Cell Biology Commons^™

Replication-Transciption Switch In Human Mitochondria, Karen Agaronyan

Graduate School of Biomedical Sciences Theses and Dissertations

Coordinated replication and expression of mitochondrial genome is critical for metabolically active cells during various stages of development. However, it is not known whether replication and transcription can occur simultaneously without interfering with each other and whether mtDNA copy number can be regulated by the transcription machinery. Human mitochondrial RNA polymerase (mtRNAP) is a central enzyme involved in gene expression in mitochondria. It generates genome-size polycistronic transcripts and also makes replication primers at two origins of replication. MtRNAP is distantly related to phage T7 RNAP. While T7 RNAP is optimized to produce large amounts of transcripts to overcompete the bacterial …

An Arginine Finger Regulates The Sequential Action Of Asymmetrical Hexameric Atpase In The Double-Stranded Dna Translocation Motor, Zhengyi Zhao, Gian Marco De-Donatis, Chad T. Schwartz, Huaming Fang, Jingyuan Li, Peixuan Guo

Pharmaceutical Sciences Faculty Publications

Biological motors are ubiquitous in living systems. Currently, how the motor components coordinate the unidirectional motion is elusive in most cases. Here, we report that the sequential action of the ATPase ring in the DNA packaging motor of bacteriophage ϕ29 is regulated by an arginine finger that extends from one ATPase subunit to the adjacent unit to promote noncovalent dimer formation. Mutation of the arginine finger resulted in the interruption of ATPase oligomerization, ATP binding/hydrolysis, and DNA translocation. Dimer formation reappeared when arginine mutants were mixed with other ATPase subunits that can offer the arginine to promote their interaction. Ultracentrifugation …

Depletion Of The Rna Helicase Skiv2l2 Impedes Mitotic Progression And Histone Mrna Turnover In Murine Cell Lines, Alexis Marie Onderak

Dissertations (1934 -)

RNA surveillance via the nuclear exosome requires cofactors such as the helicase SKIV2L2 to process and degrade certain noncoding RNAs. This dissertation aimed to characterize the phenotype associated with RNAi knockdown of SKIV2L2 in two murine cancer cell lines: Neuro2A and P19. Skiv2l2 knockdown in Neuro2A and P19 cells induced changes in gene expression indicative of cell differentiation and reduced cellular proliferation. Analysis of the cell cycle revealed defective progression through mitosis following SKIV2L2 depletion. These results indicate that SKIV2L2 enhances mitotic progression, thereby maintaining cancer cell proliferation and preventing differentiation. Indeed, SKIV2L2 levels were found to be downregulated during …

Molecular Analysis Of Ftsz-Ring Assembly In E. Coli Cytokinesis, Kuo-Hsiang Huang

Dissertations, Theses, and Capstone Projects

An essential first step in bacterial division is the assembly of a cytokinetic ring (Z-ring) formed by the tubulin-like FtsZ at midcell. The highly conserved core domain of FtsZ has been reported to mediate assembly of FtsZ polymers in vivo and in vitro. Species-specific differences in the FtsZ C-terminal domain such as the FtsZ CTV region and interactions with several modulatory proteins such as ZapC and ZapD, restricted to certain bacterial classes, also serve as key determinants of FtsZ protofilament bundling. Here, we characterize (i) the roles of the FtsZ CTV region in mediating both longitudinal and lateral interactions …

Selective Anticancer Activity Of Hydroxyapatite/Chitosan-Poly(D,L)-Lactide-Co-Glycolide Particles Loaded With An Androstane-Based Cancer Inhibitor, Nenad Ignjatović, Katarina M. Penov-Gaši, Victoria M. Wu, Jovana J. Ajduković, Vesna V. Kojić, Dana Vasiljević-Radović, Maja Kuzmanović, Vuk Uskoković, Dragab Uskoković

Pharmacy Faculty Articles and Research

In an earlier study we demonstrated that hydroxyapatite nanoparticles coated with chitosan-poly(d,l)-lactide-co-glycolide (HAp/Ch-PLGA) target lungs following their intravenous injection into mice. In this study we utilize an emulsification process and freeze drying to load the composite HAp/Ch-PLGA particles with 17β-hydroxy-17α-picolyl-androst-5-en-3β-yl-acetate (A), a chemotherapeutic derivative of androstane and a novel compound with a selective anticancer activity against lung cancer cells. ¹H NMR and ¹³C NMR techniques confirmed the intact structure of the derivative A following its entrapment within HAp/Ch-PLGA particles. The thermogravimetric and differential thermal analyses coupled with mass spectrometry were used to assess the …

Identification Of Control Targets In Boolean Molecular Network Models Via Computational Algebra, David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Reinhard Laubenbacher

Mathematics Faculty Publications

Background: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type …

Exposures To The Environmental Toxicants Pentachlorophenol (Pcp) And Dichlorodiphenyltrichloroethane (Ddt) Modify Secretion Of Interleukin 1-Beta (Il-1Β) From Human Immune Cells, Tamara J. Martin, Margaret M. Whalen

Chemistry Faculty Research

Pentachlorophenol (PCP) and Dichlorodiphenyltrichloroethane (DDT) are environmental contaminants found in human blood. Previous studies have shown that PCP and DDT inhibit the lytic function of highly purified human natural killer (NK) lymphocytes and decrease the expression of several surface proteins on NK cells. Interleukin-1 βeta (IL-1β) is a cytokine produced by lymphocytes and monocytes, and anything that elevates its levels inappropriately can lead to chronic inflammation, which among other consequences can increase tumor development and invasiveness. Here, PCP and DDT were examined for their ability to alter secretion of IL-1β from immune cell preparations of various complexity: NK cells; monocyte-depleted …

Identification Of Microorganisms Isolated From Mars-Bound Spacecraft Using Maldi-Tof, Melanie K. Phillips

STAR Program Research Presentations

The primary goal of the Biotechnology and Planetary Protection Group (BPPG) at the Jet Propulsion Laboratory (JPL) is to prevent microbial contamination between Earth and other planetary bodies. This helps preserve the ability to study other worlds as they exist in their natural states and protects our biosphere from extraterrestrial life. The process for identifying microbes located on space-bound hardware in JPL can be more efficient and precise by using the technique called matrix-assisted laser desorption and ionization time of flight (MALDI-TOF). Once this identification technique is fully implemented, the process time will be reduced from two weeks to one …

Active Learning Outside The Classroom: Implementation And Outcomes Of Peer-Led Team-Learning Workshops In Introductory Biology, Philip Kudish, Robin Shores, A. Mcclung, Lisa Smulyan , '76, Elizabeth Ann Vallen, Kathleen King Siwicki

Biology Faculty Works

Study group meetings (SGMs) are voluntary-attendance peer-led team-learning workshops that supplement introductory biology lectures at a selective liberal arts college. While supporting all students’ engagement with lecture material, specific aims are to improve the success of underrepresented minority (URM) students and those with weaker backgrounds in biology. Peer leaders with experience in biology courses and training in science pedagogy facilitate work on faculty-generated challenge problems. During the eight semesters assessed in this study, URM students and those with less preparation attended SGMs with equal or greater frequency than their counterparts. Most agreed that SGMs enhanced their comprehension of biology and …

Genetic Diversity Among Eight Dendrolimus Species In Eurasia (Lepidoptera: Lasiocampidae) Inferred From Mitochondrial Coi And Coii, And Nuclear Its2 Markers, Alexander Kononov, Kirill Ustyantsev, Baode Wang, Victor C. Mastro, Victor Fet, Alexander Blinov, Yuri Baranchikov

Biological Sciences Faculty Research

Background: Moths of genus Dendrolimus (Lepidoptera: Lasiocampidae) are among the major pests of coniferous forests worldwide. Taxonomy and nomenclature of this genus are not entirely established, and there are many species with a controversial taxonomic position. We present a comparative evolutionary analysis of the most economically important Dendrolimus species in Eurasia.

Results: Our analysis was based on the nucleotide sequences of COI and COII mitochondrial genes and ITS2 spacer of nuclear ribosomal genes. All known sequences were extracted from GenBank. Additional 112 new sequences were identified for 28 specimens of D. sibiricus, D. pini, and D. superans from five …

Peroxiredoxin Catalysis At Atomic Resolution, Arden Perkins, Derek Parsonage, Kimberly J. Nelson, O. Maduka Ogba, Paul Ha-Yeon Cheong, Leslie B. Poole, P. Andrew Karplus

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases that guard cells against oxidative damage, are virulence factors for pathogens, and are involved in eukaryotic redox regulatory pathways. We have analyzed catalytically active crystals to capture atomic resolution snapshots of a PrxQ-subfamily enzyme (from Xanthomonas campestris) proceeding through thiolate, sulfenate, and sulfinate species. These analyses provide structures of unprecedented accuracy for seeding theoretical studies, and show novel conformational intermediates giving insight into the reaction pathway. Based on a highly non-standard geometry seen for the sulfenate intermediate, we infer that the sulfenate formation itself can strongly promote local unfolding of the active site to …

Regulation Of Nachrs And Stemness By Nicotine And E-Cigarettes In Nsclc, Courtney Schaal

USF Tampa Graduate Theses and Dissertations

Lung cancer is the leading cause of cancer-related death in both men and women, nationally and internationally and kills more people each year than breast, prostate, and colon cancers combined. Non-small cell lung carcinoma (NSCLC) is the most common histological subtype of lung cancer, and accounts for 85% of all cases. Cigarette smoking is the single greatest risk factor for lung cancer, and is correlated with 80-90% of all lung cancer deaths. Nicotine, the addictive component of tobacco smoke, is not a carcinogen and cannot initiate tumors itself; however, it is known to act as a tumor promoter, by enhancing …

The Mechanism Of Tubular Recycling Endosome Biogenesis, Shuwei Xie

Theses & Dissertations

Endocytic trafficking is a critical process for cellular homeostasis, and multiple ailments that include cardiovascular disease and cancer are related to the dysregulation of endocytic transport. As vesicles and target membranes are key to endocytic transport, lipids are essential for the regulation of endocytic trafficking pathways. We have shown that the tubular recycling endosomes (TRE) are essential for the regulation of endocytic recycling pathways. However, the mechanisms by which TRE are biosynthesized and carry out their functions remain unsolved. Studies from our lab have shown that phosphatidic acid (PA) recruits Molecule Interacting with Casl-Like protein 1 (MICAL-L1) as well as …

Role Of Ddr1 In Pancreatic Cancer, Huocong Huang

Theses & Dissertations

Pancreatic ductal adenocarcinomas are highly malignant cancers, characterized by extensive invasion into surrounding tissues, metastasis to distant organs at a very early stage, and a limited response to therapy. One of the main features of pancreatic ductal adenocarcinomas is desmoplasia, which leads to extensive deposition of collagen I. We have demonstrated that collagen I can induce epithelial-mesenchymal transition (EMT) in pancreatic cancer cells. A hallmark of EMT is an increase in the expression of a mesenchymal cadherin, N-cadherin. Our previous studies have shown that up-regulation of N-cadherin can promote tumor cell invasion and that collagen I-induced EMT is through two …

Deep Phylogenomics Of A Tandem-Repeat Galectin Regulating Appendicular Skeletal Pattern Formation, Ramray Bhat, Mahul Chakraborty, Tilmann Glimm, Thomas A. Stewart, Stuart A. Newman

NYMC Faculty Publications

BACKGROUND: A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied patterns of nodules, bars and plates, while tetrapod limbs exhibit tandem arrays of few, proximodistally increasing numbers of elements. We applied a comparative genomic and protein evolution approach to understand the origin of the galectin patterning network. Having previously observed a phylogenetic constraint on Gal-1 structure across vertebrates, we asked whether evolutionary changes of Gal-8 could have critically …

Contribution Of A Putative Up Element Dna Sequence To The Activity Of A Newly Identified Phage Promoter, Courtney Hamilton

Mahurin Honors College Capstone Experience/Thesis Projects

In transcription, a universal step in gene expression, information from a DNA sequence is copied into RNA. A key component in gene expression is the promoter sequence, a region of DNA to which RNA polymerase binds during the initiation of transcription of downstream genes. Most bacterial promoters contain a -10 and a -35 sequence that are bound by the RNA polymerase. Some promoters also contain an Upstream Promoter (UP) element. UP elements have been shown to boost promoter activity. We recently identified a new promoter in a mutant bacteriophage that grows on a bacterial host that prevents antitermination of phage …

Maternal Sleep Loss During Fetal Development Alters Offspring Endocrine Responses To Stress Throughout Life, Audrey Brown

Mahurin Honors College Capstone Experience/Thesis Projects

The hypothalamic-pituitary-adrenal (HPA) axis releases glucocorticoids, including corticosterone (CORT), in response to stress. CORT then negatively feeds back to inhibit its own production by binding to glucocorticoid receptors (GRs) in the hypothalamus and pituitary gland. The HPA axis is subject to “programming” by abnormal stimuli during early development, which may permanently alter how the HPA axis responds to stress. These altered responses have been linked to an increased risk for human psychiatric and metabolic disorders in later life, but the mechanism by which this happens is not fully understood. This study tests the hypothesis that changes to GR expression patterns …

Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots

STAR Program Research Presentations

The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few …

The Role Of E. Coli Transcript-Cleavage Factors Gre In Transcriptional Regulation Under Hyperosmotic Stress, Kseniya Obraztsova

Graduate School of Biomedical Sciences Theses and Dissertations

Escherichia coli adapts to changes in the osmotic environment through the process of osmotic response which entails synthesis of specific enzymes and transporters to accumulate essential osmoprotectants. This process is highly regulated at the level of transcription. Upon cell exposure to high salt, RNA polymerase (RNAP} rapidly dissociates from genomic DNA, while the nucleoid becomes hyper condensed. During the subsequent osmoadaptation phase RNAP reassociates with the DNA and resumes transcription. The mechanisms of transcription initiation, promoter escape and its regulation during osmoadaptation are poorly understood. Here we demonstrate that a highly conserved bacterial regulator, transcript cleavage factor GreA, is essential …

The Genetic Hierarchy Of The Heterochronic Pathway In C. Elegans, Jennifer Tsialikas

Graduate School of Biomedical Sciences Theses and Dissertations

The correct timing of developmental events is fundamental to the growth of every animal. The pathways that control developmental timing and cell-fate succession are complex and robust in a way that underscores this importance. In this work, I have shown how an early developmental regulator, LIN-14, acts to integrate the earliest aspects of development with the events that take place afterward. I have uncovered how microRNAs from two different families fit into the cascade of proteins and micro RNA regulation that defines the developmental timing pathway. Finally, my work has helped to uncover the dual-acting nature of two proteins in …