Life Sciences Commons^™

Investigating The Impact Of Transcription On Mutation Rates, Sarah Patterson

Theses and Dissertations

tRNA genes are highly transcribed and perform one of the most fundamental cellular functions. Although a universal pattern observed across all three domains of life is that highly transcribed genes tend to evolve slowly, tRNA genes have been shown previously to evolve rapidly. This rapid sequence evolution could result from relaxed selection, increased mutation rate, or a combination of both. Here, we use mutation-accumulation line sequencing data to show that tRNA genes accumulate more mutations than other gene types. Our results indicate that this elevated mutation rate is a consequence of both elevated transcription-associated mutagenesis and a lack of transcription-coupled …

Modeling X-Linked Dystonia Parkinsonism (Xdp) In Patient-Derived Medium Spiny Neurons, Shivani Aryal

Arts & Sciences Graduate Student Theses and Dissertations

X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative disorder that results in the loss of striatal medium spiny neurons (MSNs). XDP is an X-linked disorder caused by disease-specific mutations around the TAF1 gene. This thesis highlights the utility of directly reprogrammed MSNs from fibroblasts of affected XDP as a platform that captures cellular and epigenetic phenotypes associated with XDP neurodegeneration. In addition, this thesis demonstrates the neuroprotective effect of SAK3 currently tested in other neurodegenerative diseases. XDP fibroblasts from three independent patients as well as age- and sex-matched control fibroblasts were used to generate MSNs using miRNA-9/9*-124 and the transcription factors …

The Possible Neurobiological Mechanisms Influencing Ptsd According To Previous Research: A Review, Tiria Carr, Collen M. Parks

Undergraduate Research Symposium Posters

Post Traumatic Stress Disorder or PTSD is a mental health condition that's triggered by either experiencing or witnessing a terrifying event. According to the National Center for PTSD, approximately six out of one hundred people (six percent) in the United States report to have suffered PTSD either currently or. This experiment aimed to: Explore the different behavior and brain measures used to evaluate the extent of neurological change that brains with PTSD suffer; Review different experimental procedures; Aims to express a theoretical experiment from the data collected; Hypothesize an effective experimental procedure for measuring neurological change in subjects suffering from …

Hazards And Perceptions Of Cigarette And E-Cigarette Waste, Jossalyn Rogalski

Honors Theses

No abstract provided.

Determining The Potential Of Sonic Bloom In Inducing Rice Resistance (Oryza Sativa) Against The Attack Of Bacterial Leaf Blight Disease Caused By Xanthomonas Oryzae, Azka Algina, Syifaa Yunita Yulianti, Rohimatus Syamsyiah, Veadora Yasminingrum, Bergas Frenli Nur Vendi, Vira Kusuma Dewi

Jurnal Kultivasi

Xanthomonas oryzae which causes bacterial leaf blight disease is one of the main pathogens that attack rice crops. The threat of losing rice yields due to X. oryzae needs to be avoided by implementing appropriate control strategies. Sonic bloom has the potential to induce plant immunity against diseases. Hence, this study aimed to examine the potential of sonic bloom in inducing rice resistance to bacterial leaf blight. The experiment was arranged in a Randomized Block Design (RBD) with five treatments and three replications. The treatments consisted of several frequencies, namely PR (0.5 - 1 kHz and inoculated with X. oryzae), …

The Application Of Florpyrauxifen-Benzyl 25 G/L, A New Auxin Synthetic Herbicide, To Control And Inhibit The Growth Of Water Hyacinth Weed (Eichhornia Crassipes (Mart). Solms), Nita Nur Rezkia, Denny Kurniadie, Dedi Widayat

Jurnal Kultivasi

Water hyacinth is an invasive species that spreads rapidly and causes several issues in aquatic habitats; therefore, efforts are required to eradicate weeds in aquatic ecosystems. Aquatic weed control in Indonesia using herbicide is very limited, so it can be an alternative for aquatic weed control management. This research goal was to examine the effectiveness of the herbicide with active agent Florpyrauxifen-benzyl 25 g/L in controlling and inhibiting the rapid growth of (E. crassipes). This research was carried out at the Ciparanje Greenhouse and Weed Science Laboratory, Faculty of Agriculture Universitas Padjadjaran, West Java, Indonesia, from August to October 2022. …

Evaluation Of Physiological Quality Of Seed On Yield Of Yellow And Black Soybean Treated With Biological Seed Coating, Muhamad Kadapi, Priscilla Olga Salim, Sumadi

Jurnal Kultivasi

The demand for soybeans as one of cereal commodities increases every year, however, to meet the production and demand level is still challenging in Indonesia. One of the causes of low soybean production is stress during cultivation, lack of nutrients, or poor quality of soybean seeds. One solution is to increase seed protection by coating the seeds with an environmentally friendly biological seed coating. This study aims to obtain the best biological seed coating for increasing soybean seed viability, vigor, and yield. The research was conducted at the Faculty of Agriculture Experimental Station of Universitas Padjadjaran, Jatinangor from August to …

Ewsr1::Atf1 Orchestrates The Clear Cell Sarcoma Transcriptome In Human Tumors And A Mouse Genetic Model, Benjamin B Ozenberger, Li Li, Emily R Wilson, Alexander J Lazar, Jared J Barrott, Kevin B Jones

Faculty, Staff and Student Publications

Clear cell sarcoma (CCS) is a rare, aggressive malignancy that most frequently arises in the soft tissues of the extremities. It is defined and driven by expression of one member of a family of related translocation-generated fusion oncogenes, the most common of which is EWSR1::ATF1. The EWSR1::ATF1 fusion oncoprotein reprograms transcription. However, the binding distribution of EWSR1::ATF1 across the genome and its target genes remain unclear. Here, we interrogated the genomic distribution of V5-tagged EWSR1::ATF1 in tumors it had induced upon expression in mice that also recapitulated the transcriptome of human CCS. ChIP-sequencing of V5-EWSR1::ATF1 identified previously unreported motifs …

Evaluating Clinical Outcomes In Patients Being Treated Exclusively Via Telepsychiatry: Retrospective Data Analysis, Cheryl Person, Nicola O'Connor, Lucy Koehler, Kartik Venkatachalam, Georgia Gaveras

Faculty, Staff and Student Publications

BACKGROUND: Depression and anxiety are highly prevalent conditions in the United States. Despite the availability of suitable therapeutic options, limited access to high-quality psychiatrists represents a major barrier to treatment. Although telepsychiatry has the potential to improve access to psychiatrists, treatment efficacy in the telepsychiatry model remains unclear.

OBJECTIVE: Our primary objective was to determine whether there was a clinically meaningful change in 1 of 2 validated outcome measures of depression and anxiety-the Patient Health Questionnaire-8 (PHQ-8) or the Generalized Anxiety Disorder-7 (GAD-7)-after receiving at least 8 weeks of treatment in an outpatient telepsychiatry setting.

METHODS: We included treatment-seeking patients …

Phenotyping Emt And Met Cellular States In Lung Cancer Patient Liquid Biopsies At A Personalized Level Using Mass Cytometry, Loukia G Karacosta, Danny Pancirer, Jordan S Preiss, Jalen A Benson, Winston Trope, Joseph B Shrager, Arthur Wai Sung, Joel W Neal, Sean C Bendall, Heather Wakelee, Sylvia K Plevritis

Faculty, Staff and Student Publications

Malignant pleural effusions (MPEs) can be utilized as liquid biopsy for phenotyping malignant cells and for precision immunotherapy, yet MPEs are inadequately studied at the single-cell proteomic level. Here we leverage mass cytometry to interrogate immune and epithelial cellular profiles of primary tumors and pleural effusions (PEs) from early and late-stage non-small cell lung cancer (NSCLC) patients, with the goal of assessing epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) states in patient specimens. By using the EMT-MET reference map PHENOSTAMP, we observe a variety of EMT states in cytokeratin positive (CK+) cells, and report for the first time MET-enriched CK+ …

The Defined Tlr3 Agonist, Nexavant, Exhibits Anti-Cancer Efficacy And Potentiates Anti-Pd-1 Antibody Therapy By Enhancing Immune Cell Infiltration, Seung-Hwan Lee, Young-Ho Choi, Soon Myung Kang, Min-Gyu Lee, Arnaud Debin, Eric Perouzel, Seung-Beom Hong, Dong-Ho Kim

Faculty, Staff and Student Publications

Nexavant was reported as an alternative to the TLR3 agonist of Poly(I:C) and its derivatives. The physicochemical properties, signaling pathways, anti-cancer effects, and mechanisms of Nexavant were investigated. The distinctive characteristics of Nexavant compared to that of Poly(I:C) were demonstrated by precise quantification, enhanced thermostability, and increased resistance to RNase A. Unlike Poly(I:C), which activates TLR3, RIG-I, and MDA5, Nexavant stimulates signaling through TLR3 and RIG-I but not through MDA5. Compared to Poly(I:C), an intratumoral Nexavant treatment led to a unique immune response, immune cell infiltration, and suppression of tumor growth in various animal cancer models. Nexavant therapy outperformed anti-PD-1 …

Analysis Of Vulnerability And Risk Of Maize (Zea Mays L.) Production Decrease On Rainfed Land In Garut Regency Due To Climate Change And Its Strategic Adaptation Options, Ruminta, Yassa Sabilla, Fiky Yulianto Wicaksono, Agus Wahyudin

Jurnal Kultivasi

Climate change, especially air temperature and rainfall, impacts the agricultural sector, one of which is the reduction of maize production. As an anticipatory effort to reduce maize production due to climate change, a study is needed to identify the possible hazard, vulnerability, and risk of maize yield reduction at the sub-district level in the largest maize-producing center in West Java, Garut Regency. After identifying areas with high or very high levels of potential yield reduction risk, a strategic adaptation that can be applied to deal with climate change can be identified. The method used in this research is descriptive quantitative. …

The Effects Of Intermittent Fasting On Female Athletes: A Systematic Review, Courtnie Scarbrough

Theses and Dissertations

The intermittent fasting diet has a historical past, but recently, it has regained popularity as a weight loss strategy for the general public. Athletes have also picked up this specialized diet in search of a competitive edge. There are ample studies testing athletes of all levels, but most do not include females or report sex-specific results. This systematic review aimed to identify current research on the effects of intermittent fasting in the understudied population of female athletes. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a comprehensive search was conducted in three databases, including PubMed, Cochrane, …

Factors In Depopulation Trends Among Young Adults In Rural Areas In Mississippi, Katherine H. Ellard

Theses and Dissertations

The purpose of this study was to determine why young adults are leaving rural Mississippi towns and not returning to those areas. Research objectives were to 1) describe the characteristics of young adults who have left rural areas in the last ten years , 2) identify specific reasons why young adults choose to leave where they were raised, and 3) identify factors that would attract young people to return to rural areas in Mississippi.

Findings from this study indicated young adults were leaving rural areas for better educational and job opportunities, but some were relocating to other areas within Mississippi …

The Influence Of At-Planting Insecticide Treatments On Tobacco Thrips, (Thysanoptera:Thripidae), And Reniform Nematode, (Tylenchida:Hoplolaimidae), In Conventional And Thryvon Cotton Systems, Walker Brett Farmer

Theses and Dissertations

One of the objectives of this research was to evaluate the need for an additional imidacloprid seed treatment on ThryvOn^® (Bayer Crop Science^®, St. Louis, MO) cotton to effectively manage tobacco thrips, Frankliniella fusca (Hinds). While evaluating thrips densities and damage ratings, ThryvOn cotton continued to display reduced damage and thrips populations than non-ThryvOn. Thrips populations and damage ratings were consistently reduced when incorporating a higher rate of imidacloprid, but they were not reduced enough to justify the higher rates of imidacloprid. Another objective of this research was to evaluate the impact of aldicarb (AgLogic Chemical^{® …}

Developing A Precision Agriculture Framework To Assess Financial Viability Of Decisions In Farming And Conservation, Jennifer Sublett

Theses and Dissertations

Agricultural producers are invested in managing the impacts of crop damage on their yields and profit. When damage occurs early enough in an agricultural growing season, farmers have the option to replant their corn stand in an effort to recoup some of the lost profits. In this thesis two different types of naturally occurring damage, wildlife depredation and persistent weed or insect patches, were simulated on two representative regions of Mississippi. These data were then used to assess the financial viability of a range of damage mitigation methods, including partial replanting, enrollment into a government conservation buffer, and no action. …

Conventional And Strip-Tillage Systems With Fertilizer Placement In Irrigated And Dryland Corn And Soybean In The Mississippi Delta, James Chad Hankins

Theses and Dissertations

Years of intensive tillage operations and heavy winter rainfalls have taken a toll on the soils in the Mississippi Delta causing compaction and nutrient losses due to runoff. The purpose of this research was to determine the effects of tillage systems and P and K fertilizer placement methods on corn and soybean production, as well as soil properties in the Mississippi Delta. The tillage treatments included conventional tillage, conventional tillage with subsoiling, and strip-tillage. The fertilizer placement treatments included a non-treated control, incorporated with tillage, and broadcast after tillage. Strip-tillage treatments reduced soil compaction and maintain nutrient levels while improving …

Insights Into The Challenges Posed By Climate Change And Land Competition To Brazil’S Midwest Pulpwood Market, Roberto Hajime Sant Anna Kimura

Theses and Dissertations

I investigated the effect of climate change in one of the few expanding markets in the world in Brazil. In the last decades the demand for pulpwood increased from zero to 11 million tons, leading to an expansion of 700 thousand hectares of Eucalyptus plantation. In 2024, a new mill will start operating increasing the consumption of wood fiber by 8.2 million tons (+49%). I used mathematical programming to investigate how different scenarios of productivity and land will affect the market. My results showed that around 946,000 hectares (+124%) of additional timberland will be necessary in the upcoming decades. The …

Effects Of Wet Aging On Water-Soluble Flavor Compounds, Descriptive Flavor, Consumer Acceptability, And Willingness-To-Pay Of Beef Longissimus Lumborum Steaks, Shangshang Wang

Theses and Dissertations

This study examined the effects of wet aging on water-soluble flavor compounds, descriptive flavor, consumer acceptability, and willingness-to-pay of beef strip steaks. Twenty USDA Select boneless beef loins (NAMP #180) were dorsally divided into four equal portions, which were randomized to receive either 0, 7, 14, or 21 d of wet aging. Short-chained peptide concentration increased from 4.11 mg/g on d 0 to 5.12 mg/g on d 7 (P = 0.011) and subsequently increased to 7.14 mg/g on d 21 (P < 0.001). Cooked beef contained 1.85 mg/g less short-chained peptides than raw beef (P < 0.001). Wet aging for 21 d increased the concentrations of amino acids, which are precursors for the Maillard reaction, including methionine, threonine, cystine, serine, tryptophan, and phenylalanine (P < 0.001). Wet aging decreased the nucleotide concentrations (P ≤ 0.003) and increased hypoxanthine concentration, a compound that imparts bitter flavor (P …

Heirs' Property Disputes On Forestlands, Partition Actions, And The Determinants Of Court Verdicts, Mahesh Prasad Tiwari

Theses and Dissertations

Heirs' property is generated through the intergenerational transfer of a property to several co-owners when the original owner dies without a will. Such co-owners hold undivided fractional interest in the entire land but lack a clear title. Co-owners face several legal, financial, and technical constraints to manage the forestlands and often seek partition of the land. However, the legal environment and empirical assessment of partition actions on forestlands owned as heirs' property has not been examined. This thesis evaluates statutory laws relevant to forestland partition and the factors instrumental in adjudicating partition lawsuits. The findings reveal that partition lawsuits are …

Increased Coding Potential Of Bovine Herpesvirus 1, Victoria Jefferson

Theses and Dissertations

Bovine respiratory disease (BRD) costs the cattle industry millions of dollars in costs in treatment and loss every year in the United States. A significant pathogen often contributes to BRD is Bovine Herpesvirus 1 (BoHV-1), a double stranded DNA virus with the ability to establish latency in the trigeminal ganglia and neurons. Primary infection with BoHV-1 results in immunosuppression that increases the risk of secondary bacterial infection and pneumonia. Because herpesviruses infect their hosts for life and can be reactivated in times of stress, BoHV-1 can present a recurring risk of BRD. The following research aims to expand the knowledge …

Advancing Salamander Conservation Efforts In Zoos And Aquaria Through Assisted Reproductive Technologies (Art), Devin Marie Chen

Theses and Dissertations

Salamanders are one of the most at-risk taxa in the world due to habitat destruction, pollution, climate change, invasive diseases, and more. This has led to a need for conservation breeding programs that are often associated with zoos and aquaria. Salamanders can be difficult to breed in captivity, though, due to their dependence on specific environmental cues and other unknown factors that stimulate sperm and egg production. To overcome these challenges, assisted reproductive technologies (ART) such as exogenous hormone administration, sperm cryopreservation, and in-vitro fertilization have been developed to increase offspring propagation and maintain genetic diversity. If genetically robust populations …

Of Changing Climate And Habitat: Range-Wide Individual Growth And Local Patterns Of Phenology And Landscape Use In A Threatened Pit-Viper, James Helferich

Theses and Dissertations

Over the 21st century, climate change and wetland habitat loss will pose major threats to the Eastern Massasauga (Sistrurus catenatus), a federally threatened and Great Lakes region endemic rattlesnake. I collected capture-recapture data from sites across the range and modeled the effect of climatic variables on growth rate and asymptotic size. I found that high snow residence time was associated with larger asymptotic sizes but slower growth, while high spring precipitation increased growth rate. I then projected future growth and size under different carbon emission scenarios. Given the threat posed by successional encroachment of woody vegetation, I used spatially explicit …

Towards Understanding The Interactions Between Ospreys And Human-Made Structures In The Tennessee River Valley, Natasha Karina Murphy

Theses and Dissertations

Raptor nests on human-built structures represent a significant source of conflict as they can result in bird mortality, fires, structure damage, service distribution, or power outages when falling nest materials or animals connect with energized conductors. Power companies, such as the Tennessee Valley Authority (TVA), wish to mitigate these conflicts to avoid service disruptions. In this dissertation, I present my work towards understanding and mitigating the interactions between Ospreys (Pandion haliaetus) and human-made structures. To achieve this, I explored multiple elements of conflict identification, monitoring, and basic ecology of the target species to better inform conflict mitigation. In Chapter I, …

Moisture Effects On Visible Near-Infrared And Mid-Infrared Soil Spectra And Strategies To Mitigate The Impact For Predictive Modeling, Francis Hettige Chamika Anuradha Silva

Theses and Dissertations

Instrumental disparities and soil moisture are two of the key limitations in implementing spectroscopic techniques in the field. This study sought to address these challenges through two objectives. The first objective was to assess Visible-near infrared (VisNIR) and mid-infrared (MIR) spectroscopic approaches and explore the feasibility of transferring calibration models between laboratory and portable spectrometers. The second objective addressed the challenge of soil moisture and its impact on spectra. The portable spectrometers demonstrated comparable performance to their laboratory-based counterparts in both regions. Spiking with extra-weight, was the most effective calibration transfer method eliminating disparities between instruments. The samples were rewetted …

Occupational And Environmental Factors Influencing Morale Of United States Federal Wildland Firefighters, Rachel M. Granberg, Ting Shen, Seth W. Pearson, Robin M. Verble

Psychological Science Faculty Research & Creative Works

Background. Wildland firefighters have physically and psychologically demanding jobs that can result in social, economic and health-related stress. Previous studies have examined the physiological and physical effects of a career in wildland fire, but fewer studies have addressed psychological effects, and to date, none have directly analyzed the hiring and work experiences of wildland firefighters. Aims. We surveyed work experiences, health and well-being, and morale of wildland firefighters, explored factors that can improve recruitment and retention, and summarized broad patterns. Methods. We conducted a voluntary anonymous survey of 708 federal wildland firefighters via an online platform over 2 months in …

Hypothalamic Manipulation Of The Anuran Hpg Axis: Alternative Hormones And A Non-Invasive Administration Route For Amphibian Assisted Reproductive Technologies (Art), Erin Michelle Saylor

Theses and Dissertations

Amidst the amphibian extinction crisis, in situ and ex situ amphibian species conservation initiatives utilize assisted reproductive technologies for optimal genetic management of captive and wild populations. Development of effective, simple, low-cost methods for obtaining gametes for artificial fertilization, sperm biobanking, or natural breeding alleviates obstacles for institutions or programs to apply reproductive technologies. Objectives herein include investigating the efficacy of alternative hormones for inducing spermiation, an alternative hormone administration route for inducing ovulation, exploring the physiological effects of hormone therapy, and utilizing sperm from deceased animals for biobanking.

Development Of An Automated Delivery System To Apply Copper Sulfate Crystals Using Precision Dry Fertilizer Application Technology, Kevin Charles Wise

Theses and Dissertations

The digenetic trematode, Bolbophorus damnificus, poses a substantial threat to catfish aquaculture, causing significant economic losses. Infestations lead to suppressed feed consumption, secondary bacterial infections and poor production performance. Survey data reveals widespread infestation in the in the southeastern United States. Current control strategies involve the application of a concentrated copper sulfate solution to reduce snail populations which serve as the first intermediate host of the trematode life cycle. This study aimed to improve treatment efficacy by developing a granular copper sulfate application system. A modified Gandy fertilizer applicator, equipped with a programmable control system, demonstrated accurate distribution of copper …

Effects Of Electrical Stimulation On Water-Soluble Flavor Compounds In Beef Semimembranosus Muscle, Chelsie Beebe

Theses and Dissertations

This study examined the effects of electrical stimulation on water-soluble flavor compounds in beef semimembranosus muscle, collected immediately after exsanguination (PRE), immediately after stimulation (POST), and 24 h postmortem (H24) from both stimulated (ES) and non-stimulated (CON) carcasses. Short-chained peptides were greater in ES at H24 (P = 0.007). Glutamic acid concentration was above its taste threshold (0.044 mmol/kg) and was less in ES at PRE and POST by 0.030 mmol/kg (P ≤ 0.028) but was similar in both ES and CON by H24 (P = 0.142). Lysine, a Strecker amino acid, was greater in ES at H24 by 0.138 …

Habitat Utilization Of Marsh And Adjacent Submerged Landscape By Fish And Macroinvertebrates In A Gulf Of Mexico Tidal Oligohaline Environment, Tia Offner

Theses and Dissertations

Estuarine habitats are considered nursery habitats for fishes and invertebrates, but oligohaline environments are critically understudied. Using a seine net and fyke nets, we sampled Back Bay, Mississippi (USA), a low salinity estuary, once a month for a year to explore the temporal use of the marsh and adjacent submerged landscape by nekton species. We also looked at whether there is evidence of habitat preference in the most numerous nekton species. We used a novel habitat usage index (HUI) to compare seine and fyke net catches of our top 10 species, and evaluated catch size in relation to maturation size. …