Life Sciences Commons^™

Virology: Mutagenizing The Proteolytic Cleavage Site In The Major Capsid Protein In Ssv1, Thejanee Liyanaarachchi

University Honors Theses

SSV1, spindle-shaped virus 1, is an archaeal virus with a unique shape that belongs to the family of fuselloviruses and infects hyperthermophilic archaea that thrive at 80°C and pH 3. SSV1 has two capsid proteins, VP1 and VP3, that presumably produce the lemon-shaped virion structure characteristic of fuselloviruses. The VP1 amino acid sequence is highly conserved among SSVs. Here, we investigate the importance of the proteolytic cleavage site in position E66 in VP1 by changing its glutamic acid to the other 19 amino acids. We have developed a new protocol for creating SSV1 mutants through HiFi Assembly (NEB) to increase …

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

Biology Faculty Publications and Presentations

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

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

Biology Faculty Publications and Presentations

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

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

Biology Faculty Publications and Presentations

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

A Bioinformatic And Biochemical Analysis Of Cruciviruses, George William Kasun

Dissertations and Theses

Cruciviruses are novel ssDNA viruses discovered through metagenomics and direct environmental DNA amplification and cloning. The genomes of cruciviruses suggest that gene transfer between RNA and DNA viruses occurred due to the presence of putative protein-encoding genes that are homologous to both ssRNA and ssDNA viruses. In order to gain a better understanding of this group of viruses both bioinformatic analyses and in vitro biochemical experiments were employed. The results of the bioinformatic analyses show that cruciviruses are a highly diverse group of ssDNA viruses. Their placement within established ssDNA phylogenies is difficult due to heterogeneity in their putative replication-associated …

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

Biology Faculty Publications and Presentations

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

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

Biology Faculty Publications and Presentations

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

Plastic-Eating Microbes: A New Potential Solution To Waste Mitigation?, Megan Forbes

University Honors Theses

Plastic waste is problematic for marine and terrestrial ecosystems due to the mass production of polyethylene terephthalate (PET) single use plastics. What is unclear is a well-thought-out solution to solve pollution problems that will not further damage the environment. Throughout this literature review, I will investigate the role microbes play in plastic degradation, and if plastic eating microbes are an effective solution to the plastic pollution problem. Polyethylene terephthalate (PET) is the chemical name for polyester. It is a clear, strong, and lightweight plastic that is typically used for food and beverage packaging, and other single-use purposes. The most well …

Selenium Probes For The Detection Of Thioredoxin Reductase Activity, Tendai Joseph Mafireyi

Dissertations and Theses

The identification and quantification of proteins and enzymatic activity in living tissues frequently requires the use of invasive procedures such as biopsy. These techniques can inhibit measurements of protein levels in real-time, and the disruption of tissue can lead to the loss of important information concerning the spatial distribution and differential activities in various cell types. The use of small organic fluorescent probes that rely on activation or accumulation within a tissue embody robust methods of detection that address these issues. This dissertation describes the design, synthesis and evaluation of fluorescent probes that can detect the enzyme thioredoxin reductase (TrxR). …

Mitonuclear Mismatch Is Associated With Increased Male Frequency, Outcrossing, And Male Sperm Size In Experimentally-Evolved C. Elegans, Brent William Bever

Dissertations and Theses

We provide the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. In partial support of a tenet of the mitonuclear sex hypothesis, which predicts that outcrossing will be favored in cases of mitonuclear mismatch, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested--nuclear isp-1, mitochondrial …

Mechanisms Of Substrate Recognition By The Cul3-Based E3 Ligase, Katia Graziella De Oliveira Rebola

Dissertations and Theses

Cul3-based E3 ligase is responsible for regulating a variety of cellular pathways, many of which are known to have profound effects on the proper function of multicellular organisms. Although progress over the past years has been truly impressive, our understanding of the mechanisms of E2 recruitment and selection by the BCR complex and all the roles that Cul3 plays on kidneys remains in its infancy. To explore these aspects, this dissertation aims to analyze the Cul3 complex using two different approaches: (1) We used the powerful tool of chimeric analysis to map the essential domain binding characteristics of Cul3 taking …

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

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 …

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 …

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

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

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 …

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, …

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

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 …

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 …

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 …

Exploring Mirna Function And Host Response To Coxiella Burnetii Infection, Madhur Sachan

Dissertations and Theses

Alveolar macrophages attempt to control bacterial infection through a spectrum of defense processes, including induction of apoptosis, autophagy, inflammatory response, and nutrient sequestration. MicroRNAs (miRNAs), a class of small non-coding RNAs, are involved in a spectrum of physiological processes, including immune response to intracellular infections. However, whether microRNAs have any functions in host response to Coxiella burnetii infection is unknown. Coxiella burnetii is a highly infectious intracellular pathogen that causes Q fever, a zoonosis with a worldwide occurrence. In this work, I investigated the functions of miRNAs in host response to C. burnetii infection and found that miRNAs are an …

Understanding The Metabolic Regulation Of Trained Immunity By Palmitic Acid, Khaleda Aqaei, Brooke A. Napier

McNair Symposium

Sepsis is an inflammatory disease that occurs when the body’s response to an infection becomes dysregulated, and infection-fighting processes of the body damage tissues via inflammation, resulting in organ failure and death. Currently, the role for diet in regulating sepsis susceptibility and severity is not fully understood. The Western Diet (WD), the most prevalent diet worldwide, is high in saturated fatty acids (SFAs) and sucrose, and low in fiber. Previously, we have used a lipopolysaccharide (LPS)-induced sepsis mouse model to show that mice fed a Western Diet (WD) or a diet enriched only in SFAs (Ketogenic Diet; KD), experience increased …

Hybrid-Lipid Coated Silver Nanoparticles As An Antimicrobial, Alexandria Murphy, Marilyn R. Mackiewicz, Michael S. Bartlett

McNair Symposium

Silver has been known to be an antimicrobial for hundreds of years, but wasn’t thought to be useful in the medical field until the 1960’s. In more recent years people have been designing different methods of synthesis for silver nanoparticles, yet none of these methods prevent the oxidized silver (Ag+), which is toxic. As the use of silver nano materials for antimicrobial activity has expanded there has been an increase in interest in the medical field, and how silver nanoparticles can be used as an antimicrobial without having toxic effects. While there is a large availability of silver nanoparticles (AgNp’s) …

The Effect Of Apremilast On Circadian Rhythm In The Ventral Tegmental Area, Courtney Ledford, Angela Ozburn

McNair Symposium

Chronic binge drinking negatively impacts society and is a leading cause of preventable deaths. The purpose of the experiment is to determine if regulation of circadian rhythms in the ventral tegmental area (VTA) will contribute to less ethanol consumption. The VTA plays a major role in addiction. A simple genetic animal model examines iHDID-1 mice and their binge-like drinking intake. The mice undergo Drinking in the Dark (DID) for 6 weeks prior to administration of apremilast or saline treatment at weeks 7 and 8. The mice are exposed to DID and sacrificed at two separate time points (ZT 3 and …

Efficacy Of Curcumin In Asthma: A Systematic Review And Meta Analysis, Tabitha Grow, Adam Sadowski

McNair Symposium

Over 23 million people are affected by asthma in the United States and 262 million individuals globally. Asthma, if poorly controlled, is associated with significant morbidity as well as increased risk for mortality. Asthma involves several complex inflammatory pathways and processes including an increase in immune cell activation. Curcumin, the active constituent found in turmeric, has been studied in numerous in-vivo and in-vitro studies to generate anti-inflammatory effects in pulmonary diseases and, more recently, an increase in clinical data has become available. Since the most recent review assessing the role of curcumin in pulmonary disorders, additional clinical trials have been …

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 …

Experiences Of Undergraduates And Graduate Teaching Assistants In Biology Course-Based Undergraduate Research Experiences, Emma Crystal Goodwin

Dissertations and Theses

Evidence of positive student outcomes from course-based undergraduate research experiences (CUREs) has sparked implementation of CUREs in introductory biology laboratory courses, as one approach to boosting student engagement in research. In a CURE, students collaborate with other students and instructors on a research project, where they conduct novel scientific research that has relevance to a local or scientific community. However, previous research rarely considers that graduate teaching assistants (GTAs) often teach introductory labs. The classroom role of GTAs expands in a CURE--they no longer need to simply teach a lab class, but also to serve as research mentors. GTAs, who …

Nesting Habits Of Cavity Nesting Bees And Wasps In Portland, Oregon, Stefanie Kay Steele

Dissertations and Theses

Native bees are threatened by habitat loss through urbanization, however, there is increasing interest in creating bee nesting habitat in urban areas. Few studies have determined what species are present in the region, or examined the role of nest height or cavity size in attracting the approximate one-third of native bees that nest in cavities. To determine what species were present, and whether they showed preferences for nesting at a certain height or cavity width, we set up artificial wooden cavity nest blocks across fourteen locations in the greater Portland, OR area. Wooden posts were erected with nest blocks at …