Biology Commons^™

X-Linked Ubiquitin-Specific Peptidase 11 Increases Tauopathy Vulnerability In Women, Yan Yan

USF Tampa Graduate Theses and Dissertations

Women experience significantly higher tau burden and increased risk for Alzheimer’s disease (AD) than men, yet the underlying mechanism for this vulnerability has not been explained. Here, we demonstrate through in vitro and in vivo models, as well as human AD brain tissue, that X-linked ubiquitin specific peptidase 11 (USP11) augments pathological tau aggregation via tau deubiquitination initiated at lysine-281. Removal of ubiquitin provides access for enzymatic tau acetylation at lysines 281 and 274. USP11 escapes complete X-inactivation, and female mice and people both exhibit higher USP11 levels than males. Genetic elimination of usp11 in a tauopathy mouse model preferentially …

Speciation Jigsaw Activity, Erika Crispo

Open Educational Resources

What is a species? Why are there so many species on the planet? The question of why we have different species of organisms was the key thesis of Charles Darwin’s most famous book, On the Origin of Species.While several definitions of what constitutes a species exists, the most common definition lies within thebiological species concept. This concept states that different species exist when two individuals of different sexes are unable to reproduce with one another to yield viable offspring in the wild. A major limitation of this definition is that it can only be applied to sexually reproducing organisms that …

Seqcode: A Nomenclatural Code For Prokaryotes Described From Sequence Data, Brian P. Hedlund, Maria Chuvochina, Philip Hugenholtz, Konstantinos T. Konstantinidis, Alison E. Murray, Marike Palmer, Donovan H. Parks, Alexander J. Probst, Anna-Louise Reysenbach, Luis M. Rodriguez-R, Ramon Rossello-Mora, Iain C. Sutcliffe, Stephanus N. Venter, William B. Whitman

Life Sciences Faculty Research

Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and …

Circadian Clock Controls Rhythms In Ketogenesis By Interfering With Ppar Alpha Transcriptional Network, Volha Mezhnina, Oghogho P. Ebeigbe, Nikkhil Velingkaar, Allan Poe, Yana I. Sandlers, Roman Kondratov

Biological, Geological, and Environmental Faculty Publications

Ketone bodies are energy-rich metabolites and signaling molecules whose production is mainly regulated by diet. Caloric restriction (CR) is a dietary intervention that improves metabolism and extends longevity across the taxa. We found that CR induced high -amplitude daily rhythms in blood ketone bodies (beta-hydroxybutyrate [beta OHB]) that correlated with liver beta OHB level. Time-restricted feeding, another periodic fasting-based diet, also led to rhythmic beta OHB but with reduced amplitude. CR induced strong circadian rhythms in the expression of fatty acid oxidation and ketogenesis genes in the liver. The transcriptional factor peroxisome-proliferator-activated-receptor alpha (PPAR alpha) and its transcriptional target hepatokine …

Generation Of Mycobacterium Smegmatis Model Systems For Testing Inhibitors Of The Mycobactin Siderophore Of Mycobacterium Tuberculosis, Gabrielle A. Germain

Dissertations, Theses, and Capstone Projects

Mycobacterium tuberculosis (Mtb) is the pathogenic bacterium causative of tuberculosis. According to the 2021 World Health Organization (WHO) Global Tuberculosis (TB) Report, there were approximately 5.8 million TB cases in 2020, and 1.3 million TB deaths among HIV negative people in that year. The rise of multi-drug resistant Mtb strains has increased the need for more potent microbials against this pathogen. Biosynthesis of iron scavenging molecules, known as siderophores (e.g., mycobactin and carboxymycobactin), has been identified as a potential drug target candidate since iron acquisition has been directly linked to the survival and virulence of Mtb. Salicyl-AMS (Sal-AMS) is …

Arabidopsis Shoot Gravitropism Requires The Mediator Coactivator Complex, Gabriella Newton

Honors Theses

Gravitropism is a plant response to gravity in directing the growth of its organs, such as the root and the stem. Gravity is sensed by statocytes, unique cells that contain starch-filled amyloplasts, which trigger gravitropic growth response by modulating the distribution of growth hormone auxin in the elongation zone of the stem and root. Despite the fact that multiple factors have been identified as key regulators of shoot negative gravitropism, how these factors are regulated at the transcriptional level is largely unknown. In this study, we explore the role of transcriptional machinery in regulating shoot gravity sensing and responses by …

Identification Of Secondary Structural Elements Contained Within The Intrinsically Disordered N-Terminal Tail Of The Bloom’S Syndrome Helicase., Vivek Somasundaram

USF Tampa Graduate Theses and Dissertations

The Bloom’s Syndrome Helicase (BLM) is one of five human RecQ helicases and is necessary for maintenance of genome stability. Whilst a crystal structure exists for the C-terminal domain of BLM, very limited structural knowledge is known about the intrinsically disordered N-terminal tail. This lack of insight exists, despite the fact that the N-terminus of BLM is essential for the overall biological activity of BLM. Here we provide an Nuclear Magnetic Resonance spectroscopy based approach that we used to identify two distinct ⍺-helices contained within the first 100 residues of BLM. In addition, we propose a mutagenesis-based approach involving rationally …

Intermediates In Sars-Cov-2 Spike–Mediated Cell Entry, Tara C. Marcink, Thomas Kicmal, Emily Armbruster, Zhening Zhang, Gillian Zipursky, Kate L. Golub, Mohab Idris, Jonathan Khao, Jennifer Drew-Bear, Gael Mcgill, Tom Gallagher, Matteo Porotto, Amédée Des Georges, Anne Moscona

Advanced Science Research Center

SARS-CoV-2 cell entry is completed after viral spike (S) protein–mediated membrane fusion between viral and host cell membranes. Stable prefusion and postfusion S structures have been resolved by cryo–electron microscopy and cryo–electron tomography, but the refolding intermediates on the fusion pathway are transient and have not been examined. We used an antiviral lipopeptide entry inhibitor to arrest S protein refolding and thereby capture intermediates as S proteins interact with hACE2 and fusion-activating proteases on cell-derived target membranes. Cryo–electron tomography imaged both extended and partially folded intermediate states of S2, as well as a novel late-stage conformation on the pathway to …

Ewing Sarcoma Transcriptome: Identification Of Foxn3 As A Novel Target Of Ews-Fli1, Natasha Kreiling

Theses & Dissertations

Ewing Sarcoma is an aggressive cancer characterized by a fusion gene formed from a chromosomal translocation between a RNA binding protein and a transcription factor. The most common fusion gene is EWS-FLI1 a potent oncogenic transcription factor responsible for initiating genome instability. EWS-FLI1 promotes tumor growth by dysregulating several genes and pathways. We have identified FOXN3, an important gene in cell cycle control and development, as being suppressed by EWS-FLI1. In the future, a better understanding of FOXN3 and its ability to act as a tumor suppressor in EWS will unravel novel mechanisms of EWS pathogenesis, potential biomarker and drug …

N6-Methyladenosine Rna Modifications In Myogenesis / Narrative Competence And Cognitive Mapping As A Culturally Sustaining Pedagogy In The Education Of Emergent Bilinguals, Marina Danielle Infantado

Legacy Theses & Dissertations (2009 - 2024)

Myogenesis involves skeletal muscle stem cells (MuSCs) that produce and regenerate skeletal muscle during regular growth and repair. However, when this system fails to function normally, it can lead to musculoskeletal diseases like Duchenne Muscular Dystrophy (DMD). Therefore, it is important to study the molecular mechanisms behind this developmental process in order to seek therapies and solutions for these types of diseases. Our interest lies in the field of epitranscriptomics, which focuses on post-transcriptional ribonucleic acid (RNA) modifications, particularly N6-methyladenosine (m6A), which involves the addition of a methyl group to the adenosine nucleotide, a process that is mediated by the …

Parallel Networks That Govern The Transcriptional Response To Stress, Serene Anne Durham

Legacy Theses & Dissertations (2009 - 2024)

The transcription factor, p53, plays a pivotal role in the oversight of many stimulus-dependent pathways. Its ability to respond to a wide variety of cellular stress stimuli by activating a broad range of target genes has led it to be characterized as a stress-dependent transcription factor. Our research focuses on deconvoluting the varied transcriptional response to distinct stress signals in an attempt to define the regulatory strategies leading to gene activation after cell stress. We have found that distinct stress response networks, some of which are p53-independent, are converging at activation of a common set of target genes. Our data …

Hsp- 70 Mediated Nervous System Enhancement By Etas, Taylor Carter

Theses (2016-Present)

Neurodegenerative disease in the CNS is usually a product of increased oxidative stress in the brain. In this study we tested the ability of an asparagus supplement ETAS to help reduce oxidative stress in the normal brains of Balb C mice. Oxidative stress pathways (Heat shock proteins) are usually cumulative in the damage they cause when disrupted. We treated normal Balb C mice with ETAS and had control groups with no ETAS supplementation in their regular diet. We then sacrificed the mice and conducted microarray studies to compare oxidative stress pathway genes. We also characterized the effects of regular oxidative …

College Of Natural Sciences Newsletter, July & August 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 5

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Resources for Student Success
Page 4 Welcome to New Faculty & Staff
Page 5 Summer Activities in CNS
Page 9 Celebrating the lives of those who touched the College
Page 10 Media Coverage of CNS
Page 12 Open PRAIRIE Data
Page 13 Snaps from he start of the semester
Page 14 Science as Art Competition

Development Of A Ph-Triggered Cargo Delivery System With Esxa Mutants, Shuchen Chen

Open Access Theses & Dissertations

Tuberculosis (TB) is a communicable disease caused by Mycobacterium tuberculosis (Mtb). It was the leading cause of human death generated by a single infectious agent before the Coronavirus (COVID-19) pandemic. Mtb has a special mechanism to evade the hostâ??s immune system and utilize macrophages as reservoirs. Latent TB infections have been a threat to public health. Liposome has been widely used for drug delivery. Immunoliposomes are special liposome carriers coated with ligands, such as antigens, targeting certain cells or organs to regulate the uptake of liposome. By constructing the liposome components, or surface modification, cargo release of liposome can be …

Eluication Of Lipid Metabolic Pathways In Differentiating Giardia Lamblia Using High Resolution Mass Spectrometry, Cameron Ellis

Open Access Theses & Dissertations

Giardia lamblia is an intestinal protozoan found worldwide, including the U.S. This parasite exists in two morphologic stages - a replicative trophozoite and a relatively dormant yet viable cyst. While exposures of cysts to gastric acid during passage through the human stomach induces excystation, factors in the small intestine, where trophozoites colonize trigger encystation or cyst formation. Transformation into cyst stage is essential for Giardia to survive in the environment for months before infecting new hosts. Because of its small genome size (11.7 Mb), metabolic pathways in Giardia are highly reduced. As far as lipid metabolism is concerned, only limited …

Mtorc1 And Mtorc2 Complexes Regulate The Untargeted Metabolomics And Amino Acid Metabolites Profile Through Mitochondrial Bioenergetic Functions In Pancreatic Beta Cells, Ghada A. Soliman, Rinat Abzalimov, Ye He

Advanced Science Research Center

Background: Pancreatic beta cells regulate bioenergetics efficiency and secret insulin in response to glucose and nutrient availability. The mechanistic Target of Rapamycin (mTOR) network orchestrates pancreatic progenitor cell growth and metabolism by nucleating two complexes, mTORC1 and mTORC2. Objective: To determine the impact of mTORC1/mTORC2 inhibition on amino acid metabolism in mouse pancreatic beta cells (Beta-TC-6 cells, ATCC-CRL-11506) using high-resolution metabolomics (HRM) and live-mitochondrial functions. Methods: Pancreatic beta TC-6 cells were incubated for 24 h with either: RapaLink-1 (RL); Torin-2 (T); rapamycin (R); metformin (M); a combination of RapaLink-1 and metformin (RLM); Torin-2 and metformin (TM); compared to the control. …

Leafing Through Literature: Late Embryogenesis Abundant Proteins Coming Of Age – Achievements And Perspectives, Itzell E. Hernandez-Sanchez, Israel Maruri Lopez, Coral Martinez-Martinez, Brett Janis, Juan Francisco Jimenez Bremont, Alejandra A. Covarrubias, Michael A. Menze, Steffen P. Graether, Anja Thalhammer

Faculty and Staff Scholarship

To deal with increasingly severe periods of dehydration related to global climate change, it becomes increasingly important to understand the complex strategies many organisms have developed to cope with dehydration and desiccation. While it is undisputed that late embryogenesis abundant (LEA) proteins play a key role in the tolerance of plants and many anhydrobiotic organisms to water limitation, the molecular mechanisms are not well understood. In this review we recap the current knowledge of the physiological roles of LEA proteins and discuss their potential molecular functions. As these are ultimately linked to conformational changes in the presence of binding partners, …

Regulation Of The Heat Shock Response Via Lysine Acetyltransferase Cbp-1 And In Neurodegenerative Disease In Caenorhabditis Elegans, Lindsey N. Barrett

USF Tampa Graduate Theses and Dissertations

The decline of proteostasis is a hallmark of aging that is, in part, affected by the dysregulation of the heat shock response (HSR), a highly conserved cellular response to proteotoxic stress in the cell. The heat shock transcription factor HSF-1 is well-studied as a key regulator of proteostasis, but mechanisms that could be used to modulate HSF-1 function to enhance proteostasis during aging are largely unknown. In this study, we examined lysine acetyltransferase regulation of the HSR and HSF-1 in C. elegans. We performed an RNA interference screen of lysine acetyltransferases and examined mRNA expression of the heat-shock inducible gene …

Increasing The Resilience Of Plant Immunity To A Warming Climate, Jong Hum Kim, Christian Castroverde, Shuai Huang, Chao Li, Richard Hilleary, Adam Seroka, Reza Sohrabi, Diana Medina-Yerena, Bethany Huot, Jie Wang, Sharon Marr, Mary Wildermuth, Tao Chen, John Macmicking, Sheng Yang He

Biology Faculty Publications

Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone, is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism. Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B (phyB) and EARLY FLOWERING 3 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates (GDACs) …

College Of Natural Sciences Newsletter, May & June 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 4

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3-4 The path to a Doctorate Degree
Page 4 American Indian Student Center Native Graduate Honoring Ceremony
Page 5 Celebrating the lives of those who touched the College
Page 6 Media coverage of CNS
Page 7 Open PRAIRIE
Page 8-10 CNS Graduation Festivities
Page 11-14 Spring 2022 Dean's List
Page 16 Richard and Janice Vetter Endowed Professorship in Biotechnology.position

Optimization Of Palmitic Acid Production In Chloroidium Sp. Utex 3007 As A Sustainable Source Of Palm Oil Alternative, Amnah Salem Alzahmi

Theses

The increase in palm oil consumption and production has resulted in removing up to 90% of trees in some tropical forests. The green microalgae Chloroidium sp. UTEX 3007 can be an alternative sustainable source of palm oil due to its high palmitic acid content. The objective of this study was to generate a mutant Chloroidium population that is capable of producing and accumulating elevated levels of palmitic acid and to characterize the obtained populations’ lipid contents. The palmitic acid production optimization in Chloroidium sp. UTEX 3007 was conducted via a workflow of ultraviolet (UV) mutagenesis and sorting of high-lipid producing …

Bodipy-Based Light-Responsive Materials, Zhaoxiong Wan

Dissertations

The energy required for life on our planet is provided by light. In science, light is an important and powerful tool for measuring and modifying substances. For example, under the effect of illumination, light-responsive materials can change their physical and chemical properties. Photochemistry is a branch of research to study the effects of light irradiation on chemical structures and reactions. Some photochemical changes could lead to chemical bond dissociation (such as in photosynthesis) and structure isomerization (such as in the retina). Photochemistry has a strong relationship with human lives and it is essential in many ways. Among photophysics, fluorescence emission …

The Effects Of Aging On Wound Healing And Limb Regeneration In The Axolotl, Hande Sahin

Graduate Masters Theses

The Mexican axolotl is capable of regenerating various parts of its body and maintains this capacity throughout its entire life. Although this ability is sustained through adulthood, multiple regenerative processes appear to be negatively affected by aging. Here, we focus on evaluating the effect of aging on the rate of wound healing and limb regeneration. We have developed new in vivo, and ex vivo assays to characterize wound healing and identify differences between young and aged animals during this process. We have also characterized morphological features of mature skin from both groups of animals and although there are no obvious …

Du Undergraduate Showcase: Research, Scholarship, And Creative Works: Abstracts, Emma Aggeler, Elena Arroway, Daisy T. Booker, Justin Bravo, Kyle Bucholtz, Megan Burnham, Nicole Choi, Spencer Cockerell, Rosie Contino, Jackson Garske, Kaitlyn Glover, Caroline Hamilton, Haley Hartmann, Madalyne Heiken, Colin Holter, Leah Huzjak, Alyssa Jeng, Cole Jernigan, Chad Kashiwa, Adelaide Kerenick, Emily King, Abigail Langeberg, Maddie Leake, Meredith Lemons, Alec Mackay, Greer Mckinley, Ori Miller, Guy Milliman, Katherine Miromonti, Audrey Mitchell, Lauren Moak, Megan Morrell, Gelella Nebiyu, Zdenek Otruba, Toni V. Panzera, Kassidy Patarino, Sneha Patil, Alexandra Penney, Kevin Persky, Caitlin Pham, Gabriela Recinos, Mary Ringgenberg, Chase Routt, Olivia Schneider, Roman Shrestha, Arlo Simmerman, Alec Smith, Tessa Smith, Nhi-Lac Thai, Kyle Thurmann, Casey Tindall, Amelia Trembath, Maria Trubetskaya, Zachary Vangelisti, Peter Vo, Abby Walker, David Winter, Grayden Wolfe, Leah York

DU Undergraduate Research Journal Archive

Abstracts from the DU Undergraduate Showcase.

A Review Of Current Methods In Avian Dietary Analysis And Their Integrated Application To Characterize The Trophic Niche Of Louisiana Waterthrush (Parkesia Motacilla)., Brandon Hoenig

Electronic Theses and Dissertations

Characterizing a species’ dietary composition presents an avenue to understand many facets of its ecological niche and can provide essential information for the species’ long-term conservation. To date, the vast majority of diet studies have relied on direct identification of prey during foraging observations or from diet samples to characterize the dietary habits of birds. However, advancements in laboratory-based approaches have revolutionized the field of trophic ecology by allowing researchers to indirectly infer dietary habits with higher resolution across greater time scales. Here, I apply two of these laboratory-based techniques, namely DNA metabarcoding and stable isotope analysis, to characterize the …

Determining The Distribution Of Elemental Compounds And Oxidative Potential Across Fine Particulate Matter (Pm2.5) Filters, Allie Michelle Sidwell

Honors Theses

Fine particulate matter (PM_2.5) is a complex mixture of particles and sorbed chemicals that poses serious, adverse effects on human health such as increasing cardiovascular and respiratory morbidity and mortality. There is ongoing research into the impacts of PM_2.5 of differing chemical compositions, sampling location, and the mechanisms for the observed health effects. To conduct these analytical and toxicology studies of PM_2.5, researchers often split filters into sections. This process allows multiple, often destructive, assays to be performed. Our previous research showed chemical composition differences across PM_2.5 filters. The goal of our study was …

Development And Analysis Of Next-Generation Polymeric And Bio-Ceramic Based Orthopedic Scaffolds By Advanced Manufacturing Techniques, Sudeep K. Gummadi

ETD Archive

Gliomas express mutant isocitrate dehydrogenases producing excessive amounts of D 2-hydroxyglutarate (D2HG) and releasing some of it into the environment. The immune surveillance is reduced as a result, however, the mechanisms behind lymphocyte suppression by the D2HG stereoisomer remain unknown. I incubated Jurkat T cells with D2HG at concentrations present within and surrounding gliomas, or its obverse L2HG stereoisomer, and quantified 2HG isomers within washed cells by TSPC derivatization with stable isotope-labeled D2HG and L2HG internal standards, HPLC separation, and mass spectrometry. D2HG was found in quiescent cells in double the amount of L2HG. External D2HG or L2HG increased the …

Evaluation Of Diaphragmatic Movement In The Respiratory System Of An Emphysema Patient, Aubri Ford

Honor’s College Freeman Research Journal

Respiration is an essential part of life. The diaphragm is the main muscle involved in the process of respiration. However, respiratory diseases such as emphysema alter the function of the diaphragm which sometimes leads to respiratory failure and death. This review compiles studies concerning emphysema and how the morphological changes in the lungs (i.e. hyperinflation) caused by the disease affect the diaphragm. The first major point covers the risks associated with developing the disease as a component of Chronic Obstructive Pulmonary Disease (COPD). Next, the paper outlines the pathophysiology of emphysema within the lungs, the methods used to diagnose emphysema, …

Time Course Investigation Of The Dermal Leukocyte Response To Lipoteichoic Acid In Chickens, Ian Gilbert

Animal Science Undergraduate Honors Theses

Lipoteichoic acid (LTA) is component of the cell wall of Gram-positive bacteria that stimulates inflammation during bacterial infection. However, few studies have investigated the in vivo immune response to LTA, and none of the in vivo studies done have been performed in birds. For this project, the pulp (a skin-derivative) of growing feathers (GFs) of chickens were used as a test site to investigate the in vivo effects of intradermally injected LTA. In Study 1, the pulp of 12 GFs of 11-week-old Light-brown Leghorn (LBL) males were injected with 10 μL of differing concentrations of LTA (0.1, 1.0, 10, 100 …

Characterization Of Fgf1/Fgf2 Heterodimer With Mutation R136e, Brett Haley

Biological Sciences Undergraduate Honors Theses

Fibroblast growth factors are a family of heparin binding proteins that are involved in a broad spectrum of physiological functions, such as angiogenesis, cell proliferation, cell differentiation, and wound healing. Fibroblast growth factor 1 (FGF-1) is a member of the FGF superfamily and can bind universally to fibroblast growth factor receptors. Fibroblast growth factor 2 (FGF-2) is similar in structure to FGF-1 but has been shown to have a potent effect on angiogenesis. A physiologically stable dimerization of these two growth factors could prove to induce desirable effects in the instance of wound healing. In this study, we have designed …