Digital Commons Network^™

Mammalian Trait Evolution: Macroevolutionary And Comparative Genomic Analyses Of Diet And Ursid-Specific Adaptations, Matthew David Pollard

Electronic Theses and Dissertations Archive

Complex traits such as diet have shaped the evolutionary success of species, driving the diversity of form and function that we observe across the tree of life. My research investigates the genomic and macroevolutionary forces behind diet and other complex traits, revealing how they mediate evolutionary change across Mammalia. I utilized two complementary approaches for understanding the evolution of diet in mammals. First, I created two continuous dietary variables—degree of carnivory and degree of dietary specialization—to quantify the impact of diet on mammalian speciation. I found that degree of carnivory, rather than dietary specialization, significantly influenced speciation, but did not …

Investigation And Computational Analysis Of The Iqd Gene Family In Common Bean (Phaseolus Vulgaris L.): Expression Profiling Under Salt Stress, Tarik Kirlioğlu, Aybüke Okay, Emi̇ne Sümer Aras, İlker Büyük

Turkish Journal of Botany

Common bean is one of the most nutritionally important legumes because of its high-quality protein content. While its genome has been widely studied however, the IQD gene family has not been extensively investigated in common bean to date. The IQD proteins (IQ-67 domain), a type of calmodulin-binding protein, are involved in plant growth and development, as well as the plant's response to environmental stressors. In this study, thirty-six PvIQD genes were discovered and their proteins were found to be classified into four groups according to the phylogenetic tree. The proteins which are encoded by PvIQD genes with similar exon-intron pattern …

Primary Distribution And Rt-Pcr-Based Detection Of Citrus Dwarfing Viroid (Cdvd) In Citrus Cultivars Of Pakistan, Zia Ul Haq, Amjad Ali, Syed A.H. Naqvi, Faheem Shehzad Baloch, Ummad U.D. Umar

Turkish Journal of Botany

Viroid diseases have emerged as a significant threat to citrus orchards globally. In Pakistan, viroid infections have rapidly spread across different citrus cultivar, posing serious challenges to the survival of orchards. This study encompasses the determination of the prevalence and detection of Citrus dwarfing viroid (CDVd) in both reported and newly introduced citrus cultivars in Pakistan using RT-PCR. RNA was extracted from 122 infected citrus samples and examined for the presence of viroids following the successful optimization of newly designed CDVd primers (CDVd AF1/AR1). This led to the confirmation of CDVd in 72 samples (59.01%).. Biological indexing was performed using …

Functional Characterization Of Haloarchaeal Udp-Glucose 4-Epimerase And 3-Hydroxybutyryl-Coa Dehydrogenase Genes In Nicotiana Tabacum, Çi̇ğdem Otur, Sezer Okay, Aslihan Kurt Kizildoğan

Turkish Journal of Botany

The objective of the studyAbiotic stress poses a significant threat to plant survival. In response to the challenging conditions, plants have evolved various resistance mechanisms. Recently, genetic strategies have become increasingly prevalent in efforts to enhance abiotic stress tolerance and develop stress-resistant plant varieties. In this study, we employed heterologous expression of two metabolism-related haloarchaeal genes in the Nicotiana tabacum genome to improve its mechanism for salt and drought tolerance.Experimental procedure(s)The U2642 and CL165 genes encoding 3-hydroxybutyryl-CoA dehydrogenase and UDP-glucose 4-epimerase, respectively, were subcloned into the pIPKb004 vector under the control of Cauliflower mosaic virus 35S (CaMV35S) promoter using the …

Genome-Wide Identification And Characterization Of The Lea Gene Family In Common Bean And The Role Of The Dehydrin Gene Pvhdn3 In Enhancing Salt And Drought Tolerance In Transgenic Tobacco Plant., Gökhan Gökdemi̇r, Zafer Seçgin, Karam Mostafa, Mohamed Farah Abdulla, Musa Kavas

Turkish Journal of Botany

Global climate change exposes crops to numerous abiotic and biotic stress factors, significantly threatening their growth, development, and overall productivity. Among the various abiotic stresses, salt and drought are the most detrimental, having a severe impact on yield stability. Late Embryogenesis Abundant proteins (LEA) represent a broad and varied class of polypeptides that accumulate in response to cellular dehydration across diverse organisms. Nonetheless, there has been a scarcity of studies on this protein family in common beans prior to this investigation. In this study, we identified 69 members of the LEA gene family in common bean, characterized by conserved LEA …

Phylogenomics Of The Tribe Leonureae Reveals A New Genus: Paraleonurus (Lamiaceae, Lamioideae), Mei-Lin Qian, Ya-Ping Chen, Tuncay Di̇rmenci̇, Yue Zhao, Guo-Xiong Hu, Fei Zhao, Ferhat Celep, Bo Li, Chunlei Xiang

Turkish Journal of Botany

With approximately 80 species across six genera (Leonurus, Lagopsis, Panzerina, Lagochilus, Chaiturus, and Loxocalyx), the tribe Leonureae represents one of the most morphologically diverse tribes within the subfamily Lamioideae of Lamiaceae. Previous studies indicated that Leonurus and Lagopsis are not monophyletic, and relationships among and within these genera remain unclear due to limited sampling and DNA markers. In this study, we present the most comprehensive phylogenomic analyses of Leonureae based on complete plastome sequences and 127 nuclear loci retrieved from next-generation sequencing data. Our results provide strong evidence for the monophyly of Leonureae, which can be further divided into six …

Heterologous Expression Of Haloarchaeal Transporter Genes In Nicotiana Tabacum Under Salt And Drought Stresses, Çi̇ğdem Otur, Musa Kavas, Aslihan Kurt Kizildoğan

Turkish Journal of Botany

The objective of the study: Climate change and human activities impose severe biotic and abiotic stresses that threaten plant survival. To cope with these extreme conditions, plants have evolved various resistance mechanisms. In recent years, genetic approaches have been increasingly employed to enhance abiotic stress tolerance and develop stress-resistant plants. In this study, we introduced three transporter-related genes from extreme haloarchaea, which thrive in saturated NaCl environments, into the Nicotiana tabacum genome to improve its salt and drought tolerance mechanisms.E xperimental procedure(s) : The U2845, U3508, and CL165 genes were subcloned into the pIPKb004 vector, which includes the cauliflower mosaic …

Artificial Intelligence-Based Methodologies For Early Diagnostic Precision And Personalized Therapeutic Strategies In Neuro-Ophthalmic And Neurodegenerative Pathologies, Rahul Kumar, Ethan Waisberg, Joshua Ong, Phani Paladugu, Dylan Amiri, Jeremy Saintyl, Jahnavi Yelamanchi, Robert Nahouraii, Ram Jagadeesan, Alireza Tavakkoli

SKMC Student Presentations and Publications

Advancements in neuroimaging, particularly diffusion magnetic resonance imaging (MRI) techniques and molecular imaging with positron emission tomography (PET), have significantly enhanced the early detection of biomarkers in neurodegenerative and neuro-ophthalmic disorders. These include Alzheimer's disease, Parkinson's disease, multiple sclerosis, neuromyelitis optica, and myelin oligodendrocyte glycoprotein antibody disease. This review highlights the transformative role of advanced diffusion MRI techniques-Neurite Orientation Dispersion and Density Imaging and Diffusion Kurtosis Imaging-in identifying subtle microstructural changes in the brain and visual pathways that precede clinical symptoms. When integrated with artificial intelligence (AI) algorithms, these techniques achieve unprecedented diagnostic precision, facilitating early detection of neurodegeneration and …

Understanding Sequence Determinants Of Functional Protein Dynamics Using Biophysical Simulations And Experiments, Upasana Lakshmi Mallimadugula

Arts & Sciences Graduate Student Theses and Dissertations

Mutations in the sequence of proteins associated with a disease often increase its risk or severity. They can also be a barrier to developing effective therapeutics for such diseases. One way in which mutations affect function is by altering dynamics that elude structural studies. Observing these changes requires methods that can report on movements of the protein on various timescales and is an ongoing challenge in biophysics and biochemistry. In this study I will use both experimental and computational techniques that can report on such dynamics to explore how small sequence changes shift the conformational landscape and consequently the function …

Avian Adaptation To Thermal Gradients, Justin Wheeler Baldwin

Arts & Sciences Graduate Student Theses and Dissertations

Life on Earth has adapted to extremely different temperatures worldwide. However, across distant branches of the tree of life, animals in similar temperature environments often share similar phenotypic traits. Specifically, traits that bear on the ratio between an individual’s surface area (e.g. appendage length) and its volume (e.g. body size) are particularly important for temperature regulation and are codified in canonical biogeographical rules. Although these global patterns of finding larger-bodied (Bergmann’s Rule) and shorter-limbed (Allen’s Rule) animals in colder regions are widely upheld, they also show substantial variation. It remains poorly understood why some animals conform to these biogeographical rules …

Sustainable Plastics From Plastic Metabolisms: Leveraging Purple Non-Sulfur Bacteria For Polyhydroxyalkanoate Synthesis, Eric Michael Conners

Arts & Sciences Graduate Student Theses and Dissertations

Purple non-sulfur bacteria (PNSB) are a taxonomically diverse group of gram-negative bacteria representing some of Earth’s most metabolically versatile life, with many genera capable of switching between the four major metabolic modes – chemoheterotrophy, chemoautotrophy, photoheterotrophy, and photoautotrophy. Today, we exploit this diversity to explore fundamental questions about microbial metabolism. At the same time, many researchers are eager to use PNSB as tools for biotechnological innovations. Yet there exists a gap between fundamental biology and applied science. Part of the challenge is that we rely on a handful of model organisms – namely, members of the genera Rhodopseudomonas and Rhodobacter …

Small- And Medium-Sized Enterprises Strategies For Sustainability And Profitability Beyond 5 Years, Bawi Ming

Walden Dissertations and Doctoral Studies

Up to 80% of small- and medium-sized enterprises (SMEs) fail within the first 5 years due to factors like financial mismanagement, market challenges, and insufficient long-term planning. To prevent these failures, organizational leaders must adopt effective sustainability strategies, as SME closures lead to job losses, economic instability, and lost innovation opportunities. Grounded in the resource-based view and general systems theories, the purpose of this qualitative pragmatic inquiry project was to explore successful strategies that SME leaders in Maryland used to sustain their businesses beyond their initial 5 years. Data were collected from six SME leaders using semistructured interviews and reviews …

Does Emotion Regulation Capacity Moderate Social Anxiety Risk Given Experiences Of Racial Microaggressions In Black/African American Undergraduate Students?, Alisha M. Sylvester

Honors College Theses

Racial microaggressions are intentional or unintentional slights toward members of a marginalized community that may come in the form of verbal, behavioral, or environmental insults. Black/African Americans experience racial microaggressions frequently, and these experiences threaten mental health. Specifically, experiencing more racial microaggressions is linked with a risk for social anxiety. However, not all individuals within the community go on to experience social anxiety. Therefore, the present study sought to identify which individuals are more vulnerable to social anxiety given experiences of racism. Poorer emotion regulation (i.e., the ability to manage emotions) is a known risk factor for anxiety. Thus, I …

The Activity And Origin Of The Chitinases In The Gut Of The Mediterranean House Gecko, Alec John

Masters Theses (Archived)

Chitin is a major component of the exoskeleton of arthropods as well as the cell wall of fungi. This amino polysaccharide polymer provides structure and protection to these organisms and represents a significant barrier to digestion of arthropod prey and fighting fungal infections. Chitinases are enzymes that break down chitin. Smaller insectivores, based upon the higher surface-to-volume ratio of their even smaller prey, ingest a large amount of chitin per unit prey item. Therefore, they represent high-likelihood opportunities to bio prospect for novel chitinases that may be effective against pathogenic fungi. Fungal infections are notoriously difficult to treat, and they …

Addressing Non-Stationary Fishery Dynamics And Demographic Complexity In Integrated Stock Assessment Models, Matthew L. Cheng

Fisheries

Integrated stock assessment models are complex non-linear statistical models that fit a variety of fishery-dependent and independent data sources to estimate the status and trends of fish populations, providing recommendations for sustainable harvest levels. Given their complexity, simplifying assumptions are necessary in stock assessment models to balance model parsimony versus complexity, while also considering data limitations. In this dissertation, I investigated considerations for addressing non-stationary fishery dynamics and evaluated the consequences of oversimplified assumptions of fishery dynamics and sex-specific demography in stock assessment models. Using Alaska sablefish (Anoplopoma fimbria) as a case-study, I developed a generalized framework to standardize fishery-dependent …

Combining Alaska Forage Fish Data From Research Surveys And Predator Diets To Assess Forage Fish Response To Climatic Regime Shifts, Lindsay Turner

Fisheries

Forage fish play a crucial role in the marine ecosystems of Alaska through the transfer of energy from lower trophic levels to marine predators. Understanding and quantifying Alaskan forage fish responses to rapid climatic shifts is needed to inform adaptive management strategies under a warmer and more variable future in Alaska. However, data on the occurrence and abundance of forage fish in Alaska are limited due to the diversity of life history strategies and patchy distribution that make their capture in fisheries-independent surveys difficult. In this thesis, I address current gaps in the data available on forage fish through the …

Generative Ai And Professional Technical Writers: A Mixed-Method Study, Jarrett Schaefer

Theses and Dissertations

This research investigates how professional technical writers use AI technology in their work today, which tools they are using, and which tasks they use them for. Using a mixed-methods research design, the study involved 21 participants completing a survey hosted in Qualtrics, and three participants interviewed over Zoom. Quantitative analysis was performed on the survey data, and the researcher used grounded theory to analyze the transcripts of the interview participants. The findings offer insight into how professional technical communicators use these tools and their attitudes toward including AI technologies in future pedagogies. While most participants had used AI technology in …

Innovations In Plant Genome Editing And Biotechnology: Addressing Global Agricultural Challenges, Bayram Ali̇ Yerli̇kaya, Karam Mostafa, Abdullah Aydin, Seher Yerli̇kaya, Momna Mehmood, Ni̇sa Nur Yilmaz, Kubi̇lay Yildirim, Musa Kavas

Turkish Journal of Botany

Developments in genome editing and plant biotechnology in recent years, especially CRISPR-Cas9 and RNA interference (RNAi) technologies, offer essential tools for solving global agricultural problems that are worsened by climate change and the increasing food demand caused by the rising world population. This review focuses on the urgent need to feed a growing global population. It explores how key biotechnological tools can enhance crop resilience and nutritional quality amid climate variability and extreme weather. The applicability of CRISPR-Cas technologies in the development of climate-friendly, more nutritious, and higher-yielding crops has opened a biotechnological avenue for the development of both transgenic …

Advancements In Qtl Mapping And Gwas Application In Plant Improvement, Muhammad Tanveer Altaf, Muhammed Tatar, Amjad Ali, Waqas Liaqat, Parnaz Mortazvi, Ceyhun Kayihan, Fati̇h Ölmez, Muhammad Azhar Nadeem, Jazib Javed, Jin-Ying Gou, Meng-Lu Wang, Ummad Ud Din Umar, Hayri̇ye Yildiz Daşgan, Cemal Kurt, Mehtap Yildiz, Sheikh Mansoor, Abdelfattah A. Dababat, Nafiz Çeli̇ktaş, Faheem Shehzad Baloch

Turkish Journal of Botany

Molecular markers play a crucial role in modern plant breeding by enabling the precise identification of genetic loci associated with important agronomic traits. This article focuses on the advancements in Quantitative Trait Locus (QTL) mapping and Genome-Wide Association Studies (GWAS), which are pivotal in identifying and dissecting complex traits such as stress tolerance, yield improvement, and nutrient efficiency. Through QTL mapping, significant genetic regions linked to desired traits are identified, while GWAS leverages larger populations for higher resolution in genetic association studies. The integration of next-generation sequencing, CRISPR, and transcriptomics technologies has revolutionized the precision and efficiency of these methods, …

Identification Of Genes Associated With Zinc And Copper Concentrations In Walnut (Juglans Regia L.) By Gwas Analysis, Berfi̇n Nazlican Kaman, Bülent Yağmur, Erdal Orman, Muhammed Bahatti̇n Tanyolaç, Duygu Ateş

Turkish Journal of Botany

154 walnut genotypes from various geographic regions were analyzed in the study. Micronutrient concentrations of zinc (Zn) ranged from 1.61 to 8.98 mg/100 g, and the concentrations of copper (Cu) varied between 0.12 and 0.38 mg/100 g. 16,473 SNPs were generated using Diversity Array Technology (DArT) for genome-wide association (GWAS) studies. The Mixed Linear Model (MLM) utilizing the Q + K model revealed seven associated markers for the element Zn in 2021 and four in 2022. The MLM (Q + K) model indicated two associated markers for the element Cu in 2021 and three in 2022. The markers found in …

Gene Expression Changes In The Seagrass Cymodocea Nodosa Individuals In Response To Aquatic Acidification, Enes Göksal, Esra Öztürk Yi̇ği̇t

Turkish Journal of Botany

Human activities have caused a rise in atmospheric carbon dioxide (CO2) levels, leading to greater absorption of CO2 by oceans and causing ocean acidification. This phenomenon, marked by a reduction in pH, represents substantial risks to marine ecosystems, including seagrass meadows. Seagrasses are vital elements of coastal ecosystems, performing important functions in carbon storage, stabilizing shorelines, and preserving biodiversity; however, reactions to ocean acidification are not well understood, especially in terms of molecular.This research study examined alterations in gene expression within seagrass meadows, namely the species Cymodocea nodosa, in reaction to simulated ocean acidification conditions. Climate chamber system to adjust …

Cultivation Protocols For The Red Seaweeds, Devaleraea Mollis And Palmaria Hecatensis From Alaska, Muriel Dittrich

Marine Biology

Species diversification is crucial for the long-term viability, competitiveness, and sustainability of the seaweed farming industry in the United States. This study investigated the effects of temperature (4, 8 and 12 °C), photoperiod (8L:16D, 12L:12D and 16L:8D), and irradiance (20, 40, 100 ± 10 μmol photons m-2 s-1) on the specific growth rate (SGR) of Devaleraea mollis and Palmaria hecatensis from Alaska. Outputs were used to adjust indoor cultivation protocols for D. mollis and develop the first protocols for Palmaria hecatensis. This study also explored the use of two relatively low-cost commercial nutrient products (F/2 and Jack's Special 25-5-15) as …

Spatial And Temporal Variability Of Carbohydrate Compositions In Cultivated Alaria Marginata, Nereocystis Luekteana, And Saccharina Latissima, Cameron Jardell

Marine Biology

Carbohydrates derived from Laminariales (kelp), including polysaccharides and sugar alcohols, present significant market opportunities for nascent mariculture industries. These carbohydrates can enhance crop biomass value through extractive processing, with applications in medicine, manufacturing, health supplements, and bio-plastics. The relative abundance and composition of carbohydrates in kelp can vary depending on species, life history, tissue type, season, and environmental conditions. In Alaska, mariculture of kelp focuses on three species: Alaria marginata, Nereocystis luetkeana, and Saccharina latissima. This study assessed the relative abundance of carbohydrates (glucan, mannitol, alginate, and fucoidan) in these species, as well as the sulfate content of fucoidan and …

Exploring The Population Structure And Genetic Diversity In Apple Germplasm Using Ipbs-Retrotransposon Markers, Aigul Madenova, Angsagan Kuan, Amjad Ali, Muhammad Azhar Nadeem, Muhammad Tanveer Altaf, Balnur Kabylbekova, Dinara Kaldybaeva, Ti̇mur Turdi̇yev, Faheem Shahzad Baloch

Turkish Journal of Botany

The apple (Malus domestica [Suckow] Borkh) is economically and culturally significant worldwide, thriving in temperate regions. This study examined genetic variations among 52 apple accessions from three research centers in Kazakhstan using the iPBS-retrotransposons marker system. Out of 35 screened markers, 12 highly polymorphic markers were selected for PCR amplification, resulting in 280 bands, 279 of which were polymorphic, yielding a 99.64% polymorphism rate. Genetic diversity indices showed substantial variation: effective number of alleles (ne=1.655), Shannon's information index (I=0.373), gene diversity (h=0.549), and an average genetic distance of 1.2. The analysis of molecular variance (AMOVA) indicated that 98.80% of the …

Role Of Sulfur Metabolism In Acquiring Of Boron Tolerance In Arabidopsis Thaliana, Seda Yi̇rmi̇beş, Ceyhun Kayihan, Nuran Çi̇çek, Yasemi̇n Ekmekçi̇

Turkish Journal of Botany

The purpose of this study was to assess whether sulfate applications (pre- and combined) caused the changes of tolerance against boron (B) toxicity in Arabidopsis thaliana at physiological, biochemical and molecular levels. Plants were germinated and grown on MS medium for 12 days, and then, sulfate pre-treatment groups (PS-B) were transferred to sulfate-containing media for 3 days. Subsequently, PS-B, combined (S+B) and un-treated application groups were transferred to medium containing 3 and 5 mM B for 10 days. Leaf area, plant biomass and total chlorophyll content decreased significantly depending on the accumulation of B. Toxic levels of B adversely affected …

Icc Agenda 12-17-24, Angela Brock

Individual Course Committee (ICC)

No abstract provided.

Completed Aa/As Degrees, Angela Brock

General Education Committee

No abstract provided.

Influence Of Loading Methods On Compression Modulus Of Red Sandstone Soil Solidified With Biological Enzyme And Cement, He Liang, Zhang Haixiang, Guan H Ongxin, Li Huili, Yang Hairong, Liu Hongfu

Journal of China & Foreign Highway

There are various methods to test the modulus of cement-stabilized mixtures.The stiffness performance of cement-stabilized materials will be affected after adding biological enzymes.In order to systematically analyze the influence of loading conditions on the compression modulus of the red sandstone soil solidified with biological enzyme and cement，compressive modulus tests were conducted on the red sandstone soil solidified with biological enzyme and cement by using three static modulus test methods including monotonic loading method of middle section，stepwise loading and unloading method of top surface，and stepwise loading and unloading method of middle section，as well as dynamic modulus method of top surface and …

The Pace Of Biological Aging Partially Explains The Relationship Between Socioeconomic Status And Chronic Low Back Pain Outcomes, Edwin N Aroke, Jai Ganesh Nagidi, Vinodh Srinivasasainagendra, Tammie L Quinn, Fiona B A T Agbor, Kiari R Kinnie, Hemant K Tiwari, Burel R Goodin

2020-Current year OA Pubs

INTRODUCTION: Having a lower socioeconomic status (SES) is a predictor of age-related chronic conditions, including chronic low back pain (cLBP). We aimed to examine whether the pace of biological aging mediates the relationship between SES and cLBP outcomes - pain intensity, pain interference, and physical performance.

METHODS: We used the Dunedin Pace of Aging Calculated from the Epigenome (DunedinPACE) software to determine the pace of biological aging in adults ages 18 to 85 years with no cLBP (n = 74), low-impact pain (n = 56), and high-impact pain (n = 77).

RESULTS: The mean chronological age of the participants was …

Clover (Clostridium Difficile Vaccine Efficacy Trial) Study: A Phase 3, Randomized Trial Investigating The Efficacy And Safety Of A Detoxified Toxin A/B Vaccine In Adults 50 Years And Older At Increased Risk Of Clostridioides Difficile Infection, Curtis J Donskey, Erik R Dubberke, Et Al.

2020-Current year OA Pubs

BACKGROUND: Clostridioides difficile infection (CDI) causes substantial mortality and healthcare burden. We assessed the detoxified toxin-A/B PF-06425090 vaccine for primary CDI prevention.

METHODS: This phase 3 observer-blinded study randomized (1:1) ≥50-year-olds at increased CDI risk (N = 17 535) to receive 3 PF-06425090 or placebo doses (0, 1, and 6 months). Primary end points were first CDI episode (≥3 unformed stools within 24 hours; central laboratory-confirmed toxin A/B positive) ≥14 days post-dose 3 (PD3; first primary) and post-dose 2 (PD2; second primary). CDI duration, need for CDI-related medical attention (secondary end points), and antibiotic use (post hoc analysis) PD3 were …