Over the past decade, it has come to light that many published scientific findings cannot be reproduced. This has led to the replication crisis in science. Many researchers feel that they can no longer trust much of what they read in scientific journals, and the public is becoming ever more...
Exploring and quantifying the parameters regarding contact guidance may provide valuable insight to the precise mechanisms controlling cell movement, especially in a three-dimensional environment. The objective of this project was to quantify the relationship between MDA-MB-231 cell morphogenesis and the geometry of the cell’s local microenvironment, which was modeled by...
Uveitis is a serious ophthalmological disorder characterized by intraocular infiltration of inflammatory cells. In most cases, uveitis is derived from the adaptive immune response. More specifically, CD4+ T lymphocytes play an important role in the pathogenesis of uveitis by recognizing uveitogenic antigen and orchestrating the immune response. While it is...
Osmotic stress is a common challenge faced by organisms in environments with variable salinity or aridity. Understanding the evolutionary mechanisms underlying adaptation to osmotic stress may have wide applications, including management of populations experiencing climate change, or engineering industrial organisms involved in processes such as fermentation. While Saccharomyces cerevisiae is...
Global warming and on-going depletion of fossil fuels have stimulated research to develop renewable sources of energy. Current renewable energy use comprises only 10% of the energy consumed in the US and is focused mostly on generating electricity. The majority of the energy consumed by the US transportation sector is...
The aging process is a biological phenomenon in mammals that heavily contributes to the onset of chronic diseases. While there are many theories that attempt to explain the biological onset of aging, one emerging theory involves chronic inflammation. Chronic inflammation has been previously linked to several age-related diseases and is...
Water samples along the Washington, Oregon and California coastline were collected using high resolution sampling and analyzed to determine particulate organic carbon and nitrogen concentrations. Over 28 days during August 2011, nearly 1500 samples were collected aboard the R/V Wecoma (W1108C) using a semi-automated filtration system. Additional subsurface samples were...
There are clues that suggest human breast cancer cells use collagen fibers to migrate, and vinculin is a transmembrane protein associated with how cells attach to their environment. Therefore, immunostaining for the vinculin will shed some light in how human breast cancer cells are attaching to their environment. Immunostaining for...
Antisense morpholino oligomers are synthetic macromolecules can modify gene expression. While these compounds have great potential to treat a broad range of human diseases, they suffer from poor cellular delivery. Conjugating cell-penetrating peptides onto these morpholinos is one option of addressing delivery, however development remains slow due to the cost...
This study sought to explore the differences between the varied academic advising models in the College of Science at Oregon State University through the feedback of its undergraduate students and advisors. Using parallel surveys of students and their academic advisors, it found that the decentralized and centralized models each had...
Glioblastoma is a malignant brain tumor that has extremely poor prognoses with a 5 year survival rate of less than 5%. The low survival rates of glioblastoma patients is attributed to glioblastoma cells being extremely resistant to radiotherapy and chemotherapy as well as being very invasive. We previously identified calpain...
Fer1L6 is an uncharacterized member of the ferlin family of proteins, a group of large, calcium sensitive proteins with emerging roles in vesicle trafficking and various disease states. The presence of Fer1L6 has been identified within the C2C12 cell line of mouse skeletal muscle. To determine the protein’s subcellular location...
A specific tyrosine post-translational modification, called 3-nitro-tyrosine (nitroTyr), has been known to be present on an essential calcium signaling protein called calmodulin (CaM) during oxidative stress. While protein-bound 3-nitro-tyrosine has long been considered a biomarker of OS, it is also hypothesized to be a mechanism for protein signaling. However, purification...
Base-pairing interaction are the fundamental blocks of an RNA structure. With increased ability to determine the structure of RNA molecules, an accurate and informative way of classifying these interactions would help to study RNA structure at many levels. Apart from the well-known complementary base pairs and wobble pairs, other interactions...
The role of the high density lipoprotein (HDL) molecule is currently an area of great interest within the scientific community. Previously, mouse and human studies have demonstrated an inverse association between HDL cholesterol (HDL-C) levels and cardiovascular disease. Recent clinical trials, which increased HDL-C, have failed to reduce the number...
Many people die yearly worldwide due to diseases associated with aging, and if the
process of aging in humans was more understood, the health of these patients could be
improved. While many biochemical actions are involved with the aging process, loss of
proteostasis has been called one of the most...
Cells are constantly bombarded with mutagens, both endogenous and exogenous in origin. Endogenous sources of mutation include reactive oxygen species formed during aerobic respiration, replication errors by DNA polymerase, and spontaneous deamination and depurination (Jackson 2009). Exogenous sources of mutation include UV and ionizing radiation, aflatoxins, and polycyclic aromatic hydrocarbons...
A unique, permanent root-growth arrest phenotype was observed in UV-B irradiated Arabidopsis thaliana roots lacking the DNA damage response kinase ATR. Segregation analysis suggests the dependence of this phenotype on another, unidentified gene, termed ursu. High-throughput sequencing technologies were used to map and identify the causal ursu mutation. Illumina HiSeq...
Heavy chronic alcohol consumption has been linked to a myriad of
detrimental skeletal effects. Many studies have been conducted to examine
the effects of alcohol abuse upon cancellous bone. However, little is known
about its effect upon cortical bone. The skeleton is comprised of
approximately 80% cortical bone and thus...
It is no doubt that the face of Ernesto "Che" Guevara is recognized
globally as it appears on currency, merchandise, at protest marches, and in art.
However, there is little agreement on what this handsome face represents or what
the Argentine revolutionary fought for. Some view Guevara as a humanitarian...
Amyotrophic Lateral Sclerosis (ALS) is a relatively rare neurodegenerative disorder that is fatal 2-4 years after the onset of the disease. Population studies are being done in order to help reveal candidates for further studies of disease etiology, disease progression, as well as to further understand racial and ethnic variations....
DNA segments in the fungus Fusarium graminearum were identified as possible genes encoding for chromodomain proteins (CDPs), and targeted for genetic manipulation. Targeted single-gene deletion strains, as wells as GFP-S tag fusion strains, were generated from wildtype F. graminearum protoplasts, and verified strains were screened for phenotypic differences, such as...
The preconditioning agent poly-ICLC has recently been shown to protect against cerebral injury in the mouse model, when administered systemically prior to ischemic insult. However, the mechanism by which poly-ICLC provides neuroprotection is currently unknown, but it has been shown to protect against ischemia-induced bloodbrain barrier (BBB) disruption. Inflammation contributes...
A study was conducted to evaluate the developmental toxicity of three commonly detected mycotoxins in food (deoxynivalenol, patulin, and zearalenone) using the zebrafish (Danio rerio) model. Mycotoxin exposures were carried out at five concentrations (0.0064, 0.064, 0.64, 6.4, and 64 μM). Morphological and photomotor screenings were conducted at 24 hours...
Polycyclic aromatic hydrocarbons (PAHs), including benzo[a]pyrene (B[a]P), are environmental pollutants linked to increased disease susceptibilities. Alpha-Tocopherol (αT) supplementation decreases B[a]P-DNA adducts in smokers, particularly women; but the mechanism is unknown. To test the hypothesis that αT protection from B[a]P exposure is gender-dependent, male and female rats received 7 daily subcutaneous...
Auxotrophic strains of the fungus Fusarium graminearum were generated in order to increase
the number of functional selectable markers and improve the utility of the model organism.
Single metabolic genes, the sequences encoding for enzymes required for the production of
specific essential metabolites, were deleted in F. graminearum, and then...
A compound series capable of reversing the antiviral effect of Ribavirin (RBV) against H1N1 was
identified from a high throughput screen designed to discover compounds capable of increasing the
fidelity of the RNA-dependent RNA polymerase (RDRP) n ribovirus quasispecies. Two lead compounds,
RIC-1 (EC50 of 78.4 nM) and RIC-2 (EC50...
Oxygenated polycyclic aromatic hydrocarbons (OPAHs) are a class of environmentally prevalent compounds with little known information on their effect in vivo. In a recent study conducted using zebrafish as a model, 38 OPAHs were screened for toxicity. This investigation focuses on two of these OPAHs, 7,12-B[a]AQ and BEZO. Both 7,12-B[a]AQ...
The process of expressing a gene involves not just binding of proteins and enzymes to DNA to produce first RNA and eventually proteins, but rather association of these transcription factors with chromatin and structural proteins called histones. When histone H3 is trimethylated at lysine 27 to produce H3K27me3, gene silencing...
M. avium is an opportunistic pathogen that primarily infects macrophages. In order to survive within the macrophage, M. avium secretes proteins into the host cell cytoplasm to inhibit specific functions such as phagosome acidification, altering pathways as well as initiating apoptosis. However, little is known about how those secreted proteins...
Glioblastoma multiforme is a devastating primary brain tumor with a median five year survival rate of less than 5%. It is a cancer that is resistant to current cancer treatments, such as surgery and chemotherapy, as well as one that is prone to recurrence after surgical removal. This highlights the...
Autophagy, a homeostatic degradation pathway, has a role in promoting cell survival under stress conditions, but can also promote cell death under conditions of sustained stress. This project investigates the cytotoxic potential of coibamide A and other natural products in autophagy-deficient and wild-type mouse embryonic fibroblasts (MEFs). Wild-type MEFs were...
Koi herpesvirus (KHV), is a highly pathogenic virus causing high mortality in common carp and koi, especially in fry. One of the unique features of herpesvirus infections is their ability to become latent following initial infection. During latent infection, only viral genome persists in the host and remains dormant in...
Several compounds have been recently identified which are effective against dengue virus, a tropical arbovirus highly prevalent in southeast Asia and central America. Initial intrinsic fluorescence characterization of the mechanism of action of compound B reveals binding affinity to the dengue capsid protein. A molecular beacon unwinding assay and malachite...
The purpose of this honors thesis research project is to investigate the molecular causes of childhood and infant T-cell acute lymphoblastic leukemias. T-cells are the work horses of the immune system, and like any organ, must develop properly to be fully functional. Improper development of thymocytes into T-cells can lead...
Pseudomonas aeruginosa is a gram-negative nosocomial pathogenic bacterium known for its resilience against antibiotics. The bacterium infects over 50,000 patients each year in the United States, with 13% of reported cases involving multi-drug-resistant strains of Pseudomonas. This research discovered several fungal natural products with promising activity against Pseudomonas aeruginosa. The...
Atopic Dermatitis (AD) is a widespread skin disorder, affecting some 20% of the world’s population. Though the precise molecular underpinnings are still being understood, changes in lipid composition within the epidermal stratum corneum (SC) layer have been shown to be closely linked with AD. Previous studies have identified several specific...
Gluten intolerance is a condition that affects a significant portion of the world’s
population. While awareness about the condition has recently increased, the condition
remains poorly understood and therefore commonly mis- and underdiagnosed. In this
paper, I examine the challenges in obtaining a gluten intolerant diagnosis and attempt to
capture...
Polycomb Repressive Complex 2 (PRC2) is a histone methyltransferase that initiates facultative heterochromatin formation by trimethylating histone H3 on lysine 27 (H3K27me3). Mutations within its three primary subunits, KMT6, EED, and SUZ12, result in inherited diseases and sporadic cancers. In the fungus Fusarium graminearum, deletion of the gene encoding the...
In recent years, non-coding DNA has received much attention within the scientific
community. This attention has not only illuminated the mystery behind functionally
important regions like the centromere, but has also brought to light additional important
questions regarding centromere mechanisms, inheritance, and cellular recognition by the
kinetochore, a protein complex...
The steroid hormone estrogen plays a crucial role in regulating certain mammalian tissues, especially female reproductive systems. Estrogen effects physiological changes in the cell by altering transcription activity for certain target genes, as a consequence of interactions between estradiol-17β (E2) and its nuclear receptor (nER). This mechanism of cellular control...
Academic performance of student athletes is an of interest topic in the current climate of rising university athletics expenses. This project academic population of Oregon State University student athletes with that of the general undergraduate population using grade point averages (GPA). Samples were compared using team, gender, college, and sport...
The planar peptide model has guided our understanding and interpretation of protein crystal structures since its origin in the 1950s. It is well understood that deviations from this model occur, but the majority of peptides are planar, as measured by the standard omega torsion angle. Here, we report the first...
In this investigation, six different endogenous thyroid hormone derivatives—T₄, T₃, TA₄, TA₃, T₁-Amine, and N-Acetylated T₁-Amine—were tested to gain insight into their permeability coefficients and efflux ratios across a monolayer of Madin-Darby Canine Kidney (MDCK II) cells. The results indicate that T₃ and T₄ were unable to traverse the membrane...
The purpose of this study was to examine pregnant Puerto Rican women’s perspectives on the Zika virus threat. Using data collected from open-ended, semi-structured interviews and observational field notes, we aimed to understand the degree to which Zika contributes to maternal stress. How concerned are pregnant women in Puerto Rico...
As organisms age they lose the ability to respond to both exogenous and endogenous stresses, therefore placing them at a greater risk for the development of many diseases. The transcription factor Nrf2 is responsible for the induction of many oxidative stress response genes and therefore 3proteins. Additionally, Nrf2-mediated stress response...
The purpose of this meta-synthesis was to investigate why students from the U.S. receive the scores they do on the international TIMSS and PISA science exams. This work sought to shed light on the perceived disparity between science performance of U.S. students and students from other countries. To do so,...
An ideal labeling reaction between protein and surface should generate a protein-patterned surface with control over the orientation of the desired protein. Controlling orientation would generate a homogeneous, un-fouled protein surface and allow for maximum efficiency in regards to the activity, reactivity, and stability of the protein. In this research...
The gut microbiome influences human disease including Type 2 diabetes, obesity and metabolic syndrome and interacts with the innate immune system. The human cathelicidin antimicrobial peptide (hCAMP), an important component of the innate immune system, and vitamin D and xanthohumol, a natural compound found in beer hops, regulate its expression....