Digital Commons Network^™

Biophysical And X-Ray Structural Studies Of The (Gggtt)3ggg G-Quadruplex In Complex With N-Methyl Mesoporphyrin Ix, Linda Yingqi Lin , '20, S. Mccarthy, Barrett M. Powell , '18, Yanti Manurung , '20, Irene M. Xiang , '18, W. L. Dean, B. Chaires, Liliya A. Yatsunyk

Chemistry & Biochemistry Faculty Works

The G-quadruplex (GQ) is a well-studied non-canonical DNA structure formed by G-rich sequences found at telomeres and gene promoters. Biological studies suggest that GQs may play roles in regulating gene expression, DNA replication, and DNA repair. Small molecule ligands were shown to alter GQ structure and stability and thereby serve as novel therapies, particularly against cancer. In this work, we investigate the interaction of a G-rich sequence, 5’-GGGTTGGGTTGGGTTGGG-3’ (T1), with a water-soluble porphyrin, N-methyl mesoporphyrin IX (NMM) via biophysical and X-ray crystallographic studies. UV-vis and fluorescence titrations, as well as a Job plot, revealed a 1:1 binding stoichiometry with an …

The Positive And Negative Effects Of Photography On Wildlife, Joy Smith

Undergraduate Honors Theses

No abstract provided.

Malaria Parasite Plasmepsins: More Than Just Plain Old Degradative Pepsins, Armiyaw S. Nasamu, Alexander J. Polino, Eva S. Istvan, Daniel E. Goldberg

Open Access Publications

No abstract provided.

Assaying Three-Dimensional Cellular Architecture Using X-Ray Tomographic And Correlated Imaging Approaches, Peter O. Bayguinov, Max R. Fisher, James A. J. Fitzpatrick

Open Access Publications

No abstract provided.

Comprehensive Profiling Of Extracellular Rna In Hpv‑Induced Cancers Using An Improved Pipeline For Small Rna‑Seq Analysis, Fangjia Tong, Arlise Andress, Gongyu Tang, Ping Liu, Xiaowei Wang

Open Access Publications

No abstract provided.

Acvr1/Jak1/Jak2 Inhibitor Momelotinib Reverses Transfusion Dependency And Suppresses Hepcidin In Myelofibrosis Phase 2 Trial, Stephen T. Oh, Et Al.

Open Access Publications

No abstract provided.

Distribution, Density, Movement, And Support For Management Of Mountain Sucker, Pantosteus Jordani, In The Black Hills Of South Dakota, Seth J. Fopma

Electronic Theses and Dissertations

Mountain Sucker, Pantosteus jordani, is a cold-water species native to the Intermountain West. Fringe populations of Mountain Sucker have experienced declines in recent decades. The population of Mountain Sucker found in the Black Hills of South Dakota represents the eastern fringe of the species’ native range. Recognized as both an indicator of biologic health and as a species of greatest conservation need in South Dakota, recent studies have suggested significant declines in both distribution and abundance. Despite the recent study of Mountain Sucker in the region, increased understanding of Mountain Sucker ecology is needed to effectively manage for the conservation …

Profiling Transcription And Retrotransposition Of Mouse L1 Subfamilies, Lingqi Kong

Electronic Theses and Dissertations

Transposable elements, also called jumping genes, comprise almost 45% of the human genome. In contrast, only 1% of the human genome is protein-coding sequences. The function and advantages of maintaining such massive copies of transposable elements in the human genome are still unclear. Long interspersed element 1 (L1), the most substantial group and the only active autonomous transposable element in the human genome, has revealed its unique roles in many diseases. The insertional mutagenesis induced by L1 retrotransposition events could threaten human genomic stability and generate unexpected mutations. L1 overexpression has been documented in both somatic and germline cells and, …

Evaluating Prevalence And Mortality Of External Injuries On Loggerhead (Caretta Caretta) And Green (Chelonia Mydas) Sea Turtles In Florida, Usa, Aleah Marie Ataman

USF St. Petersburg campus Master's Theses (Graduate)

Anthropogenic threats, such as bycatch, boat strikes, and pollution, account for two to three times more sea turtle mortality events than natural causes. The goals of this study were to: (1) determine prevalence and cause of external traumatic injuries on nesting loggerhead sea turtles (Caretta caretta) in Juno Beach, Florida and (2) conduct an analysis of historical rehabilitation data from Florida Fish and Wildlife Conservation Commission (FWC) to calculate mortality of loggerhead and green (Chelonia mydas) turtles injured by boats. During the 2019 nesting season, 300 loggerheads were tagged and examined for external injuries. All injuries were categorized based on …

What's In My Histological Dyes Anyway?, Ashley Post

Undergraduate Honors Thesis Collection

There are many different dyes that are used for biological research, but not much is commonly known about the origins of the dyes or how they are synthesized. Our dyes of interest were Coomassie Blue G and Rhodamine B. Coomassie Blue G is a blue colored dye used mainly for SDS-PAGE (gel electrophoresis) in biological research. Rhodamine B is used for its ability to fluoresce under ultraviolet light. Both of these dyes have been used for research purposes for many years despite researchers who use the dyes not having little background knowledge regarding the purity of the manufactured dyes. We …

The Roles And Benefits Of Using Undergraduate Student Leaders To Support The Work Of Summit-P, Janet Bowers, Bryan D. Poole, Caroline Maher-Boulis, Ashley Schwartz, Angelica Bloomquist, Erica Slate Young

Journal of Mathematics and Science: Collaborative Explorations

The article by Poole, Turner, and Maher-Boulis (2020) describes one way in which undergraduates have been used to support the SUMMIT-P goal of investigating examples of how mathematics and statistics are applied in partner discipline courses. Two other universities in the SUMMIT-P consortium, San Diego State University and Oregon State University, also use undergraduates in different ways to support the work of integrating science applications into math classes. In this article, we compare and contrast these three uses to further highlight this somewhat untapped resource.

Feelings Of Incompleteness As Linking Obsessive-Compulsive Disorder And Autism Spectrum Disorder: An Examination Using A Computerized Approach-Avoidance Task, Sarah R. Lee

Graduate Research Theses & Dissertations

This dissertation examines the construct of incompleteness as it relates to both Obsessive-

Compulsive Disorder (OCD) and Autism Spectrum Disorder (ASD). Incompleteness is a

construct which was developed to describe symptoms of OCD which are not accounted for using

a traditional, harm-avoidance and fear-based conceptualization. Unlike harm-avoidance based

OCD, in which an individual engages in compulsions to prevent some feared outcome,

individuals with incompleteness-based OCD engage in compulsions to resolve an internal feeling

that their experience is uneven, asymmetrical, incomplete, or not-just-right.

Recently, researchers have begun to examine feelings of incompleteness in the context of

other disorders, such as ASD. …

Comparability Of Raman Spectroscopic Configurations: A Largescale Cross-Laboratory Study, Shuxia Guo, Hugh Byrne, Shiyamala Duraipandian, Fiona Lyng, Claudia Beleites, Ute Neugebauer

Articles

The variable configuration of Raman spectroscopic platforms is one ofthe major obstacles in establishing Raman spectroscopy as a valuable physicochemicalmethod within real-world scenarios such as clinical diagnostics. For such real worldapplications like diagnostic classification, the models should ideally be usable to predictdata from different setups. Whether it is done by training a rugged model with data frommany setups or by a primary-replica strategy where models are developed on a‘primary’setup and the test data are generated on‘replicate’setups, this is only possible if the Raman spectra from different setups are consistent, reproducible, and comparable.However, Raman spectra can be highly sensitive to the …

Spatially Fractionated Radiation Therapy: History, Present And The Future, Weisi Yan, Mohammad K. Khan, Xiaodong Wu, Charles B. Simone Ii, Jiajin Fan, Eric Gressen, Xin Zhang, Charles L. Limoli, Houda Bahig, Slavisa Tubin, Waleed F. Mourad

Department of Radiation Oncology Faculty Papers

No abstract provided.

Chemical Composition And Antimicrobial And Antioxidant Activity Of Helichrysum Italicum (Roth) G.Don Subspecies Essential Oils, Silviya Mollova, Hafize Fidan, Daniela Antonova, Dimitar Bozhilov, Stanko Stanev, Iliana Kostova, Albena Stoyanova

Turkish Journal of Agriculture and Forestry

The chemical composition and the antimicrobial and antioxidant activity of essential oils from two Helichrysum italicum (Roth) G.Don subspecies grown in Bulgaria were investigated. As a result, 95 compounds with concentrations above 0.05% were detected by GC/MS and 46 of them, mainly mono- and sesquiterpenes, representing 79.81% and 85.51% of the total content of the samples, were identified. The main constituents of the essential oil from Helichrysum italicum subsp. microphyllum (plant origin from Bosnia) were monoterpene α-pinene (20.84%) and sesquiterpene γ-curcumene (16.53%), followed by β-selinene (5.59%), ar-curcumene (4.39%), trans-caryophyllene (4.35%), β-diketone italidione I (4.32%), α-selinene (4.28%), and neryl acetate (3.81%). …

Bmp And Tgfß Use And Release In Bone Regeneration, Zeynep Bal, Junichi Kushioka, Joe Kodama, Takashi Kaito, Hideki Yoshikawa, Petek Korkusuz, Feza Korkusuz

Turkish Journal of Medical Sciences

A fracture that does not unite in nine months is defined as nonunion. Nonunion is common in fragmented fractures and large bone defects where vascularization is impaired. The distal third of the tibia, the scaphoid bone or the talus fractures are furthermore prone to nonunion. Open fractures and spinal fusion cases also need special monitoring for healing. Bone tissue regeneration can be attained by autografts, allografts, xenografts and synthetic materials, however their limited availability and the increased surgical time as well as the donor site morbidity of autograft use, and lower probability of success, increased costs and disease transmission and …

Hormonal Regulation Of Glycine Decarboxylase And Its Metabolic Outcomes, Ruta Milind Jog

Wayne State University Dissertations

The amino acid glycine is involved in generation of multiple critical metabolites including glutathione, heme, and creatinine. Interestingly, in both humans and rodents, circulating glycine levels are significantly reduced in obesity, glucose intolerance, type II diabetes and non-alcoholic fatty liver disease. The glycine cleavage system is the predominant glycine degradation pathway in humans. The rate-limiting enzyme of glycine cleavage system is glycine decarboxylase (GLDC), and loss-of-function mutations of GLDC cause hyperglycinemia. Here, we show that GLDC gene expression is upregulated in livers of mouse models of diabetes and diet-induced obesity as well as in the fasted state in normal animals. …

Polygenic Risk Score Analysis Revealed Shared Genetic Background In Attention Deficit Hyperactivity Disorder And Narcolepsy, Nagahide Takahashi, Tomoko Nishimura, Taeko Harada, Akemi Okumura, Damee Choi, Toshiki Iwabuchi, Hitoshi Kuwabara, Shu Takagi, Yoko Nomura, Jeffrey H. Newcorn, Nori Takei, Kenji J. Tsuchiya

Publications and Research

Attention deficit hyperactive disorder (ADHD) is a highly heritable neurodevelopmental disorder, and excessive daytime sleepiness is frequently observed in ADHD patients. Excessive daytime sleepiness is also a core symptom of narcolepsy and essential hypersomnia (EHS), which are also heritable conditions. Psychostimulants are effective for the symptomatic control of ADHD (primary recommended intervention) and the two sleep disorders (frequent off-label use). However, the common biological mechanism for these disorders has not been well understood. Using a previously collected genome-wide association study of narcolepsy and EHS, we calculated polygenic risk scores (PRS) for each individual. We investigated a possible genetic association between …

Development Of 3d Porous Chitosan-Based Platform For In Vitro Culture, Kailei Xu

Electronic Theses and Dissertations, 2020-2023

Three-dimensional (3D) cell cultures have been widely used in biological research since two-dimensional (2D) cultures have many limitations including alteration of cell morphology, metabolic pathways and gene expression. Therefore, the application of 2D cell cultures in pharmaceutical companies for drug screening causes reproducibility issues in animal studies, which strongly influences the efficiency of drug development. The aim of my studies is to develop 3D cell culture models to better mimic the extracellular matrix (ECM) in tumor microenvironment, not only for deeper understanding of interaction between cells and ECM, but also for the application in drug screening. Three different compositions of …

Life History Metrics Of Wahoo (Acanthocybium Solandri) From The Northern Gulf Of Mexico, Erik T. Lang, Chris A. Levron, Cijii D. Marshall, Brett J. Falterman

Gulf and Caribbean Research

Wahoo (Acanthocybium solandri) are highly sought in recreational and commercial fisheries in the Gulf of Mexico (GOM), yet the harvest of Wahoo is currently unmanaged in the GOM region outside of Florida waters. Life history metrics are critical to stock assessments and science-based management. Between 2014-2017, Louisiana Department of Wildlife and Fisheries (LDWF) biologists collected Wahoo otoliths and ovaries (n=198) from the northern GOM Wahoo recreational fishery based in Venice, LA to estimate life history metrics of age, growth, and maturity. A protocol was developed to section and age the small, fragile otoliths. A 2-parameter Von Bertalanffy growth …

Fluorescence Microscopy With Tailored Illumination Light, Jialei Tang

Electronic Theses and Dissertations, 2020-2023

Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from single molecule imaging to long-term observation of living organisms. While numerous fluorescence imaging techniques have been developed over the past decades, there is always an inevitable tradeoff among the spatial resolution, imaging speed, contrast, photodamage and the total cost when it comes to choose the appropriate microscope. A main goal of my dissertation research is to develop state-of-the-art microscope systems that exhibit unprecedented performance in …

Methods To Integrate Genetic And Clinical Data For Disease Subtyping, Diana Mabel Diaz-Herrera

Wayne State University Dissertations

Enormous efforts have been made to collect genetic and clinical data from cancer patients to advance the understanding of disease development and progression. Processing and analyzing these flows of data is challenging. Many computational methods have been proposed to help different fronts of biology and medicine. The integration of clinical and genetic data using computational methods towards personalized medicine is considered the future for oncology studies, and this thesis contributes in this direction. This thesis presents three new data integration approaches to elucidate granular and meaningful disease sub-types from high-dimensional complex genetic and clinical variables, which is an essential step …

Three-Dimensional Geometric Morphometric Sex Determination And Modeled Fragmentary Analysis Of The Human Pubic Bone, Katherine Scot Baca

Graduate Student Theses, Dissertations, & Professional Papers

Geometric morphometrics has become a more popular method in anthropology as three-dimensional data and research become more widely recognized and accessible. This research provides a refined method utilizing 3-D geometric morphometric analysis to determine sex from the human pubic bone. The study used a sample of N=378 individual pubic bones from the University of New Mexico Maxwell Documented Collection. Eight landmarks were digitized on each individual bone using a Microscribe Digitizer. Results from the Principal Components Analysis provide promising clustering between male and female groups, as well as indications that the method may be ancestry-specific, and that parity may have …

Efficacy Of Seaweed (Sargassum Sp.) Extract To Prevent Vibriosis In White Shrimp (Litopenaeus Vannamei) Juvenile, Indriyani Nur Mulyadi, Wa Iba

Fisheries, Animal and Veterinary Sciences Faculty Publications

Background and Objectives: Marine algae, especially brown algae (Sargassum sp.), is a natural compound plant capable of being prophylactic and immunostimulant. This study was aimed to evaluate the efficacy of seaweed (Sargassum sp.) extract to improve resistance and immune response of juvenile white shrimps (Litopenaeus vannamei ) infected by Vibrio algynolyticus .

Materials and Methods: The ethanolic extract of seaweed was used to evaluate its antibacterial effect by immerse the juvenile shrimp at a dose level of 0 (control), 150, 250 and 350 ppm for 3 h. Shrimp immune response was observed based on total haemocyte count (THC) and differential …

Chemical Investigations Of Pectic Oligosaccharides From Vaccinium Macrocarpon, Zhiyuan Peng

Open Access Master's Theses

Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are a serious problem worldwide, especially for females. Previous research in our laboratory suggests that cranberry pectic oligosaccharides (cPOS) can reverse dormant phenotypes in UPEC and therefore could prove useful in the prevention of recurrent UTIs. This thesis focused on the purification and structure determination of purified pectic oligosaccharides from cranberry hull extract. The research helped established the structures of cPOS, provided high purity materials for biological testing, and enabled further studies on the effect of different degrees of polymerization (DP) in preventing dormant phenotypes in UPEC. More specifically, cPOS …

Copper/N-Acetylcysteine Coated Iron Oxide Nanoparticles Synthesis, Characterization, And Antimicrobial Activities, Danya Belnour

Electronic Theses and Dissertations, 2020-2023

In recent years, there is a growing interest in developing metal based antimicrobial nanomaterials suitable for agricultural and biomedical applications. For centuries, Copper (Cu) biocide has been used for protecting a wide variety of crops from devastating bacterial and fungal diseases. However, prolonged and aggressive use of Cu led to the development of resistance and accumulation in soil. The latter has been linked to aquatic toxicity due to soil Cu leaching. Furthermore, copper build up in soil causes phytotoxicity and reduces uptake of micronutrient Zn through the root system. In biomedical field, Cu has been historically used as an antimicrobial …

How Landscape Change Affects Commercial And Recreational Fishermen’S Perceptions And Place Meanings, Talya Syvann Ten Brink

Open Access Dissertations

It is critical to plan for environmental change in order to mitigate its adverse effects on human wellbeing. This series of manuscripts examines the impacts of landscape change on commercial and recreational fishermen. Each manuscript provides a unique perspective on place meaning and place change. Using a mixed methods approach, data were collected and analyzed on fishermen’s perceptions of familiar places and on the changes that these places undergo. The first manuscript investigates the impact of offshore wind farms on commercial and recreational fishermen, using the first offshore wind farm in North America – the Block Island Wind Farm (Rhode …

Assessment Of Heat Stress For Outdoor Work Conditions In Saudi Arabia, Jamal Alanazi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Outdoor workers have an increased risk of heat stress in Saudi Arabia since it is one of the hottest places in the Middle East. Recently, the government decided to limit outdoor work hours during the months of June, July, and August every year, and banned working under the direct sunlight from 12:00 to 03:00 p.m., although outdoor workers in the petroleum, natural gas, or emergency maintenance work industries are exempt from this prohibition. Traditionally, the efforts by safety and health professionals to mitigate work-related heat injury has been directed toward the assessment of environmental heat stress (e.g., wet-bulb globe temperature), …

The Role Of Genotype In Saccharomyces Cerevisiae Resistance To 4-Methylcyclohexanemethanol, Michael C. Ayers

Graduate Theses, Dissertations, and Problem Reports (ETD)

The chemical 4-methylcyclohexanemethanol (MCHM) spilled in the Elk River near Charleston, WV in January 2014, impacting the drinking water of 300,000 residents. Initial studies on MCHM following the spill attempted to characterize its toxicological effects in animals, but largely ignored characterization of its effects on cellular pathways and metabolism. In this study, I used this chemical as a novel stressor for the model eukaryote S. cerevisiae to explore the relationship of genotype and stress phenotypes. Initial exploration characterized the stress phenotype of MCHM in yeast through growth assays, cell cycle analysis, and transcriptomic data. MCHM exposure caused cells to arrest …

Protein/Peptide Characterization Using Mass Spectrometry And Molecular Dynamics Simulations, Ahmad Kiani Karanji

Graduate Theses, Dissertations, and Problem Reports (ETD)

Mass spectrometry (MS) based-techniques and molecular dynamics (MD) simulations have been used to characterize protein/peptide structure as well as their interactions with lipid vesicles and detergents. Chapter 1 introduces an introduction to the concepts and tools that were used in this work. In Chapter 2, the dominant gas-phase conformer of [M+3H]3+ ions of the model peptide Acetyl-PSSSSKSSSSKSSSSKSSSSK are examined with ion mobility spectrometry (IMS), gas-phase hydrogen deuterium exchange (HDX), and mass spectrometry (MS) techniques. This section furthers the development of a protein structural prediction tool by providing information about gas-phase ion conformers of two model peptides having different solution conformational …