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Evolutionary Analyses Of Sequence And Structure Space Unravel The Structural Facets Of Sod1, Sourav Chowdury, Dwipanjan Sanyal, Sagnik Sen, Vladimir N. Uversky, Ujjwal Maulik, Krishnananda Chattopadhyay

Molecular Medicine Faculty Publications

Superoxide dismutase (SOD) is the primary enzyme of the cellular antioxidant defense cascade. Misfolding, concomitant oligomerization, and higher order aggregation of human cytosolic SOD are linked to amyotrophic lateral sclerosis (ALS). Although, with two metal ion cofactors SOD1 is extremely robust, the de-metallated apo form is intrinsically disordered. Since the rise of oxygen-based metabolism and antioxidant defense systems are evolutionary coupled, SOD is an interesting protein with a deep evolutionary history. We deployed statistical analysis of sequence space to decode evolutionarily co-varying residues in this protein. These were validated by applying graph theoretical modelling to understand the impact of the …

Hiv Vaccine Mystery And Viral Shell Disorder, Gerard Kian-Meng Goh, A. Keith Dunker, James A. Foster, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Hundreds of billions of dollars have been spent for over three decades in the search for an effective human immunodeficiency virus (HIV) vaccine with no success. There are also at least two other sexually transmitted viruses, for which no vaccine is available, the herpes simplex virus (HSV) and the hepatitis C virus (HCV). Traditional textbook explanatory paradigm of rapid mutation of retroviruses cannot adequately address the unavailability of vaccine for many sexually transmissible viruses, since HSV and HCV are DNA and non-retroviral RNA viruses, respectively, whereas effective vaccine for the horsefly-transmitted retroviral cousin of HIV, equine infectious anemia virus (EIAV), …

Curriculum Change 2019-2020, Portland State University

Bulletin & Curriculum Change Documents

No abstract provided.

Application Of Rb/Sr Ratio In Paleo-Climate Inversion, Shupei Ouyang, Muhammad Aqeel Ashraf, Yung-Tse Hung

Civil and Environmental Engineering Faculty Publications

In order to study the intensity of chemical weathering during the formation of sedimentary strata in the site profile, the evolution of climatic environment in the region where the site profile is located was revealed. The rubidium (Rb) and strontium (Sr) values in the rubidium (Rb) and strontium (Sr) were tested and analysed. The Rb/Sr ratio has become an ideal alternative indicator in the study of regional environmental evolution. The Rb value in the strata section of Zhongba site is low, and the average value (calculated based on 202 sample values) is only 80 g/g. The Sr value was higher, …

Postures In Mobile Device Usage: Effects On Interpretation Bias, Mood, And Physical Tension, Gabriela Flores-Cruz

Honors Undergraduate Theses

Past research has shown that there is a relationship between body posture and cognitive processes. However, postures used with technological devices has not been studied more extensively. The purpose of this study was to examine posture effects when using a mobile device on interpretation bias, mood, and physical tension. Each participant was randomly assigned one of three conditions: sitting slumped, sitting upright, or lying down. Participants were asked to complete the Scrambled Sentences Task (SST), a task of unscrambling emotional and neutral sentences, to measure their interpretation bias. Additional questions were asked to measure the participant's physical tension and mood. …

The Role Of Cues And Kinematics On Social Event Perception, Estefania Berrios

Honors Undergraduate Theses

The belief that intentions are hidden away in the minds of individuals has been circulating for many years. Theories of indirect perception, such as the Theory of Mind, have since been developed to help explain this phenomenon. Conversely, research in the field of human kinematics and event perception have also given rise to theories of direct perception. The purpose of the study was to determine if intentionality can be directly perceived rather than requiring inferential processes. Prior research regarding kinematics of cooperative and competitive movements have pointed toward direct perception, demonstrating participants can accurately judge a movement as cooperative or …

Role Of T-Bet In Production Of Immunoglobulin Isotypes In An Influenza Setting, David Sidhom

Honors Undergraduate Theses

Influenza is one of the most common diseases worldwide, yet the vaccines against influenza are only 35% effective at protecting against infection. Creating a more effective vaccine requires an understanding of the foundation and the factors that contribute to a strong and protective adaptive immune response. T-bet [TBX21] is a transcription factor that plays an instrumental role in the orchestration of the type 1 immune response, which is the specialized response used by the immune system for a cell-mediated response against intracellular pathogens, such as influenza. It has yet to be explored in an influenza setting on the role T-bet …

A Meta-Analysis Of Neuromyelitis Optica Epidemiology In Latin American Nations, Brittany M. Zengotita

Honors Undergraduate Theses

Neuromyelitis Optica (NMO) is a rare, autoimmune, neurodegenerative disease selectively affecting the optic nerves and spinal cord. Relapsing NMO is nine times more prevalent in women than in men and approximately one-quarter of NMO patients have symptoms of another autoimmune disorder (National Institute of Health, 2019). NMO has not been linked to any genetic mutations and the cause of the disorder is unknown beyond the general understanding that the body produces anti-aquaporin-4 antibodies (AQP4) which mistakenly attack cells in the nervous system. NMO affects roughly one percent of that of Multiple Sclerosis (4000-8000 patients total) in the United States, but …

Effects Of Diet Quality And Temperature On Stable Fly (Diptera: Muscidae) Development, Melina Florez-Cuadros, Dennis Berkebile, Gary Brewer

Department of Entomology: Faculty Publications

The effects of diet quality and temperature on the development time and size of stable flies, Stomoxys calcitrans (L.), was evaluated. Both development time and size varied relative to diet quality and temperature, and their effects were additive. Diet quality and temperature made similar contributions to the variance in size whereas temperature was responsible for >97% of the variance in development time. Regression analysis predicted the shortest development time, egg to adult, to be 12.7 days at 32 ^◦C and 70% nutrients. Egg to adult development varied curvilinearly relative to diet quality and temperature on the degree day 10 …

Concerning The Provision For Payment Of The Expenses Of The Executive, Legislative, And Judicial Departments Of The State Of Colorado, And Of Its Agencies And Institutions, For And During The Fiscal Year Beginning July 1, 2019, Except As Otherwise Noted., Colorado General Assembly

Session Laws 2001-Present

No abstract provided.

Assessing The Value Of Grazed Corn Residue For Crop And Cattle Producers, Daren Redfearn, Jay Parsons, Mary Drewnoski, Marty Schmer, Rob Mitchell, James Macdonald, Jaymelynn Farney, Alexander Smart

Department of Agronomy and Horticulture: Faculty Publications

Integrated crop–livestock systems have included grazing perennial grasses during the spring and summer and corn (Zea mays L.) residues during the winter. Our objectives were to identify opportunities for expanded corn residue use through grazing and provide an economic assessment for value-added grazing. We estimated the economic value to the crop sector through grazing leased corn residue at over $95 million for Nebraska, South Dakota, Kansas, and North Dakota under current management. Additionally, gross economic value to the livestock sector in these states was estimated at greater than $191 million. Advantages for increased grazing use of corn residue include …

Climate-Smart Practices For Improvement Of Crop Yields In Mid-Hills Of Nepal, Roshan Subedi, Laxmi Dutt Bhatta, Erica Udas, Nand Kishor Agrawal, Keshab Datta Joshi, Dinesh Panday

Department of Agronomy and Horticulture: Faculty Publications

Farming in Nepal mostly represents the hill farming system with the dominance of small-holder farmers. In recent days, farmers in the country are impacted by climate change. Events of surface runoff, landslides, and soil erosions, along with changes in rainfall pattern and intensity have elevated a decline in crop productivity and soil fertility. Considering the situation, a pilot project on Resilient Mountain Village was implemented in Kavrepalanchowk district of Nepal from 2014–2016 with a participatory approach to demonstrate climate-smart practices. These practices include the application of locally prepared bio-fertilizer (named as “jholmal”), green manuring in rice (Oryza sativa L.) …

Drought Stress Tolerance In Wheat And Barley: Advances In Physiology, Breeding And Genetics Research, Ahmed Sallam, Ahmad M. Alqudah, Mona F. A. Dawood, P. Stephen Baenziger, Andreas Borner

Department of Agronomy and Horticulture: Faculty Publications

Climate change is a major threat to most of the agricultural crops grown in tropical and sub-tropical areas globally. Drought stress is one of the consequences of climate change that has a negative impact on crop growth and yield. In the past, many simulation models were proposed to predict climate change and drought occurrences, and it is extremely important to improve essential crops to meet the challenges of drought stress which limits crop productivity and production. Wheat and barley are among the most common and widely used crops due to their economic and social values. Many parts of the world …

Management Recommendations For Ecological Restoration On The Little River Parcel, Maya Sady Partain, Garitt Mathews

Environmental Science & Management Senior Capstones

Ecological restoration is an important aspect of land management. Data collection and ongoing monitoring help inform restoration decisions and determine their effectiveness. In this project, we followed a monitoring protocol provided by the Trinidad Coastal Land Trust to assess the 2019 status of their Little River parcel, a fifteen-acre area near the mouth of Little River in Trinidad, California. We performed a site analysis of invasive plant species and recorded their extent and location, as well as noting other observations of the ecology, topography, and biology of the site. After making our observations, we recommended land management methods woven together …

Azalea State Reserve Vegetation Management Plan, Ethan Len Reibsome, Rosebelle Abuan Ines

Environmental Science & Management Senior Capstones

This comprehensive vegetation management plan for Azalea State Reserve was produced by Humboldt State University students Ethan Reibsome and Rosebelle Ines in partnership with the California State Parks. As a capstone senior project within the Environmental Science and Management department, these students collaborated to map existing habitat types and invasive species, and created a species list. In addition, this document contains their observations and recommendations which will inform future management actions as well as the conservation of the Reserve.

Plant Hormone Signaling Lab Module, Olivia Snyder

Williams Honors College, Honors Research Projects

Course material for universities constantly needs updating and refinement. One area that required new material at The University of Akron was the Principles of Biology II course, specifically in the laboratory section. A new laboratory module was created and centered around hormone signaling in Arabidopsis thaliana. Brassinosteroid mutants were used to show students the event hormones had on plants. Students were to test root lengths by completing growth plate analysis.

Presenting A Product Design From Computer-Generated Imagery (Cgi), Mirjeta Mustafa

Theses and Dissertations

The purpose of this thesis is to determine a solution to overcome photography problems to present product design by using Computer Generated Imagery. CGI and virtual design now play a key role in the development of many materials, processes and products. Through this study has been explored, the impact of 3D render to exhibit the product design, as well as a brief history of photography and how it is used to present the product, the problems that have emerged during the use of photographs to present the product design have been discussed, and how new technologies have enabled us to …

Disruptive Mathematicians, David Bruce Guild

Theses & ETDs

This thesis addresses two problems. The first is the general lack of knowledge about the background stories of prominent mathematicians. Undergraduate mathematical instruction offers little, if any, information about the personal histories of the people who developed the material being studied. I believe learning these life stories will add depth to students' understanding of mathematical concepts by learning how the ideas developed. To address this, I will study the lives of mathematicians and the role of collaboration among them and will present the material in a tutorial. Evaluation of the effectiveness of the tutorial will be determined, in part, by …

Litter Carbon Pool Variation Between Restored And Disturbed Coastal Habitats In Manatee County Florida, Angela Mctigue

Theses & ETDs

Coastal ecosystems provide key services, such as carbon storage, but compete with development in natural areas. For this reason, increasing their value requires restoring coastal habitats that have been degraded. After the ecosystem has been restored, a goal is that it will start to store more carbon in its soils over time. Specifically, in this thesis I sought to see if litter mass and decomposition change over time in restored habitats, and if litter mass and decomposition change between restored and disturbed habitats. By using the Tea Bag Index, and analyzing the litter fall in respective disturbed and restored habitats …

Hormone Replacement Therapy Attenuates Hearing Loss: Mechanisms Involving Estrogen And The Igf-1 Pathway, Tanika T. Williamson, Bo Ding, Xiaoxia Zhu, Robert D. Frisina

Chemical, Biological and Materials Engineering Faculty Publications

Estradiol (E) is a multitasking hormone that plays a prominent role in the reproductive system, and also contributes to physiological and growth mechanisms throughout the body. Frisina and colleagues have previously demonstrated the beneficial effects of this hormone, with E-treated subjects maintaining low auditory brainstem response (ABR) thresholds relative to control subjects (Proceedings of the National Academy of Sciences of the United States of America, 2006;103:14246; Hearing Research, 2009;252:29). In the present study, we evaluated the functionality of the peripheral and central auditory systems in female CBA/CaJ middle-aged mice during and after long-term hormone replacement therapy (HRT) via …

The “Social Media Discount” And First Amendment Exceptionalism, Frank D. Lomonte

University of Memphis Law Review

No abstract provided.

Extracellular Matrix In Development And Disease, Julia Thom Oxford, Jonathon C. Reeck, Makenna J. Hardy

Biomedical Research Institute Publications and Presentations

The evolution of multicellular metazoan organisms was marked by the inclusion of an extracellular matrix (ECM), a multicomponent, proteinaceous network between cells that contributes to the spatial arrangement of cells and the resulting tissue organization. The development of an ECM that provides support in larger organisms may have represented an advantage in the face of selection pressure for the evolution of the ECM.

Prophylactic Treatment Of Hyperbaric Oxygen Treatment Mitigates Inflammatory Response Via Mitochondria Transfer, Trenton Lippert, Cesar V. Borlongan

Neurosurgery and Brain Repair Faculty Publications

No abstract provided.

Concise Review: Stem Cell Therapy For Stroke Patients: Are We There Yet?, Cesar V. Borlongan

Neurosurgery and Brain Repair Faculty Publications

Four decades of preclinical research demonstrating survival, functional integration, and behavioral effects of transplanted stem cells in experimental stroke models have provided ample scientific basis for initiating limited clinical trials of stem cell therapy in stroke patients. Although safety of the grafted cells has been overwhelmingly documented, efficacy has not been forthcoming. Two recently concluded stroke clinical trials on mesenchymal stem cells (MSCs) highlight the importance of strict adherence to the basic science findings of optimal transplant regimen of cell dose, timing, and route of delivery in enhancing the functional outcomes of cell therapy. Echoing the Stem Cell Therapeutics as …

Microrna-133a And Myocardial Infarction, Yi Xiao, Jiling Zhao, Julian P. Tuazon, Cesar V. Borlongan, Guolong Yu

Neurosurgery and Brain Repair Faculty Publications

Myocardial infarction (MI) is the leading cause of morbidity and mortality in the world. The infarcted heart displays typical cell death cascades characterized by a loss of cells and fibrotic scarring in the myocardium. Cardiac hypertrophy and fibrosis largely contribute to ventricular wall thickening and stiffening, altogether defining an adverse cardiac remodeling that ultimately leads to impaired cardiac function and subsequent heart failure. Finding a strategy to promote therapeutic, instead of detrimental, cardiac remodeling may pose as a potent MI treatment. Accumulating evidence shows that microRNAs (miRNAs) may play an essential role in cardiovascular diseases. In particular, microRNA-133a (miR-133a) is …

A Hallmark Clinical Study Of Cord Blood Therapy In Adults With Ischemic Stroke, Paul R. Sanberg, Jared Ehrhart

Neurosurgery and Brain Repair Faculty Publications

The therapeutic application of human umbilical cord blood cells has been an area of great interest for at least the last 25 years. Currently, cord blood cells are approved for reconstitution of the bone marrow following myeloablation in both young and old patients with myeloid malignancies and other blood cancers. Translational studies investigating alternative uses of cord blood have also shown that these cells not only stimulate neurogenesis in the aged brain but are also potentially therapeutic in the treatment of adult neurodegenerative disorders including amyotrophic lateral sclerosis, Alzheimer’s disease, ischemic stroke, traumatic brain injury, and Parkinson’s disease. Recent advances …

Immunomodulation With Human Umbilical Cord Blood Stem Cells Ameliorates Ischemic Brain Injury – A Brain Transcriptome Profiling Analysis, Maple L. Shiao, Ce Yuan, Andrew T. Crane, Joseph P. Voth, Mario Juliano, Laura L. Hocum Stone, Zhenghong Nan, Ying Zhang, Nicole Kuzmin-Nichols, Paul R. Sanberg, Andrew W. Grande, Walter C. Low

Neurosurgery and Brain Repair Faculty Publications

Our group previously demonstrated that administration of a CD34-negative fraction of human non- hematopoietic umbilical cord blood stem cells (UCBSC) 48 h after ischemic injury could reduce infarct volume by 50% as well as significantly ameliorate neurological deficits. In the present study, we explored possible mechanisms of action using next generation RNA sequencing to analyze the brain transcriptome profiles in rats with ischemic brain injury following UCBSC therapy. Two days after ischemic injury, rats were treated with UCBSC. Five days after administration, total brain mRNA was then extracted for RNAseq analysis using Illumina Hiseq 2000. We found 275 genes that …

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

Biology Faculty Publications and Presentations

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

Evaluation Of Genotype Quality Parameters For Sowpro90, A New Genotyping Array For Swine, Hiruni R. Wijesena, Gary A. Rohrer, Dan J. Nonneman, Brittney N. Keel, Jessica L. Petersen, Stephen D. Kachman, Daniel C. Ciobanu

Department of Animal Science: Faculty Publications

Understanding early predictors of sow fertility has the potential to improve genomic predictions. A custom SNP array (SowPro90 produced by Affymetrix) was developed to include genetic variants overlapping quantitative trait loci for age at puberty, one of the earliest indicators of sow fertility, as well as variants related to innate and adaptive immunity. The polymorphisms included in the custom genotyping array were identified using multiple genomic approaches including deep genomic and transcriptomic sequencing and genome-wide associations. Animals from research and commercial populations (n = 2,586) were genotyped for 103,476 SNPs included in SowPro90. To assess the quality …

Coding Sequences Of Sarcoplasmic Reticulum Calcium Atpase Regulatory Peptides And Expression Of Calcium Regulatory Genes In Recurrent Exertional Rhabdomyolysis, Stephanie J. Valberg, Kaitlin Soave, Zoe J. Williams, Sudeep Perumbakkam, Melissa Schott, Carrie J. Finno, Jessica L. Petersen, Clara Fenger, Joseph M. Autry, David D. Thomas

Department of Animal Science: Faculty Publications

Background: Sarcolipin (SLN), myoregulin (MRLN), and dwarf open reading frame (DWORF) are transmembrane regulators of the sarcoplasmic reticulum calcium transporting ATPase (SERCA) that we hypothesized played a role in recurrent exertional rhabdomyolysis (RER).

Objectives: Compare coding sequences of SLN, MRLN, DWORF across species and between RER and control horses. Compare expression of muscle Ca²⁺ regulatory genes between RER and control horses.

Animals: Twenty Thoroughbreds (TB), 5 Standardbreds (STD), 6 Quarter Horses (QH) with RER and 39 breed-matched controls.

Methods: Sanger sequencing of SERCA regulatory genes with comparison of amino acid (AA) …