, interview transcripts

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Dendroctonus Ponderosae (Coleoptera: Curculionidae) Observations From Wheeler Peak Campground, Great Basin National Park, Justin P. Williams, Danielle Malesky May 2023

Dendroctonus Ponderosae (Coleoptera: Curculionidae) Observations From Wheeler Peak Campground, Great Basin National Park, Justin P. Williams, Danielle Malesky

Western North American Naturalist

Mountain pine beetle (Dendroctonus ponderosae Hopkins, 1902; MPB) has been causing limber pine (Pinus flexilis E. James) mortality at Great Basin National Park, Nevada, including at Wheeler Peak Campground, for many years. Research has shown that MPB voltinism and phenology are strongly influenced by climate and can vary by location and elevation, indicating the need for localized observations to inform treatment recommendations in some cases. We used emergence cages on infested tree boles, baited Lindgren funnel traps, and ambient air temperatures to describe MPB adult flight timing over 2 years. Adult MPB flight at this high-elevation site occurred …

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Channel Island Foxes (Urocyon Littoralis) Are Viable Seed Dispersal Agents Of Toyon, Savannah L. Bartel, Juliann T. Schamel, Bridget A. Parrino, Melissa K. Marshall, John L. Orrock May 2023

Channel Island Foxes (Urocyon Littoralis) Are Viable Seed Dispersal Agents Of Toyon, Savannah L. Bartel, Juliann T. Schamel, Bridget A. Parrino, Melissa K. Marshall, John L. Orrock

Western North American Naturalist

Mammals that consume fleshy fruit and deposit viable seeds in their scat can be important agents of seed dispersal for plants. Despite the knowledge that the island fox (Urocyon littoralis) consumes large quantities of fleshy fruits, it is unknown whether seeds survive digestion by island foxes and are able to germinate. In order to evaluate whether island foxes are agents of viable seed dispersal on the Channel Islands, we collected island fox scat on Santa Cruz Island in February 2021 and conducted germination assays on digested seeds found in scat. We compared the germinability and germination rates of …

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Distribution Of Astragalus Amnis-Amissi (Fabaceae), A Plant Endemic To East-Central Idaho, Michael Daines May 2023

Distribution Of Astragalus Amnis-Amissi (Fabaceae), A Plant Endemic To East-Central Idaho, Michael Daines

Western North American Naturalist

Astragalus amnis-amissi (Fabaceae), or Lost River milkvetch, is a plant endemic to east-central Idaho for which no published surveys have been completed in the last 18 years. A search for several previously documented populations in canyons of the southern Lemhi Range and the Lost River Range, in Butte and Custer Counties, Idaho, documented the species in 4 canyons. However, it was not relocated in an unnamed canyon in the southern Lemhi Range, indicating potential extirpation of 1 of 2 previously known populations documented on land managed by the USDI Bureau of Land Management. No new populations of A. amnis-amissi were …

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Assessing The Role Of Hybridization In The Evolution Of Two Common Lineages Of Lichen-Forming Fungi, Rachel Keuler Apr 2023

Assessing The Role Of Hybridization In The Evolution Of Two Common Lineages Of Lichen-Forming Fungi, Rachel Keuler

Theses and Dissertations

Once thought to be an evolutionary dead-end, hybridization is now being detected in genomes across kingdoms, perhaps even playing an integral role in evolution. In chapter 1, I investigated the potential influences of hybridization on the evolution of a group of vagrant, asexual species in the Rhizoplaca melanophthalma species group. I sequenced the mitochondrial and nuclear genomes of 55 specimens and found well-supported nuclear phylogenies of both datasets. There were, however, multiple instances of discordance between the mitochondrial and nuclear trees, which can be caused by hybridization. PhyloNet and ABBA-BABA also detected widespread hybridization among this group. In chapter 2, …

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Superabsorbent Polymer Use In Rangeland Restoration, Shannon V. Nelson Apr 2023

Superabsorbent Polymer Use In Rangeland Restoration, Shannon V. Nelson

Theses and Dissertations

Soil moisture deficits often hinder rangeland revegetation efforts. Due to sheer numbers and germination timing, invasive annual species can easily outcompete those of desired seeded species for resources, including water. One way to increase seedling establishment may be to increase the amount of water available to seeded species. Superabsorbent polymers (SAPs) can absorb and release hundreds of times their weight in water and slowly release it. Concentrated SAP bands at or near seedling rooting depth may act as a soil water reservoir for germinating seedlings and increase rangeland seedling establishment. The objective of these studies was to evaluate the effect …

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Shannon V Nelson 2023 Dissertation Supplementary Data, Shannon Nelson, Neil C. Hansen, Matthew D. Madsen, Val Jo Anderson, Dennis L. Eggett, Bryan G. Hopkins Apr 2023

Shannon V Nelson 2023 Dissertation Supplementary Data, Shannon Nelson, Neil C. Hansen, Matthew D. Madsen, Val Jo Anderson, Dennis L. Eggett, Bryan G. Hopkins

ScholarsArchive Data

This data set includes soil matric potential and temperature data for a field trial at the Utah Test and Training Range (UTTR) evaluating the use of banded superabsorbent polymer (SAP) to increase soil moisture and seedling establishment in rangeland restoration.

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