Digital Commons Network^™

Nuclear Receptor Coactivator 3 In Endoplasmic Reticulum Stress And Stress Granule Dynamics In Pancreatic Cancer, Andrew Kisling

Theses & Dissertations

Pancreatic cancer is predicted to be the second-leading cause of cancer-related deaths within the next decade. Nuclear receptor coactivator 3 (NCOA3/SRC3/AIB1) regulates an array of metabolic and signaling pathways and has been established by our group and others as a critical regulator pancreatic cancer progression and metastasis. A recent study demonstrated NCOA3 regulation by the IRE1α-XBP1 axis of the unfolded protein response (UPR), suggesting a link between NCOA3 and cellular stress management. Furthermore, NCOA3 has been shown to directly bind to a scaffolding protein of stress granules (SGs). Since SG assembly is regulated by the UPR, we hypothesized that NCOA3 …

The Contribution Of Bioethics To Home Healthcare (Hhc) In Saudi Arabia, Saeed Alghamdi

Electronic Theses and Dissertations

This dissertation examines the contribution of bioethics to Home Healthcare (HHC) In Saudi Arabia (SA). Through exploring the critical bioethical issues that have influenced the implementation of home health care, the dissertation highlights the significance of incorporating bioethics in home health care. Organizational ethics has led to the regulation of healthcare professionals, patients, and the stakeholders within clinical care settings. Healthcare organizations and other stakeholders, such as global health bodies, should formulate laws and policies that promote bioethics in contemporary healthcare. The Kingdom of Saudi Arabia, through the Ministry of Health, should promote the adoption of home health care services …

Does Speech-To-Text Assistive Technology Paired With Graphic Organizers Improve The Written Expression Of Students With Traumatic Brain Injuries?, Kayla Cuifolo

Electronic Theses and Dissertations

A traumatic brain injury (TBI) can range from mild to severe and can cause debilitating outcomes that require children to need specialized medical or educational services post-injury. Outcomes vary and are dependent on the location of injury, age, severity, and environmental factors. Some common deficits that happen as a result of a brain injury are fine motor and executive functioning skill difficulties. Fine motor and executive functioning skills are an important component of written expression. Therefore, this current study utilized a brief experimental analysis in order to determine the effects that speech-to-text assistive technology along with a graphic organizer has …

Identifying And Knocking Out Non-Visual Opsins In The Optic Tectum Of Zebrafish Larvae, Sarah Jarrett

Undergraduate Honors Theses

Deep brain photoreceptors (DBPs) are non-visual photoreceptors found in the brains of non-mammalian vertebrates like zebrafish. While using optogenetic techniques in our lab to photo-activate the ear (by expressing the light-gated channel: channelrhodopsin) in efforts of identifying optic tectum (OT) neurons that respond to and integrate auditory and visual stimuli, we found that violet light was able to elicit OT neuronal activity. OT activity was also detected in cases when visual and auditory stimulation was not possible due to removal of the eyes and absence of the exogenously expressed channelrhodopsin, respectively. Analyzing OT single-cell sequencing data of 7day post fertilization …

Using Eugenecid And Eugenecim Computational Tools For Synthetic Biology, Wheaton L. Schroeder, Anna S. Baber, Rajib Saha

Department of Chemical and Biomolecular Engineering: Faculty Publications

Synthetic biology often relies on the design of genetic circuits, utilizing ‘‘bio parts’’ (modular DNA pieces) to accomplish desired responses to external stimuli. While such designs are usually intuited, detailed here is a computational approach to synthetic biology design and modeling using optimization-based tools named Eukaryotic Genetic Circuit Design and Modeling. These allow for designing and subsequent screening of genetic circuits to increase the chances of in vivo success and contribute to the development of an application development pipeline. For complete details on the use and execution of this protocol, please refer to Schroeder, Baber, and Saha (2021).

Characterization Of Phase Behavior In Idp Solutions By Uv-Vis Spectrophotometry And Phase Volume Fraction Measurements In Capillaries, Qing Sun

Biomedical Engineering ETDs

Intrinsically disordered proteins (IDPs) play vital roles in cell signaling and regulation by changing conformation dynamically under various stimulus. Thus, it is crucial to understand their physical properties in vitro especially liquid-liquid phase separation (LLPS). Here, we first used UV-vis spectrophotometry to investigate two of IDPs' physical properties – transition temperature (Tt) and coacervate size. This deeper insight allows us to further understand the dynamics of phase growth. We then constructed a binodal curve in the phase diagram by measurement of volume ratios in phase separated IDP solution in glass capillaries.

Nitrogenase Iron Protein Classification Using Cnn Neural Network, Amer Rez

Master's Projects

The nitrogenase iron protein (NifH) is extensively used to study nitrogen fixation, the ecologically vital process of reducing atmospheric nitrogen to a bioavailable form. The discovery rate of novel NifH sequences is high, and there is an ongoing need for software tools to mine NifH records from the GenBank repository. Since record annotations are unreliable, because they contain errors, classifiers based on sequence alone are required. The ARBitrator classifier is highly successful but must be initialized by extensive manual effort. A Deep Learning approach could substantially reduce manual intervention. However, attempts to build a character-based Deep Learning NifH classifier were …

Spaceflight And Differential Gene Expression Analysis Of Mice Quadriceps Exposed To Microgravity, Tommy Nguyen

Master's Projects

he trip to Mars and back is planned for the next 20 years. Improvement in technology and research has allowed data analysis, at a larger scale, on spaceflight specimen. However, research involving spaceflight is decentralized, as research is spread across laboratories with different methodologies. NASA’S GeneLab is a public repository for spaceflight-related omics data and promotes centralizing spaceflight RNA-Seq studies using NASA’s RNA-Seq pipeline. Jonathan Oribello, a SJSU’s Bioinformatics graduate and now an employee at GeneLab, has implemented Nextflow to NASA’s RNA-Seq pipeline. The Nextflow RNA-Seq pipeline was ran on San Jose State University’s College of Science High Performance Computing …

An Examination Of Bone Loss During Space Travel With Differential Gene Expression Analysis, Claudia Vo

Master's Projects

Spaceflight poses many risks to human health due to the harsh conditions of microgravity, cosmic radiation, and confinement. One of the impacts that spaceflight entails is bone loss, which is a risk to astronauts as future space missions will require long travel durations. To elucidate the role of genetics in spaceflight bone loss, in this study differential gene expression analysis was performed using Nextflow-RCP, an adaptation of NASA Genelab’s RNA-Seq Consensus pipeline. The dataset for this project was GLDS-241, which contained samples from mice femoral skin. To gain a comprehensive understanding of the genes involved in bone loss, the results …

Mrna-Sequencing Pipeline For Differential Gene Expression Analysis, Crystal Han

Master's Projects

Endothelial cells (ECs) line the insides of blood vessels and play a key role in the coagulation and vascular repair system. Under normal circumstances, ECs are constantly expressing anticoagulants to prevent clots and maintain healthy blood flow. But when there is an injury to the vessel, endothelial cells become centrally involved in orchestrating the complex series of events that would lead to the clotting of the wound. Thus, ECs are dynamic and respond accordingly based on changes in their local environment. Unfortunately, endothelial cells can sometimes misinterpret cues from the environment and initiate coagulation when there is no vessel damage …

Mindfulness And Meditation To Reduce Test And Evaluation Anxiety In Doctoral Nurse Anesthesia Students, Jenna L. Tebbenkamp

Doctor of Nursing Practice Projects

Abstract

Mindfulness and Meditation to Reduce Test and Evaluation Anxiety in Doctoral Nurse Anesthesia Students

Background/Information

A significant number of university students report experiencing test anxiety. Extreme anxiety has been reported as a cause of withdrawal from university studies. Certified Registered Nurse Anesthetists are required to complete an intense curriculum with tests and evaluations prior to passing a national board certifying exam, which is anxiety provoking.

Purpose

The primary objective of this project was to provide mindfulness intervention information to be utilized by the DNP students and assess desires of having a mindfulness meditation practice to alleviate academic anxiety.

Methods …

Implementation Of A Risk Assessment Tool To Increase Screening For Extragenital Gonorrhea And Chlamydia In Men Who Have Sex With Men, Andrew P. Tharp

Doctor of Nursing Practice Projects

INTRODUCTION: Gonorrhea and chlamydia account for the majority of sexually transmitted infections (STIs) in the United States and are often thought to infect only the urogenital tract. Infections can also be harbored at extragenital sites (rectum and oropharynx), and these infections can increase susceptibility to HIV. Extragenital screening recommendations exist for populations deemed high risk, including men who have sex with men (MSM); yet, routine screening is not consistently completed.

PURPOSE: To improve screening rates for extragenital gonorrhea and chlamydia in MSM within a primary care setting by using an STI risk assessment tool.

METHODS: Clinicians completed a baseline knowledge …

Viloxazine In The Treatment Of Attention Deficit Hyperactivity Disorder, Amber N. Edinoff, Haseeb A. Akuly, John H. Wagner, Megan A. Boudreaux, Leah A. Kaplan, Shadman Yusuf, Elisa E. Neuchat, Elyse M. Cornett, Andrea G. Boyer, Adam M. Kaye, Alan David Kaye

School of Pharmacy Faculty Articles

Attention deficit hyperactivity disorder (ADHD) is the most common neurodevelopmental disorder in children. Over the past twenty years, research on the disease and its characteristics and treatment options has grown exponentially. The first-line pharmacologic treatment of ADHD is stimulants, which have a response rate of ~70%. With the support of four phase 3 studies involving more than 1,000 pediatric patients 6–17 years old, the FDA has approved the non-stimulant, serotonin-norepinephrine modulating agent (SNMA) viloxazine in an extended-release capsule (viloxazine ER) for treatment of ADHD in children aged 6–17. Viloxazine modulates serotonergic activity as a selective 5-HT22B receptor antagonist and 5-HT2C …

Poor Acclimation To Experimental Field Drought In Subalpine Forest Tree Seedlings, Alex Goke, Patrick H. Martin

Biological Sciences: Faculty Scholarship

The ability of tree species to acclimate and tolerate projected increases in drought frequency and intensity has fundamental implications for future forest dynamics with climate change. Inquiries to date on the drought tolerance capacities of tree species, however, have focused almost exclusively on mature trees with scant in situ work on seedlings, despite the central role that regeneration dynamics play in forest responses to changing conditions. We subjected naturally established seedlings of co-dominant subalpine conifer species (Abies lasiocarpa and Picea engelmannii) in the southern Rocky Mountains to 2 years of in situ summer precipitation exclusion, simulating summer drought …

Effective Cancer Detection Using Higher-Order Genome Architecture And Chromatin Interactions, My Chung

Master's Projects

Cancer is a complex disease which requires interactions between cell-intrinsic alterations and tumor microenvironment. The connection between epigenetics and genomic structure plays a key role in chromatin interaction which promotes enhancer-promoter interactions for transcriptional activities. Alterations of chromatin states in oncogenic signaling pathway potentially cause cancer cell-intrinsic changes and inappropriate instructions to normal cell cycles, leading to abnormal cell growth. Resulting phenotypic changes are correlated to underlying changes in higher-order chromatin structure such as topologically associating domains (TADs) and compartments. In cancer cells, TAD structure is usually altered to facilitate the communication between enhancers and promoters in addition to higher …

Farnesol Secretion As A Possible Driving Force For Maintaining Candida Albicans As A Diploid, Kenneth Nickerson, Cory Boone, Kory Parker

Kenneth Nickerson Papers

Candida albicans is a pathogenic dimorphic fungus which is invariably found as a diploid in patients. C. albicans secretes the sesquiterpene farnesol both as a quorum sensing molecule which blocks the yeast to hypha conversion and as a virulence factor for pathogenicity. 20-25 μM farnesol kills other competing yeasts and fungi, often by triggering apoptosis, and yet wild type diploid C. albicans tolerates 300-500 μM farnesol. The recent availability of 10 haploid strains of C. albicans (5 mating type aand 5 mating type α) allowed us to compare their production of and sensitivity to farnesol. On average, the heterozygous diploid …

Engineering Advanced Micro And Nanofiber Materials For Biomedical Applications, Alec D. Mccarthy

Theses & Dissertations

At the functional crossroads of engineering and biomedical sciences lies the interdisciplinary field of biomedical engineering. Principles of biomedical engineering are vast, and the rigorous application of engineering towards clinically-relevant medicine has the ability to take novel concepts from bench to bedside. Arguably one of the most promising and productive sub-fields within the biomedical engineering discipline is biomaterial engineering. Here, novel biomaterials, synthesized from natural, synthetic, or hybrid materials, can be used in tissue repair and regeneration, hemostasis, as anatomical support and drug delivery vessels, or as diagnostic devices.

Of particular interest are applications of nanofiber and microfiber objects, which …

Review Article: Synthesis Of Fe3o4 Nanoparticle And Its Application For Glassy Carbon Electrode Modification, Agung Slamet Nugraha, Asep Bayu Dani Nandiyanto

Chimica et Natura Acta

Nanomaterials have various unique properties and characteristics so that they can apply in many sectors. One of the most popular nanoparticles today is magnetite nanoparticles. Magnetite particles have several properties such as being super magnetic, having a high saturation field, chemical stability, biocompatibility, and low production costs. The purpose of this article is to review the synthesis of magnetite nanoparticles and their application to Glassy Carbon Electrode (GCE) modification. This modified GCE can applied as an electrochemical sensor to detect various organic and inorganic substances. In this study, type synthesis methods of magnetite nanoparticles which taken from kind literature well …

Examining The Interaction Of Adverse Childhood Events, Dental Issues, Asthma And Autism, Cathy Koetting

Electronic Theses and Dissertations

Dissertation supervised by Dr. Rebecca Kronk

Purpose: Adverse childhood events (ACEs) have a profound and long-term effect on the health outcomes of many children and adults. However, few studies have focused on specific ACEs and health outcomes in children with autism spectrum disorder (ASD). The aim of the study was to investigate if ASD moderated the relationship between ACEs and specific health outcomes in children who had been the subject of a child welfare system report.

Design and Methods: Using the second National Survey of Child and Adolescent Well-Being (NSCAW II), a secondary analysis was performed on a sample of …

A Bible Study Series: The Family-Centered, Church-Supported Paradigm Shift For Raising Children In The Faith At Salem Lutheran Church, Michael J. Nielsen

Doctor of Ministry Major Applied Project

Nielsen, Michael J. “A Bible Study Series: The Family-Centered, Church-Supported Paradigm Shift for Raising Children in The Faith at Salem Lutheran Church.” Doctor of Ministry. Major Applied Project, Concordia Seminary, 2021. 160 pp.

In many Christian churches there is the question: “How do we keep our children after confirmation?” The answer is a simple one: Parents. This MAP examines the relationship of the family and the church when it comes to raising children in the faith. Biblically parents are called to be the primary faith formers in the lives of their children. A multi-part Bible study was created to teach …

Distribution, Abundance And Natural Enemies Of The Invasive Tomato Leafminer, Tuta Absoluta (Meyrick) In Kenya, G. Kinyanjui, F. M. Khamis, F. L.O. Ombura, E. U. Kenya, S. Ekesi, S. A. Mohamed

All Peer-Reviewed Publications

Tuta absoluta (Meyrick) has become a serious menace to sustainable production of tomato in Kenya. A survey was conducted between April 2015 and June 2016 to determine its distribution, abundance, infestation, and damage levels on tomato, and associated natural enemies. Trap counts of T. absoluta moths were recorded in all surveyed 29 counties, which indicated its nationwide distribution irrespective of altitude. Tuta absoluta was present in both open fields and greenhouses. The highest moth/trap/day was 115.38 ± 15.90. Highest leaf infestation was 92.22% and the highest number of mines and larvae per leaf were 3.71 ± 0.28 and 2.16 ± …

Ultrasound Modulation Of Macaque Prefrontal Cortex Selectively Alters Credit Assignment–Related Activity And Behavior, Davide Folloni, Elsa Fouragnan, Marco K. Wittmann, Lea Roumazeilles, Lev Tankelevitch, Lennart Verhagen, David Attali, Jean François Aubry, Jerome Sallet, Matthew F.S. Rushworth

School of Psychology

Credit assignment is the association of specific instances of reward to the specific events, such as a particular choice, that caused them. Without credit assignment, choice values reflect an approximate estimate of how good the environment was when the choice was made—the global reward state—rather than exactly which outcome the choice caused. Combined transcranial ultrasound stimulation (TUS) and functional magnetic resonance imaging in macaques demonstrate credit assignment–related activity in prefrontal area 47/12o, and when this signal was disrupted with TUS, choice value representations across the brain were impaired. As a consequence, behavior was no longer guided by choice value, and …

Fasting Status Of Steller Sea Lion Pups, Stephanie G. Crawford

Biological Sciences

Following population declines in species of concern, wildlife managers often seek to identify underlying causes to understand and predict population dynamics for better future management. Often, physiological and/or behavioral metrics are measurable markers of decline, and these are often detectable well before declines are measurable through population surveys. During the 1970's, 80's, and 90's Steller sea lion (SSL; Eumetopias jubatus) populations in the western portion of their breeding range declined by ~85%. Though declines in most regions have since stabilized or exhibited modest recovery, some subpopulations breeding in the Aleutian Islands continue to decline. In contrast, SSL subpopulations in eastern …

Naturally Occurring Etiologic Factors Affecting The Health Of Breeding Seabirds In The Bering Sea, Maile Branson

Biological Sciences

Seabird populations across the globe have experienced both significant instability and consistent overall declines in recent history. Seabirds in the Bering Sea of Alaska, USA appear to be severely affected by environmental changes, exhibiting large-scale shifts in behavior and distribution and increases in unusual mortality events (UMEs) in recent years. I analyze a selection of the naturally occurring pathogenic and toxicological factors affecting breeding seabirds in the Bering Sea region using an approach focusing on zoonoses and bioaccumulating toxins. Specimens were collected at three breeding colonies in the Bering Sea in 2018 and 2019, and were evaluated for the presence …

Rooted In Environmental Justice: Phytogeography And Ethnoecology Of Serianthes, Else Demeulenaere

Biological Sciences

Serianthes Benth. (Fabaceae) is one of the most endangered plant genera in the world, with 12 of the 18 species listed on the IUCN Red List of Threatened Species. Serianthes trees are culturally important to island communities of the Indo-Pacific region for canoes, boats, traditional houses, and medicine. Habitat loss and ecosystem degradation increased pressure on these trees, also threatening its Indigenous cosmology and traditional practices. This interdisciplinary study integrated genomic, biogeographic and ethnoecological approaches to develop appropriate policies that protect the Indigenous biocultural diversity of Serianthes. Phylogenomics of 401 nuclear exons and non-coding flanking regions using both a multi-species …

A Pkcα-Mediated Growth Suppressive Mek-Erk Signaling Axis In Intestinal Epithelial Cells, Navneet Kaur

Theses & Dissertations

Members of the protein kinase C (PKC) family of serine/threonine kinases are involved in regulation of fundamental cellular functions, including proliferation, differentiation, survival, migration, and transformation. Increasing evidence points to anti-proliferative and tumor suppressive role of PKCs. Our laboratory and others have reported that the classical PKC isozyme, PKCαnegatively regulates proliferation and tumorigenesis in the intestinal epithelium. Our laboratory has further determined that PKCα signaling induces a program of cell cycle withdrawal in intestinal epithelial cells that involves downregulation of the pro-proliferative proteins, cyclin D1 and Id1, and upregulation of the cyclin dependent kinase (CDK) inhibitor, p21^Cip1. Unexpectedly, …

A Public Health Ethics Approach To Substance Use Disorder, Adele Flaherty

Electronic Theses and Dissertations

The goal of the dissertation is to undertake an analysis of substance use disorders that focuses on a public health ethics perspective. The ethical argument focuses upon justifying the use of harm reduction and is primarily concerned with the current opioid crisis. While substance abuse/misuse over the course of history has been identified as a public health concern, this dissertation presents substance use disorders over the course of the lifespan, examining various contexts in which it can affect daily living and health outcomes. It achieves this by analyzing substance use disorders through the lens of the socioecological model of public …

Air Quality And Mental Health: Evidence, Challenges And Future Directions, K Bhui, J Newbury, R Latham, M Ucci, Z Nasar, B Turner, C O'Leary, Hl Fisher, E Marczylo, P Douglas, S Stansfeld, S Jackson, S Tyrrel, A Rzhetsky, R Kinnersley, P Kumar, C Duchaine, F Coulon

School of Biomedical Sciences

No abstract provided.

Coyote Management In San Francisco, Matthew Greer

Master's Projects and Capstones

As cities in North America grow, coyotes have become progressively more important species in urban ecosystems. Moreover, as coyotes increasingly use these urban spaces, human-coyote conflicts have become more common, creating a need for new management strategies. This paper will explore how the city of San Francisco could create a new coyote management plan for its highly visible coyote population. San Francisco has had a persistent coyote population since the early 2000s (Todd, 2018). Currently, the coyote population is close to 100 individuals and is still growing (J. Young, Presidio Trust, pers. comm.). To explore this topic a literature review …

The Feasibility Of Industrial Wastewater Reuse Onsite In The Tri-City Area, Shayla Bergeron

Master's Projects and Capstones

Industries typically discharge wastewater to a centralized wastewater treatment plant, but given ongoing water scarcity from repeated droughts, onsite wastewater reuse within the industrial facility’s plant is an attractive alternative. However, information on economic and technical feasibility on wastewater reuse onsite is limited. A literature review showed that membrane bioreactors are a promising wastewater reuse treatment technology due to their reduced footprint and high quality produced effluent. A watershed assessment of the Tri-City area was conducted to evaluate future water supply. A case study was then performed on industrial dischargers in the Tri-City area applying this technology. Finally, the costs …