Life Sciences Commons^™

High-Density Genetic Map Construction And Qtl Mapping Of A Zigzag-Shaped Stem Trait In Tea Plant (Camellia Sinensis), Si Chen, Chenyu Zhang, Piao Mei, Jiedan Chen, Liang Chen, Chunlei Ma

Faculty, Staff and Student Publications

The highly unique zigzag-shaped stem phenotype in tea plants boasts significant ornamental value and is exceptionally rare. To investigate the genetic mechanism behind this trait, we developed BC1 artificial hybrid populations. Our genetic analysis revealed the zigzag-shaped trait as a qualitative trait. Utilizing whole-genome resequencing, we constructed a high-density genetic map from the BC1 population, incorporating 5,250 SNP markers across 15 linkage groups, covering 3,328.51 cM with an average marker interval distance of 0.68 cM. A quantitative trait locus (QTL) for the zigzag-shaped trait was identified on chromosome 4, within a 61.2 to 97.2 Mb range, accounting for a phenotypic …

Mitochondria Regulate Proliferation In Adult Cardiac Myocytes, Kathryn A Helmin, Benjamin D Singer, Clara Bien Peek, Joseph Bass, Lauren Nelson, Sanjiv J Shah, Gaston Ofman, J Andrew Wasserstrom, William A Muller, Alexander V Misharin, G R Scott Budinger, Hiam Abdala-Valencia, Navdeep S Chandel, Danijela Dokic, Elizabeth Bartom, Shuang Zhang, Yuki Tatekoshi, Amir Mahmoodzadeh, Hossein Ardehali, Edward B Thorp, Paul T Schumacker

Faculty, Staff and Student Publications

Newborn mammalian cardiomyocytes quickly transition from a fetal to an adult phenotype that utilizes mitochondrial oxidative phosphorylation but loses mitotic capacity. We tested whether forced reversal of adult cardiomyocytes back to a fetal glycolytic phenotype would restore proliferative capacity. We deleted Uqcrfs1 (mitochondrial Rieske iron-sulfur protein, RISP) in hearts of adult mice. As RISP protein decreased, heart mitochondrial function declined, and glucose utilization increased. Simultaneously, the hearts underwent hyperplastic remodeling during which cardiomyocyte number doubled without cellular hypertrophy. Cellular energy supply was preserved, AMPK activation was absent, and mTOR activation was evident. In ischemic hearts with RISP deletion, new cardiomyocytes …

Soil Organic Matter Components And Characteristics Of Forest Soil In Spruce And Sycamore Plantations In The Temperate Region, Samuel Obeng Apori, Michelle Giltrap, Julie Dunne, Furong Tian Nanolab Research Centre, Focas Research Institute

Articles

The stability of soil organic matter (SOM) that governs soil organic carbon (SOC) storage depends on its characteristics and components, but little is known about how tree species in forest ecosystems affect SOM components and characteristics. In this study, we used FTIR spectroscopy to investigate plantations of two ecologically and economically significant tree species—namely, spruce (Picea spp.) and sycamore (Acer pseudoplatanus)—in order to determine how the different litter inputs and root-microbe interactions of these two plantations affect the functional groups, components, and characteristics of their SOM. Soil samples were taken from the topsoil (0–10 cm) and subsoil (10–20 cm). In …

Vascular Electrophysiology And Pathogenic Consequences Of Cardiovascular Katp Channel Mutations, Alex Hanson

Arts & Sciences Graduate Student Theses and Dissertations

The complex cardiovascular disorder Cantú Syndrome (CS) arises from gain-of-function (GoF) mutations in either KCNJ8 or ABCC9, the genes encoding the Kir6.1 and SUR2 subunits of cardiovascular ATP-sensitive potassium (KATP) channels, respectively. CS involves an array of cardiovascular pathologies, including cardiac hypertrophy and hypercontractility, low systemic vascular resistance, and excessively compliant, dilated, and tortuous vessels. Together, the latter features exemplify the hypomyotonic and hyperelastic components of CS vasculopathy. It was recently established that CS vasculopathy drives the associated cardiac pathologies, which are observed even in the absence of cardiac KATP GoF. In this thesis, I carried out experiments to determine …

Inducible Crispr-Targeted ‘Knockdown’ Of Human Gut Bacteroides In Mice Reveals Glycan Utilization Strategies, Zachary Beller

Arts & Sciences Graduate Student Theses and Dissertations

Learning how members of the human gut microbiota compete and cooperate for dietary nutrients, such as fiber-associated glycans, should help facilitate development of more precise nutritional recommendations for improving health. To model how bacteria prioritize the utilization of different fiber glycans in the mammalian gut, germ-free mice were colonized with a 13-member consortium of cultured, genome-sequenced human bacterial strains, including seven Bacteroides species. Animals were fed a Western diet supplemented with pea fiber. Once the consortium had time to assemble, an inducible CRISPR-based system was used to deplete the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to …

Metabarcoding The Mycobiome: An Analysis Of The Gut Mycobiome Of Babies, Daniel B. Colon, Jeremy Seto

Publications and Research

The human gut mycobiome (the fungus that lives in our gut) has been correlated with overall health and disease in humans. There are several factors that affect the human gut mycobiome including delivery method during birth (vaginal vs. c-section) and the presence or absence of antibiotics at birth. The mycobiome of 140 infants aged newborn to 18 months were tested using fecal samples from 3 different time periods (meconium, 6 months, 18 months). A total of 434 fecal samples were collected. A midwife or nurse collected the meconium samples while the child’s parents collected the samples at the 6-month and …

Casi: A Framework For Cross-Timepoint Analysis Of Single-Cell Rna Sequencing Data, Yizhuo Wang, Christopher R Flowers, Michael Wang, Xuelin Huang, Ziyi Li

Faculty, Staff and Student Publications

Single-cell RNA sequencing (scRNA-seq) technology has been widely used to study the differences in gene expression at the single cell level, providing insights into the research of cell development, differentiation, and functional heterogeneity. Various pipelines and workflows of scRNA-seq analysis have been developed but few considered multi-timepoint data specifically. In this study, we develop CASi, a comprehensive framework for analyzing multiple timepoints' scRNA-seq data, which provides users with: (1) cross-timepoint cell annotation, (2) detection of potentially novel cell types emerged over time, (3) visualization of cell population evolution, and (4) identification of temporal differentially expressed genes (tDEGs). Through comprehensive simulation …

Imaging Features Of Primary Intracranial Sarcoma With Dicer1 Mutation: A Multicenter Case Series, Rami W Eldaya, Richard J Fagan, Samir A Dagher, Angshumoy Roy, Sonika Dahyia, Max Wintermark, Thierry A G M Huisman

Faculty, Staff and Student Publications

Primary intracranial sarcoma, DICER1-mutant, is a rare, recently described entity in the fifth edition of the WHO Classification of CNS Tumors. Given the entity's rarity and recent description, imaging data on primary intracranial sarcoma, DICER1-mutant, remains scarce. In this multicenter case series, we present detailed multimodality imaging features of primary intracranial sarcoma, DICER1-mutant, with emphasis on the appearance of the entity on MR imaging. In total, 8 patients were included. In all 8 patients, the lesion demonstrated blood products on T1WI. In 7 patients, susceptibility-weighted imaging was obtained and demonstrated blood products. Primary intracranial sarcoma, DICER1-mutant, …

Early Developmental Exposure To Δ9-Tetrahydrocannabinol Causes Latent Behavioral, Growth, And Bioenergetic Effects In Danio Rerio, Astra Hahm

Honors Theses

Early developmental exposure to Δ9-tetrahydrocannabinol causes latent behavioral, growth, and bioenergetic effects in Danio rerio

(Under the direction of Dr. Kristine Willett)

Δ9-tetrahydrocannabinol (Δ9-THC) is used during pregnancy to mitigate symptoms such as nausea, pain, and insomnia. It is established that Δ9-THC exposure early in life causes adverse effects in children’s development including behavioral disorders. Our goal was to determine the latent and generational impacts on growth, behavior, and mitochondrial bioenergetics following exposure to Δ9-THC. Wildtype (5D) zebrafish were exposed to 0 (0.05% DMSO), 0.08, 0.4, or 1 µM Δ9-THC from 6-96 hours post-fertilization (hpf), then subsequently raised in clean …

Validation Of A Triple Quadrupole Lcms Instrument For Cocaine And Amphetamines, Isabel R. Nichols

Honors Theses

Despite the opioid crisis taking headlines, the abuse of cocaine and amphetamines remains rampant and laboratory instruments must be able to effectively and reliably handle the overwhelming case load. In this study, an Agilent 6475 Triple Quadrupole (QQQ) LCMS, recently acquired by the Tarrant County Medical Examiner’s Office (TCMEO) in Fort Worth, Texas, was validated for identifying and quantifying CocAmps. Results show that the instrument was fit-for-purpose and that the instrument passed all validation tests. Reproducibility was ≤ 20% RSD for 12 QC replicates, 6 of blood and 6 of urine. Accuracy was ± 20%. A 98.9% recovery was yielded …

Bioinformatic Comparison And Salinity Tolerance Of Various Cyanobacterial Strains, Lucie Rowe

Honors Theses

Cyanobacteria are an abundant and diverse group of photosynthetic prokaryotes with a long evolutionary history, which presents challenges for comprehensive taxonomic classification. Phylogenies were traditionally constructed based on the highly conserved 16S rRNA gene, but research has increasingly relied upon whole genome sequencing to elucidate evolutionary relationships, despite increased cost and time. In this thesis, publicly available genome sequences of various cyanobacterial strains were utilized to determine if the whole rRNA region, which includes the 16S, 23S, and 5S genes as well as the spacer regions between, could provide accurate, yet cost/time efficient representations of their evolutionary relationships. From phylogenetic …

Examining The Role Of Rgs2 In The Maintenance Of Diapause After Anoxic Stress In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Patrick Clouser

Student Research Symposium

Austrofundulus limnaeus live in ephemeral ponds of Venezuela. They have evolved a unique life history that includes embryonic diapause, a period of developmental dormancy, metabolic arrest, and reduced protein synthesis. Diapausing embryos are resistant to environmental stress and survive months without oxygen (anoxia). A. limnaeus’ anoxia tolerance is an important survival mechanism as they can be buried in anoxic soil during development. Analysis of RNAseq data from diapausing A. limnaeus embryos show significant down-regulation of RGS2 transcripts in anoxic embryos. RGS2 regulates G-protein receptor signaling by inhibiting associated G_a-proteins and can inhibit protein synthesis. I hypothesis that …

Evaluation Of Sleep Outcomes After Traumatic Brain Injury In Children Using Questionnaires And Actigraphy, Connie Tran, Sydney Weese, Cydni Williams Md

Student Research Symposium

Traumatic brain injuries are the result of a sudden external blunt force to the brain and can result in long-term complications or death. In pediatrics, it is the leading cause of acute and chronic sleep wake disturbances, as well as cognitive deficits, which can lead to a reduction in the quality of life. These impairments can later result in lowered performance in work and school settings or decreased psychosocial function. Although there is sufficient evidence that traumatic brain injuries contribute to is that it is unknown whether or not sleep wake disturbances contribute to an increase in the mentioned cognitive …

Dragon Pseudoscorpions Shed Light On Ancient Climate History In The Pacific Northwest, Joshua W. Hootman

Student Research Symposium

Pseudoscorpions are an ancient and diverse group of understudied arachnids, and there is much to be learned about their relationships to each other. Pseudoscorpions are one of many leaf-litter dwelling and low dispersing invertebrates that inhabit the forests of the Pacific Northwest. Previous phylogeographic studies of Pacific Northwest taxa have shed light on some of the climatic and geologic events that have shaped the area's flora and fauna. One purpose of this study is to determine if there is similar genetic structuring within the pseudoscorpion populations present in the study area, or if there is even more structure likely influenced …

Mutagenetic Analysis Of The Minor Capsid Protein Vp3 Of The Archaeal Fusellovirus Ssv1, Laura Costal Lagarde

Student Research Symposium

Viruses, while often associated with disease, are integral to life and play an important role in the microbiome. Despite their importance in medical research, archaeal viruses, particularly those found in extreme environments, are not widely understood. The Sulfolobus Spindle-Shaped Viruses (SSVs) of the Fuselloviridae family are unique among viruses in that they do not kill their host, the archaeon Sulfolobus Solfataricus in volcanic hot springs, but rather slow its growth, allowing for halo assay assessments.The study focuses on the type virus SSV1, which is predominantly composed of the Major and Minor capsid proteins vp1 and vp3, respectively. Previous study has …

Describing Shen & Shen Ming Via A Hybrid Quantum Computational Model, Alex M. Cullen, Johnny Lemau

Student Research Symposium

Definitions for Traditional Chinese Medicine (TCM) terminology within the context of quantum biology (QB) have recently been proposed. These definitions aim to elucidate concepts such as qi meridians in TCM. Our study presents a hypothesis that seeks to provide an operational definition for Spirit (Shen) and Bright Spirit (Shen Ming) in TCM via a scoping review. We propose that Shen represents physical, phenomenological proto-consciousness/consciousness in the forms of computation, such as singular particles/bits/qubits, computers, organisms, or computational strategies, whereas Shen Ming may refer to emergent, quasi-physical meta-proto-consciousness/consciousness formed by coherent relationships of multiple orchestrated/integrated units of computation; manifesting itself as …

Relationship Between Trunk Cross-Sectional Area Growth And Water Stress In Garry Oaks (Q. Garryana): A Species Of Conservation Concern, John Cochrane

Student Research Symposium

In the Pacific Northwest, Quercus garryana (Garry oak trees) support over 627 native species. Garry oak natural habitat was originally maintained by indigenous practices but has been reduced to 5-10% of its range due to change in land management strategies. To support oak conservation, we need to understand heat and water affect the growth and physiology of this species. In this study, we created a fixed linear model of trunk cross-sectional growth with water stress (Ψ), photosynthetic water-use efficiency (δ¹³C), and leaf Carbon-Nitrogen ratio. We collected branch samples from the canopies of 47-64 mature Garry oaks in the …

Improved Genome Maintenance And Dna Replication In The Anoxia Tolerant Annual Killifish, Riley A. Roth-Carter

Student Research Symposium

Timely and faithful replication of the genome is a requirement for cell survival and proliferation, with errors in this process leading to cancers and cell death. DNA replication during exposure to stressful conditions can lead to increased mutational burden, with collapsed replication forks causing mutations leading to cancers due to loss of repair capabilities during these exposures. Learning how stressful DNA replication takes places can lead to a better understanding of how resistant cancers survive similar conditions, like hypoxic tumor microenvironment, direct irradiation, and DNA damaging chemotherapeutics. Using an extremophile model, Austrofundulus limnaeus, which can survive these genotoxic stressors could …

Exploring Factors That Contribute To Stem Transfer Student Sense Of Belonging, Brittney R. Gallant, Cate Pocitari

Student Research Symposium

There is an ongoing disconnect between the number of students who enter college intending to earn a STEM degree and the number of students who persist to degree, this is particularly true for transfer students. Sense of belonging has been named as a STEM persistence factor, yet how that belonging develops for transfer students is largely unknown. Here we used a mixed-methods design to explore the experiences of STEM transfer students at PSU (n=38). Participants completed a survey prior to participating in an interview. The survey and interviews explored their science identity, sense of belonging, and involvement in STEM-related activities. …

Histone Changes As A Response To Lactic Acid Selection In Cells Of Austrofundulus Limnaeus, Lori Tran, Jason Podrabsky, Chelsea Hughes

Student Research Symposium

The killifish Austrofundulus limnaeus is an extremophile native to small temporary ponds of Venezuela. Normal embryonic development of A. limnaeus is segmented into up to three stages of metabolic depression (diapause), and both developing and diapausing embryos can survive long bouts of the complete absence of oxygen (anoxia) by using anaerobic metabolic pathways. While there has been much focus on how mutations in DNA drive evolution, environmental stress can cause heritable changes to histone post-translational modifications (hPTMs) in multiple species. However, this evolutionary role of hPTMs has never been studied in A. limnaeus. Additionally, the possible evolutionary role of extracellular …

Observing Orobanche Uniflora Parasitism Of Four Sedum Species In Relation To Soil Composition, Devin J. Forest-Hines, Sophie Wille, Noah Flick, Maxxie Barr

Student Research Symposium

Sedums are commonly selected for green roof applications due to their horizontal growth, heat and drought tolerance, water-storage capacity, and heat absorption. A potential threat to sedum health is the presence of parasitic Orobanche. Orobanche are a genus of parasitic plants that extract nutrients, water and carbohydrates from its host via root attachments. This study seeks to investigate Orobanche parasitism on the four most abundant sedum species on a Portland State University green roof in relation to soil composition. Four sedum species were propagated in clear plastic compact-disc (CD) cases containing either mineral substrate, Miracle Gro, or a seedling mix, …

Qibc Analysis On Killifish Cells Under Anoxic Conditions, Jaina Canlas

Student Research Symposium

Faithful DNA replication is vital for all living organisms. Environmental stressors can cause a multitude of mutations and DNA lesions during replication leading to cell death if not accurately repaired. The annual killifish, Austrofundulus limnaeus, has a heightened tolerance to many known genotoxic stressors, including anoxia. Embryos of the annual killifish can survive months of anoxia during the dry season when the ephemeral ponds they inhabit, completely dry. During these exposures, they have shown they are capable of repairing substantial amounts of damaged DNA. This resilience has led us to hypothesize that A. limnaeus have enhanced DNA repair capabilities. …

Annual Killifish: Eye Development And Retinal Cell Regeneration, Carmen Z. Rodriguez

Student Research Symposium

Vertebrate eye development is highly conserved. Current models have allowed the understanding of gene expression patterns that support eye development, but lack the context of extreme environmental conditions that challenge these fundamental programs. Typical vertebrate life spans can be years, but annual killifish, Austrofundulus limnaeus, are able to complete their entire adult lifespan in only weeks. Thus, A. limnaeus is a strong model for age-related macular degeneration. A. limnaeus also experiences embryonic diapause; a period of developmental dormancy. Developing/diapausing embryos of A. limnaeus are resistant to environmental stresses such as hypoxia/anoxia that would cause irreparable damage to vital organs, such …

Guide Rna Design And Delivery For Crispr/Cas9 Editing In Annual Killifish, Keria N. Moritsugu-Vandehey, Isabel Henkes, Yekaterina Chmykh, Amie Romney, Jason Podrabsky

Student Research Symposium

The CRISPR-Cas9 genome editing tool has shown to be successful in knocking out genes in model organisms such as zebrafish, turquoise killifish, and cichlid fish. CRISPR-Cas9 genome editing has been demonstrated in many species of fish, but this technology has not been verified in the annual killifish, Austrofundulus limnaeus. We hypothesize that targeted editing of the tyrosinase gene in embryos of A. limnaeus would lead to the development of fish without the ability to produce melanin, the black/brown pigment molecule. Early embryos (1-cell stage) were injected with a Cas9 cocktail containing a mix of guide RNA molecules that target …

Neuroscience Educational Interventions For Mental Health Management Within The Neurodiverse Population: A Working Model, Kadi Rae Smith, C.K. Miller, Bill Griesar, Jeff Leake

Student Research Symposium

Sociological and environmental factors such as economic disparity and cultural marginalization hinder access to educational and medical resources and must be taken into account to ensure accurate diagnoses, effective self-regulation and mental health management for neurodiverse individuals, and offset disparities in access to healthcare and education. Arbitrary attachment of stigma to traits commonly associated with neurodivergence perpetuate neuro-myths1 that have dire consequences when internalized, informing individuals’ development and sense of self. Neuroscience outreach done by NW Noggin is an active model for engaging communities with limited resources and a greater need for services to offset economic disparity. Integrated arts programming …

Selection During Reproduction In Mimulus Guttatus, Desmond C. Willson, Karla De Lima Berg, Mitch Cruzan

Student Research Symposium

A lack of genomic studies examining gametophytic selection and selective embryo abortion—which occur during the reproduction of angiosperms—leaves questions regarding the adaptive and evolutionary effects of these processes. Analyzing deviations from Mendelian segregation offers an avenue for identifying loci targeted by GS and SEA, and their contributions to purging of genetic load. However, other selective processes such as meiotic drive and cytonuclear interactions, as well as pollen and ovule abortion, can cause distortion. To distinguish the effects of GS and SEA from other causes of distortion, we will perform reciprocal crosses between highly homozygous and highly heterozygous individuals of Mimulus …

Locating Vitamin D Receptors (Vdrs) In Annual Killifish, Austrofundulus Limnaeus, Rosalia N. Tanori, Amie L. Romney, Jason E. Podrabsky

Student Research Symposium

Austrofundulus limnaeus, a species of annual killifish found in unpredictable temporary habitats in South America, has a profound ability to survive long periods without water and oxygen. This tolerance is associated with the ability to enter metabolic dormancy associated with diapause. Entrance into diapause and tolerance of environmental stress is governed by an interplay of genetic and environmental factors. The vitamin D receptor (VDR) is among these factors and plays a crucial role in determining if an embryo will enter diapause or actively develop. My work aims to identify the genomic locations of VDR proteins in the A. limnaeus genome …

Construction And Mutagenesis Of Ssv1 Mutants In Extreme Viruses, Lou Ann F. O'Connor, Jono Abshier, Kenneth M. Stedman

Student Research Symposium

Archaeal viruses with unique structures such as spindle-shaped virions are found abundantly in extreme environments like geothermal hot springs around the world. Among all spindle-shaped viruses, the model Sulfolobus Spindle-shaped Virus 1 (SSV1) is best studied. Creating the lemon-shaped or spindle-shaped virion structure are two proteins, VP1 as the major capsid protein, and VP3 as the minor capsid protein. The primary structure of VP1 consists of a proteolytic cleavage site at position 66 that is believed to be necessary for virus evolution. Recent studies showed that genetic mutation of the amino acid, glutamate (E) at position 66 in VP1 which …

The Influence Of A Ubiquitous Filter Feeder On Coastal Microbial Communities., Melissa Steinman, Moritz S. Schmid, Robert K. Cowen, Su Sponaugle, Kelly R. Sutherland, Anne W. Thompson

Student Research Symposium

Doliolids have a unique ability to impact the marine microbial community through bloom events and high filtration rates. Their predation on large eukaryotic microorganisms is established and evidence of predation on smaller prokaryotic microorganisms is beginning to emerge. We studied the retention of both eukaryotic and prokaryotic microbial taxa by wild-caught doliolids in the northern California Current system. We use qPCR to quantify the impact of doliolids on three important and globally abundant taxa: Synechococcus, SAR11 and diatoms. Doliolids were collected during bloom events identified at three different shelf locations with variable upwelling intensities. We discovered that in addition …

Variability Of Grazing By Appendicularians On Prochlorococcus, Carey Sweeney

Student Research Symposium

The marine picocyanobacterium, Prochlorococcus is the most abundant photosynthetic cell on Earth. These cells are critical to global primary productivity and are critical to biogeochemical cycles of the open ocean. While abiotic environmental factors that influence Prochlorococcus are relatively well-understood, biotic controls, especially predation, are not well-studied. Appendicularians are ubiquitous invertebrate grazers that feed on microbes including Prochlorococcus in the open ocean. However, the details of this feeding interaction have not been characterized. In a laboratory study, I showed that prey retention of Prochlorococcus increases as the life stage of the appendicularians advances and increases with increasing concentration of prey. …