Molecular Biology Commons^™

Dysfunction Of Polyamine Metabolism In Down Syndrome Related To Cellular Senescence And Β-Amyloid Production, Andres D. Sola

Electronic Theses and Dissertations

Polyamines (PA) are ubiquitous in cells and highly involved in several important cellular functions and thus the dysregulation of their biosynthetic pathway is potentially associated with the progression of age-related diseases like Alzheimer’s’ disease (AD). Though there is research describing how PA content changes in organisms as they age or in those experiencing rapid aging from increased rates of senescence, as in Down syndrome (DS), it is not clear how this connection occurs and whether modulating this pathway may reveal downstream effects on related disease progression. This study examines how the modulation of the PA biosynthetic pathway by inhibition of …

Evaluating Human Plasma Biomakers For Alzheimer's Disease; Phosphorylated-Tau 217, Phosphorylated-Tau 181, And Glial Fibrillary Acidic Protein, Mason Jonah, Mayarae N. Mugosa, Bella Hou, Emma-Nikole Krilchev, Zhengshi Yang, Dietmar Cordes, Aaron Ritter, Jefferson W. Kinney

Undergraduate Research Symposium Posters

Alzheimer’s Disease (AD) is a progressive neurodegenerative disease that is primarily identifiable by amyloid-beta (Aβ) neuronal plaques, neurofibrillary tangles (NFT) that form as aggregates of hyperphosphorylated tau (ptau) proteins clump together, and the presence of neuroinflammation; all of which are otherwise known as the hallmarks of AD pathology. Recent emerging research has discovered striking similarities between AD and diabetes mellitus pathology, illustrating how insulin deficiency and insulin resistance–both of which result in the chronic hyperglycemic state seen in the diabetic–are involved in an increase in the phosphorylation of tau. This leads to and intensifies the formation of intracellular NFTs serving …

Therapeutic Potential Of Astrocyte-Derived Extracellular Vesicles In Mitigating Cytotoxicity And Transcriptome Changes In Human Brain Endothelial Cells, Ruth Juliana Stewart

Doctoral Dissertations

Extracellular vesicles (EVs) play a major role in cell-to-cell communication via the horizontal transfer of RNA, DNA, proteins, and lipids that affect the physiological response of the recipient cells. Astrocytes are a type of glial cell that exerts a protective effect on neurons and brain endothelial cells. The astrocytes and the endothelial cells form the blood-brain barrier. Due to their nano-size and non-complex structure, EVs can efficiently cross the blood-brain barrier. This study investigated and assessed the impact of EVs on reducing oxidative DNA damage in human brain endothelial cells (HBECs). The protective potential of astrocyte-derived EVs was determined by …

Genome-Guided Isolation Of The Hyperthermophilic Aerobe Fervidibacter Sacchari Reveals Conserved Polysaccharide Metabolism In The Armatimonadota, Nancy O. Nou, Jonathan K. Covington, Dengxun Lai, Xavier Mayali, Cale O. Seymour, Juliet Johnston, Jian-Yu Jiao, Steffen Buessecker, Damon Mosier, Alise R. Muok, Nicole Torosian, Allison M. Cook, Ariane Briegel, Tanja Woyke, Emiley Eloe-Fadrosh, Nicole Shapiro, Scott G. Bryan, Savannah Sleezer, Joshua Dimapilis, Cristina Gonzalez, Lizett Gonzalez, Marlene Noriega, Matthias Hess, Ross P. Carlson, Lan Liu, Meng-Meng Li, Zheng-Han Lian, Siqii Zhu, Fan Liu, Xian Sun, Beile Gao, Ritesh Mewalal, Miranda Harmon-Smith, Ian K. Blaby, Jan-Fang Cheng, Peter K. Weber, Gabriela Grigorean, Wen-Jun Li, Anne E. Dekas, Jennifer E. Pett-Ridge, Jeremy A. Dodsworth, Marike Palmer, Brian P. Hedlund

Life Sciences Faculty Research

Few aerobic hyperthermophilic microorganisms degrade polysaccharides. Here, we describe the genome-enabled enrichment and optical tweezer-based isolation of an aerobic polysaccharide-degrading hyperthermophile, Fervidibacter sacchari, previously ascribed to candidate phylum Fervidibacteria. F. sacchari uses polysaccharides and monosaccharides for growth at 65–87.5 °C and expresses 191 carbohydrate-active enzymes (CAZymes) according to RNA-Seq and proteomics, including 31 with unusual glycoside hydrolase domains (GH109, GH177, GH179). Fluorescence in-situ hybridization and nanoscale secondary ion mass spectrometry confirmed rapid assimilation of 13C-starch in spring sediments. Purified GHs were optimally active at 80–100 °C on ten different polysaccharides. Finally, we propose reassigning Fervidibacteria as a class …

Viral Genome Delivery Across Bacterial Cell Surfaces, Stephano M. Iglesias, Fenglin Li, Federica Briani, Gino Cingolani

Department of Biochemistry and Molecular Biology Faculty Papers

In 1952, Hershey and Chase used bacteriophage T2 genome delivery inside Escherichia coli to demonstrate that DNA, not protein, is the genetic material. Over 70 years later, our understanding of bacteriophage structure has grown dramatically, mainly thanks to the cryogenic electron microscopy revolution. In stark contrast, phage genome delivery in prokaryotes remains poorly understood, mainly due to the inherent challenge of studying such a transient and complex process. Here, we review the current literature on viral genome delivery across bacterial cell surfaces. We focus on icosahedral bacterial viruses that we arbitrarily sort into three groups based on the presence and …

Repeated Shifts In Sociality Are Associated With Fine-Tuning Of Highly Conserved And Lineage-Specific Enhancers In A Socially Flexible Bee, Beryl M. Jones, Andrew E. Webb, Scott M. Geib, Sheina Sim, Rena M. Schweizer, Michael G. Branstetter, Jay D. Evans, Sarah D. Kocher

Entomology Faculty Publications

Comparative genomic studies of social insects suggest that changes in gene regulation are associated with evolutionary transitions in social behavior, but the activity of predicted regulatory regions has not been tested empirically. We used self-transcribing active regulatory region sequencing, a high-throughput enhancer discovery tool, to identify and measure the activity of enhancers in the socially variable sweat bee, Lasioglossum albipes. We identified over 36,000 enhancers in the L. albipes genome from 3 social and 3 solitary populations. Many enhancers were identified in only a subset of L. albipes populations, revealing rapid divergence in regulatory regions within this species. Population-specific enhancers …

The Divergent Responses Of Salinity Generalists To Hyposaline Stress Provide Insights Into The Colonisation Of Freshwaters By Diatoms, Kathryn J. Judy, Eveline Pinseel, Kala M. Downey, Jeffrey A. Lewis, Andrew J. Alverson

Biological Sciences Faculty Publications and Presentations

Environmental transitions, such as the salinity divide separating marine and fresh waters, shape biodiversity over both shallow and deep timescales, opening up new niches and creating opportunities for accelerated speciation and adaptive radiation. Understanding the genetics of environmental adaptation is central to understanding how organisms colonise and subsequently diversify in new habitats. We used time-resolved transcriptomics to contrast the hyposalinity stress responses of two diatoms. Skeletonema marinoi has deep marine ancestry but has recently invaded brackish waters. Cyclotella cryptica has deep freshwater ancestry and can withstand a much broader salinity range. Skeletonema marinoi is less adept at mitigating even mild …

Engineering The Coherent Phonon Transport In Polar Ferromagnetic Oxide Superlattices, In Hyeok Choi, Seung Gyo Jeong, Do-Gyeom Jeong, Ambrose Seo, Woo Seok Choi, Jong Seok Lee

Chemical and Materials Engineering Faculty Publications

Artificial superlattices composed of perovskite oxides serves as an essential platform for engineering coherent phonon transport by redefining the lattice periodicity, which strongly influences the lattice-coupled phase transitions in charge and spin degrees of freedom. However, previous methods of manipulating phonons have been limited to controlling the periodicity of superlattice, rather than utilizing complex mutual interactions that are prominent in transition metal oxides. In this study on oxide superlattices composed of ferromagnetic metallic SrRuO3 and quantum paraelectric SrTiO3 , phonon modulation by controlling the geometry of superlattice in atomic-scale precision is realized, demonstrating the coherent phonon engineering using structural and …

Diverse Pathways In Gpcr-Mediated Activation Of Ca2+ Mobilization In Hek293 Cells, Francesco De Pascali, Asuka Inoue, Jeffrey L. Benovic

Department of Biochemistry and Molecular Biology Faculty Papers

G protein-coupled receptors transduce extracellular stimuli into intracellular signaling. Ca²⁺ is a well-known second messenger that can be induced by G protein-coupled receptor activation through the primary canonical pathways involving Gα_q- and Gβγ-mediated activation of phospholipase C-β (PLCβ). While some G_s-coupled receptors are shown to trigger Ca²⁺ mobilization, underlying mechanisms remain elusive. Here, we evaluated whether G_s-coupled receptors including the β₂-adrenergic receptor (β₂AR) and the prostaglandin EP₂ and EP₄ receptors (EP₂R and EP₄R) that are endogenously expressed in human embryonic kidney 293 …

The Effect Of Nerolidol On The Renal Dysfunction Following Bilateral Ureteral Obstruction In The Rat, Harun Rashed Toumi

Theses

This thesis addressed nerolidol’s potential therapeutic and protective effects on bilateral ureteral obstruction-induced uropathy in rats. Obstructive uropathy stands as a notable contributor to acute kidney injury (AKI), accounting for 5-10% of all AKI cases worldwide, with a particularly high prevalence among the elderly, constituting 22% of AKI cases in this age group. Urinary tract obstruction, often attributed to factors such as kidney stones, urinary tract deformities and benign/malignant growths such as benign prostatic hyperplasia (BPH) in older men can lead to detrimental outcomes if left untreated, potentially progressing to kidney failure and even mortality. The severity of the kidney …

A Phenotypic Characterization Of Staphylococcus Aureus Bacteremia Clinical Isolates, Sara Dj Daniels

USF Tampa Graduate Theses and Dissertations

Staphylococcus aureus is a human pathogen of serious concern because of its ability to cause serious and wide-ranging disease. Of particular concern is the ability of S. aureus to cause bacteremia (SAB), allowing the bacteria to disseminate and spread to various organs. This study addressed this issue through the phenotypic characterization of two methicillin-resistant S. aureus (MRSA) clinical isolates taken from patients with sustained complicated bacteremia at Tampa General Hospital, referred to as SA1097 and SA1098. A battery of phenotypic tests was conducted on these strains, including a growth curve, hemolysis and proteolysis screenings, cytotoxicity assays using human neutrophils, blood …

Rictor, A Mtorc2 Protein, Regulates Lymphatic Valve Formation And Maintenance Through The Akt-Foxo1 Signaling Axis, Richa Banerjee

USF Tampa Graduate Theses and Dissertations

The lymphatic vasculature maintains tissue fluid homeostasis by absorbing interstitial fluid to form lymph and transporting it back to the bloodstream. Collecting lymphatic vessels have lymphatic valves (LVs) that prevent the retrograde flow of lymph generated by hydrostatic pressure from the blood vasculature. Backflow and accumulation of lymph leads to a lymphatic pathology called lymphedema. This implicates the involvement of defective LVs in the pathogenesis of lymphedema and warrants the study of lymphatic valve development and maintenance. The LVs are formed through a process called mechanotransduction which signals through the intracellular PI3K-AKT pathway in lymphatic endothelial cells. However, the activation …

Selective Pericyte Recruitment To Ec-Lined Tubes, Vessel Assembly Enhancement Through Pericyte Timp-3 Induction, And Pericyte Tbx2 In Capillary Formation And Maturation, Ksenia Marilyn Yrigoin Kaluguina

USF Tampa Graduate Theses and Dissertations

Capillaries, the smallest blood vascular networks, are formed by narrow and elongated endothelial cell (EC)-lined tubes with associated pericytes anchored to the abluminal tube surface. Our laboratory demonstrated that dynamic interactions between ECs and pericytes during capillary tube network assembly are required for basement membrane matrix deposition and maturation. We have also shown that key EC-derived factors promote pericyte recruitment, proliferation, and pericyte-induced basement membrane formation during capillary assembly. In the first section, we aim to identify if vascular smooth muscle cells (VSMCs) respond to the same factors and have the same invasive ability as pericytes since they are both …

Ferroptotic Cardiomyocytes Regulate Angiogenesis In The Regenerative Mouse Heart After Myocardial Infarction Through Direct And Indirect Mechanisms, Rebecca Ashley Stairley

MUSC Theses and Dissertations

Cardiovascular diseases (CVDs) are the leading cause of death in the United States, and heart attack occurs every 40 seconds in the US. A myocardial infarction (MI), or heart attack, results in ischemic injury and cardiomyocyte (CM) death. Mature mammalian CM renewal in the heart is insufficient to repopulate the lost tissue. However, the neonatal mouse heart retains its regenerative capacity through the first week of life, providing a valuable model to identifying regenerative factors.

Recent work by our lab revealed that the main mechanism of CM death in the heart post-MI is ferroptosis. In this study, we investigate the …

Post-Transcriptional Methylation Of Mitochondrial-Trna Differentially Contributes To Mitochondrial Pathology, Sunita Maharjan, Howard Gamper, Yuka Yamaki, Thomas W. Christian, Robert Y. Henley, Nan-Sheng Li, Takeo Suzuki, Tsutomu Suzuki, Joseph A. Piccirilli, Meni Wanunu, Erin L. Seifert, Douglas C. Wallace, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual sequence motifs and require post-transcriptional modifications to stabilize their fragile structures. However, whether a modification that stabilizes a wild-type (WT) mt-tRNA would also stabilize its pathogenic variants is unknown. Here we show that the N¹-methylation of guanosine at position 9 (m¹G9) of mt-Leu(UAA), while stabilizing the WT tRNA, has a destabilizing effect on variants associated with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes). This differential effect is further demonstrated, as removal of the m¹G9 …

Electric Potential Energy Optimized 3d Radial Sampling Trajectories For Mri, Christopher Huynh, Datta Singh Goolaub, Christopher K Macgowan

Faculty, Staff and Students Publications

A novel method for creating “golden” 3D center-out radial MRI sampling trajectories was developed and analyzed. This method, called ELECTRO (ELECTRic potential energy Optimized), uses repulsive forces to minimize electric potential energy. An objective function , the electric potential energies of all subsets of consecutive readouts in a 3D radial trajectory, and its reduced form were minimized using a multi-stage optimization strategy. A metric called normalized mean nearest neighbor angular distance (NMNA) was proposed for describing distributions of points on a sphere. ELECTRO and other relevant golden trajectories were compared in silico using NMNA and point spread function analysis. Consecutive …

Effects Of Cadherin Mediated Contact Normalization On Oncogenic Src Kinase Mediated Gene Expression And Protein Phosphorylation, Rachel E Nicoletto, Cayla J Holdcraft, Ariel C Yin, Edward P Retzbach, Stephanie A Sheehan, Amanda A Greenspan, Christopher M Laugier, Jason Trama, Caifeng Zhao, Haiyan Zheng, Gary S Goldberg

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Nontransformed cells form heterotypic cadherin junctions with adjacent transformed cells to inhibit tumor cell growth and motility. Transformed cells must override this form of growth control, called "contact normalization", to invade and metastasize during cancer progression. Heterocellular cadherin junctions between transformed and nontransformed cells are needed for this process. However, specific mechanisms downstream of cadherin signaling have not been clearly elucidated. Here, we utilized a β-catenin reporter construct to determine if contact normalization affects Wnt signaling in transformed cells. β-catenin driven GFP expression in Src transformed mouse embryonic cells was decreased when cultured with cadherin competent nontransformed cells compared to …

Hepatic Targets To Control Blood Glucose And Potentially Aid In The Treatment Of Diabetes, Rena A. Velissarios

PANDION: The Osprey Journal of Research and Ideas

Maintaining glucose homeostasis is extremely important to remain in good health and prevent disease. This homeostasis is achieved via the regulation of hepatic metabolic pathways like gluconeogenesis and glycogenesis by insulin, which is expressed during high blood glucose. Insulin is responsible for facilitating the uptake of glucose into other tissues from the blood, as well as signaling whether to stimulate or slow glucose metabolism in the liver. Hyperglycemia is one of the main effects of diabetes, a disease characterized by the body’s inability to produce or respond to insulin. Without insulin, hepatic glucose output continues and blood glucose accumulates, causing …

Cryo-Em Analysis Of Pseudomonas Phage Pa193 Structural Components, Stephano M. Iglesias, Chun-Feng Hou, Johnny Reid, Evan Schauer, Renae Geier, Angela Soriaga, Lucy Sim, Lucy Gao, Julian Whitelegge, Pierre Kyme, Deborah Birx, Sebastien Lemire, Gino Cingolani

Department of Biochemistry and Molecular Biology Faculty Papers

The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various clinical settings, commonly called phage therapy, to address this growing public health crisis. Here, we describe a high-resolution structural atlas of a therapeutic, contractile-tailed Pseudomonas phage, Pa193. We used bioinformatics, proteomics, and cryogenic electron microscopy single particle analysis to identify, annotate, and build atomic models for 21 distinct structural polypeptide chains forming the icosahedral capsid, neck, contractile tail, and baseplate. We identified a putative scaffolding protein stabilizing the interior of the capsid 5-fold …

Conditional Deletion Of Ceacam1 In Hepatic Stellate Cells Causes Their Activation, Harrison T. Muturi, Hilda E. Ghadieh, Suman Asalla, Sumona G. Lester, Getachew D. Belew, Sobia Zaidi, Raziyeh Abdolahipour, Abhishek P. Shrestha, Agnes O. Portuphy, Hannah L. Stankus, Raghd Abu Helal, Stefaan Verhulst, Sergio Duarte, Ali Zarrinpar, Leo A. Van Grunsven, Scott L. Friedman, Robert F. Schwabe, Terry D. Hinds, Jr., Sivarajan Kumarasamy, Sonia M. Najjar

Markey Cancer Center Faculty Publications

Objectives: Hepatic CEACAM1 expression declines with advanced hepatic fibrosis stage in patients with metabolic dysfunction-associated steatohepatitis (MASH). Global and hepatocyte-specific deletions of Ceacam1 impair insulin clearance to cause hepatic insulin resistance and steatosis. They also cause hepatic inflammation and fibrosis, a condition characterized by excessive collagen production from activated hepatic stellate cells (HSCs). Given the positive effect of PPARg on CEACAM1 transcription and on HSCs quiescence, the current studies investigated whether CEACAM1 loss from HSCs causes their activation.

Methods: We examined whether lentiviral shRNA-mediated CEACAM1 donwregulation (KD-LX2) activates cultured human LX2 stellate cells. We also generated LratCre þ Cc1fl/fl mutants …