Cell Biology Commons^™

Quantitative Comparison Of Cis-Regulatory Element (Cre) Activities In Transgenic Drosophila Melanogaster, William A. Rogers, Thomas M. Williams

Biology Faculty Publications

Gene expression patterns are specified by cis-regulatory element (CRE) sequences, which are also called enhancers or cis-regulatory modules. A typical CRE possesses an arrangement of binding sites for several transcription factor proteins that confer a regulatory logic specifying when, where, and at what level the regulated gene(s) is expressed. The full set of CREs within an animal genome encodes the organism′s program for development¹, and empirical as well as theoretical studies indicate that mutations in CREs played a prominent role in morphological evolution^2-4. Moreover, human genome wide association studies indicate that genetic variation in CREs …

Protein Trap Lines Of Drosophila To Demonstrate Spatio-Temporal Localization Of Proteins In An Undergraduate Lab, Oorvashi Roy Puli, Amit Singh

Biology Faculty Publications

The objective of this teaching note is to generate a laboratory exercise, which allows students to get a hands-on experience of a cell biology technique. The short duration of the laboratory classes is the biggest challenge with the development of a cell biology lab for an undergraduate curriculum. Therefore, it is necessary to design a laboratory exercise that enables the students to carry out cell biological assays in the desired time. This laboratory exercise focuses on tracking protein expression levels along a spatial (space) and temporal (time) axis in developing Drosophila melanogaster organ primordium. Here we use the protein trap …

The Role Of Receptor Tyrosine Kinase Axl In Pancreatic Ductal Adenocarcinoma And Its Regulation By Hematopoietic Progenitor Kinase 1, Xianzhou Song

Dissertations & Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDA) is one of the most aggressive malignancies with less than 5% of five year survival rate. New molecular markers and new therapeutic targets are urgently needed for patients with PDA. Oncogenic receptor tyrosine kinase Axl has been reported to be overexpressed in many types of human malignancies, including diffuse glioma, melanoma, osteosarcoma, and carcinomas of lung, colon, prostate, breast, ovary, esophagus, stomach, and kidney. However, the expression and functions of Axl in PDA are unclear. We hypothesized that Axl contributes to the development and progression of PDA. We examined Axl expression in 54 human PDA samples …

Laboratory Diagnosis Of Clostridium Difficile Infection: Can Molecular Amplification Methods Move Us Out Of Uncertainty?, Fred C. Tenover, Ellen Jo Baron, Lance R. Peterson, David Persing

Biology Faculty Publications

The laboratory diagnosis of Clostridium difficile infection (CDI) continues to be challenging. Recent guidelines from professional societies in the United States note that enzyme immunoassays for toxins A and B do not have adequate sensitivity to be used alone for detecting CDI, yet the optimal method for diagnosing this infection remains unclear. Nucleic acid amplification tests (NAATs) that target chromosomal toxin genes (usually the toxin B gene, tcdB) show high sensitivity and specificity, provide rapid results, and are amenable to both batch and on-demand testing, but these tests were not universally recommended for routine use in the recent guidelines. …

Molecular Systematics Of The Middle American Genus Hypopachus (Anura: Microhylidae), Eli Greenbaum, Eric N. Smith, Rafael O. De Sá

Biology Faculty Publications

We present the first phylogenetic study on the widespread Middle American microhylid frog genus Hypopachus. Partial sequences of mitochondrial (12S and 16S ribosomal RNA) and nuclear (rhodopsin) genes (1275 bp total) were analyzed from 43 samples of Hypopachus, three currently recognized species of Gastrophryne, and seven arthroleptid, brevicipitid and microhylid outgroup taxa. Maximum parsimony (PAUP), maximum likelihood (RAxML) and Bayesian inference (MrBayes) optimality criteria were used for phylogenetic analyses, and BEAST was used to estimate divergence dates of major clades. Population-level analyses were conducted with the programs NETWORK and Arlequin. Results confirm the placement of Hypopachus …

Mcnamara 2011 Mpmicro - Multi-Probe Microscopy (10/31/2011), George Mcnamara

George McNamara

Multi-Probe Microscopy is an ~1500 page Word document summarizing what I know and/or found interesting in light microscopy, fluorescence microscopy and digital image analysis, from 1995-2005. Very little has been updated since 2005.

Brassinosteroid-Mediated Stress Tolerance In Arabidopsis Thaliana, Tawhidur Rahman

Electronic Thesis and Dissertation Repository

Brassinosteroids (BRs) are a group of steroidal plant hormones that are essential for proper plant development and also promote stress tolerance. Without BRs, plants are dwarfs and infertile. To understand the molecular mechanisms underlying BR-mediated stress tolerance, global gene expression analysis of untreated and 24-epibrassinolide (EBR)-treated Arabidopsis thaliana seedlings under non-stress and heat stress (HS) conditions was carried out. Microarray data analysis indicated that stress-related genes were predominant within the EBR up-regulated gene data set. Furthermore, several of these genes were abscisic acid (ABA) and jasmonic acid (JA) related. Measurements of endogenous hormones showed significant increases in the levels ABA …

Activation Of Jnk Signaling Mediates Amyloid-Ss- Dependent Cell Death, Meghana Tare, Rohan Modi, Jaison Nainaparampil, Oorvashi Roy Puli, Shimpi Bedi, Pedro Fernandez-Funez, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Background: Alzheimer's disease (AD) is an age related progressive neurodegenerative disorder. One of the reasons for Alzheimer's neuropathology is the generation of large aggregates of Aß42 that are toxic in nature and induce oxidative stress, aberrant signaling and many other cellular alterations that trigger neuronal cell death. However, the exact mechanisms leading to cell death are not clearly understood.

Methodology/Principal Findings: We employed a Drosophila eye model of AD to study how Aß42 causes cell death. Misexpression of higher levels of Aß42 in the differentiating photoreceptors of fly retina rapidly induced aberrant cellular phenotypes and cell death. We found that …

Interspecies Comparison Of Αii-Spectrin Abundance Between Chinook Salmon And Steelhead, Brielle D. Kemis, Ann L. Miracle, Katie A. Wagner, Christa M. Woodley

STAR Program Research Presentations

Salmonids, such as Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss), are a staple economic, recreational, tribal, and environmental resource, yet many populations are unsustainable. This study was part of a broad scale effort to monitor the impact of downstream migration obstacles on juvenile salmonid health and survival, which is an essential step towards increasing Smolt-to-Adult Return ratios (SARs). The objective of this study was to determine if juvenile Chinook salmon and steelhead exhibit differing quantities of alphaII-Spectrin Breakdown Products (SBDPs) over two consecutive spring migration periods, indicative of neurogenesis rate and/or biological response to head …

Downregulation Of Pax2 Suppresses Ovarian Cancer Cell Growth, Huijuan Song

Dissertations & Theses (Open Access)

PAX2 is one of nine PAX genes regulating tissue development and cellular differentiation in embryos. PAX2 promotes cell proliferation, oncogenic transformation, cell-lineage specification, migration, and survival. Unattenuated PAX2 has been found in several cancer types. We therefore sought to elucidate the role of PAX2 in ovarian carcinomas. We found that PAX2 was expressed in low-grade serous, clear cell, endometrioid and mucinous cell ovarian carcinomas, which are relatively chemoresistant compared to high grade serous ovarian carcinomas. Four ovarian cancer cell lines, RMUGL (mucinous), TOV21G (clear cell), MDAH-2774 (endometrioid) and IGROV1 (endometrioid), which express high-levels of PAX2, were used to study the …

A Cell Biological Determination Of Integrator Subunit Localization, Sarah B. May

Dissertations & Theses (Open Access)

Uridine-rich small nuclear (U snRNAs), with the exception of the U6 snRNA, are RNA polymerase II (RNAPII) transcripts. The mechanism of 3’ cleavage of snRNAs has been unknown until recently. This area was greatly advanced when 12 of the Integrator complex subunits (IntS) were purified in 2005 through their interaction with the C-terminal domain (CTD) of the large subunit (RpbI) of RNAPII. Subsequently, our lab performed a genome-wide RNAi screen that identified two more members of the complex that we have termed IntS13 and IntS14. We have determined that IntS9 and 11 mediate the 3’ cleavage of snRNAs, but the …

Mechanism Of Transcriptional Suppression Of A Phytochrome A Epiallele In Arabidopsis Thaliana, Gulab D. Rangani

Graduate Theses and Dissertations

Cytosine methylation in DNA is an integral part of epigenetically controlled regulatory networks in eukaryotes. Both plants and vertebrates display DNA methylation in the gene coding region; however, its role in gene expression is not well understood. Gene promoter, on the other hand, remains largely unmethylated. Acquisition of methylation in promoter results in transcriptional suppression of the gene. The goal of this research is to study the effect of coding region methylation in gene expression using a unique gene model, phyA'. phyA' is a transcriptionally suppressed epiallele of the Arabidopsis thaliana Phytochrome A gene, which contains methylation in CG sites …

Mechanical Test Methods For Assessing Porcine Carotid And Uterine Artery Burst Pressure Following Ex Vivo Ultrasonic Ligature Seal And Transection, Carissa M. Krane, Margaret Pinnell, Courtney Gardner, Mercedes Thompson, James Coleman, Robert Wilkens

Biology Faculty Publications

A test method was developed to identify those variables important for assessing the performance of ultrasonic surgical devices in ex vivo ligature sealing of porcine carotid and uterine arteries. Ruggedness testing using a small sample size in pilot experiments was conducted using a newly developed test method in an effort to assess the usefulness of this methodology and to identify test variables that might warrant further testing. The development of this test method included the use of a custom-designed prototypic tension device for load-controlled ex vivo vessel stretching during saline perfusion and subsequent seal and transection of porcine arteries with …

Science Boot Camp For Librarians: Cpd On A Shoestring, Maxine G. Schmidt, Rebecca Reznik-Zellen

Maxine G Schmidt

Science Boot Camp for Librarians was envisioned as a casual but intensive immersion event into selected scientific subjects that employ networked computing capabilities for research and collaboration. The goal of the event is to provide librarians with networking opportunities, but more importantly, to give them some of the context and ocabulary of a discipline to enable them to better engage faculty and research scientists with regard to escience. A half-day is devoted to each of three topics chosen for that year’s camp. A local faculty member provides an overview of the research area, and a second describes a single project …

Septin Filaments Exhibit A Dynamic, Paired Organization That Is Conserved From Yeast To Mammals, Bradley S. Demay, Xiaobo Bai, Louisa Howard, Patricia Occhipinti, Rebecca A. Meseroll, Elias T. Spiliotis, Rudolf Oldenbourg, Amy S. Gladfelter

Dartmouth Scholarship

The septins are conserved, GTP-binding proteins important for cytokinesis, membrane compartmentalization, and exocytosis. However, it is unknown how septins are arranged within higher-order structures in cells. To determine the organization of septins in live cells, we developed a polarized fluorescence microscopy system to monitor the orientation of GFP dipole moments with high spatial and temporal resolution. When GFP was fused to septins, the arrangement of GFP dipoles reflected the underlying septin organization. We demonstrated in a filamentous fungus, a budding yeast, and a mammalian epithelial cell line that septin proteins were organized in an identical highly ordered fashion. Fluorescence anisotropy …

Endo-Porter–Mediated Delivery Of Phosphorodiamidate Morpholino Oligos (Pmos) In Erythrocyte Suspension Cultures From Cope's Gray Treefrog Hyla Chrysoscelis, Venkateshwar Mutyam, Matthew V. Puccetti, James Frisbie, David L. Goldstein, Carissa M. Krane

Biology Faculty Publications

Cope's gray treefrog, Hyla chrysoscelis, is a freeze-tolerant anuran that accumulates cryoprotective glycerol during cold acclimation. H. chrysoscelis erythrocytes express the aquaglyceroporin HC-3, which facilitates transmembrane glycerol and water movement. Aquaglyceroporins have no pharmacological inhibitors, and no genetic knockout tools currently exist for H. chrysoscelis. A phosphorodiamidate morpholino oligo (PMO)–mediated expression knockdown approach was therefore pursued to provide a model for testing the role of HC-3. We describe a novel procedure optimized for specific, efficient knockdown of HC-3 expression in amphibian erythrocyte suspensions cultured at nonmammalian physiological temperatures using Endo-Porter. Our protocol includes three critical components: pre-incubation at 37°C, …

Design Of A Factorial Experiment With Randomization Restrictions To Assess Medical Device Performance On Vascular Tissue, Wiebke Diestelkamp, Carissa M. Krane, Margaret Pinnell

Biology Faculty Publications

Background: Energy-based surgical scalpels are designed to efficiently transect and seal blood vessels using thermal energy to promote protein denaturation and coagulation. Assessment and design improvement of ultrasonic scalpel performance relies on both in vivo and ex vivo testing. The objective of this work was to design and implement a robust, experimental test matrix with randomization restrictions and predictive statistical power, which allowed for identification of those experimental variables that may affect the quality of the seal obtained ex vivo.

Methods: The design of the experiment included three factors: temperature (two levels); the type of solution used to perfuse the …

The Role Of Phosphoinositide Signaling In Breast Cancer Metastasis Suppressor 1-Mediated Metastasis Suppression Of Human Breast Carcinoma Cells, Sitaram Harihar

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Breast cancer is the most common non-skin cancer in women and the second most common cause of cancer-related death in U.S. women. Despite numerous advances in treatment strategies against breast cancer, the presence of undetected distant metastasis of the primary tumor remains the main cause of mortality. Current screening and detection methods such as mammograms are simply not sensitive enough to detect formation of metastasis. Further, currently available therapies against metastatic breast cancer do not provide a complete cure for the disease. Thus, understanding the biology and molecular factors involved in cancer metastasis will help aid in preventing the onset …

Cop 9 Signalosome Subunit 6 Stabilizes Cop1, A Novel E3 Ubiquitin Ligase For 14-3-3Σ, Hyun Ho Choi

Dissertations & Theses (Open Access)

14-3-3σ, a gene upregulated by p53 in response to DNA damage, exists as part of a positive-feedback loop which activates p53 and is a human cancer epithelial marker downregulated in various cancer types. 14-3-3σ levels are critical for maintaining p53 activity in response to DNA damage and regulating signal mediator such as Akt. Here, we identify Mammalian Constitutive Photomorphogenic 1 (COP1) as a novel E3 ubiquitin ligase for targeting 14-3-3σ through proteasome degradation. We show for the first time that COP9 signalosome subunit 6 (CSN6) associates with COP1 and is involved in 14-3-3σ ubiquitin-mediated degradation. Mechanistic studies show that CSN6 …

Stem Cell Biology And Strategies For Therapeutic Development In Degenerative Diseases And Cancer, Angel A. Alvarez '98

Doctoral Dissertations

Stem cell biology is an exciting field that will lead to significant advancements in science and medicine. We hypothesize that inducing the expression of stem cell genes, using the embryonic stem cell gene nanog, will reprogram cells and dedifferentiate human mesenchymal stem cells into pluripotent stem cells capable of neural differentiation. The aims of initial studies are as follows:

Aim 1: Demonstrate that forced expression of the embryonic stem cell gene nanog induces changes in human mesenchymal stem cells to an embryonic stem cell-like phenotype.

Aim 2: Demonstrate that induced expression of nanog up-regulates the expression of multiple embryonic stem …

Modulation Of Glutamate-Mediated Neuronal Cell Death By Neurosteroids, Benjamin J. Phelps

Undergraduate Theses and Capstone Projects

Traumatic brain injury (TBI) is a major cause of death and permanent disability in the United States. Approximately 1.7 million cases of TBI are reported annually. After an injury to the head, excessive glutamate, an excitatory neurotransmitter, is released into the extracellular fluid resulting in the excitotoxic death of neuronal tissue. Recent studies have suggested neurosteroids, may serve as an effective means by which to modulate excitotoxicity via the excitatory neurotransmitter alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA). Using mixed astrocyte-neuronal cell cultures (14-16 DIV) exposed to increasing concentrations of AMPA as the model for TBI, the experiments examined the effect of the neurosteroids, …

Mechanical Forces And Tumor Cells: Insight Into The Biophysical Aspects Of Cancer Progression, Indrajyoti Indra

Wayne State University Dissertations

Mechanical forces play an important role in the regulation of cellular behavior and physiological processes including adhesion, migration, proliferation, tissue repair, embryogenesis and development. In addition, a number of diseases including cancer, have been linked to changes in cellular and extracellular mechanical properties. However, whether a correlation exists between the progression of cancer towards metastasis and mechanical factors has not been clearly defined. Additionally, how a cell responds to changes in extracellular mechanical cues as it gains metastatic abilities is poorly understood. To address these questions, we have utilized a panel of murine breast cancer cell lines with progressive metastatic. …

Nociceptin Is A Chemorepellent In Tetrahymena Thermophila, Nathanael Braun, Thomas Lampert, Breanne Gibson, Cheryl Nugent, Heather G. Kuruvilla

Science and Mathematics Faculty Presentations

Tetrahymena thermophila are free-living, ciliated, eukaryotic organisms that respond to stimuli by moving toward chemoattractants and avoiding chemorepellents. Chemoattractant responses involve faster ciliary beating, which propels the organisms forward more rapidly. Chemorepellent signaling involves ciliary reversal, which disrupts forward swimming, and causes the organism to jerk back and forth, swim in small circles, or spin in an attempt to get away from the repellent. Many food sources, such as proteins, are chemoattractants for Tetrahymena, while a variety of compounds are repellents. Repellents in nature are thought to come from the secretions of predators, or from ruptured organisms, which may serve …

Examination Of The Mitochondrial Health Of The Basigin Null Mouse Retina, Kristine Anne V. Pablo

UNF Graduate Theses and Dissertations

Basigin gene products are cell adhesion molecules that are expressed by photoreceptor cells, Müller cells and endothelial cells of the mammalian retina. Previous studies have suggested that a lactate shuttle exists between the photoreceptor cells and the Müller cells, with Basigin being an essential component in this shuttle. Deletion of the Basigin gene in mice results in blindness with an eventual retinal degeneration. It was hypothesized that the lactate shuttle between photoreceptors and Müller cells does not form in Basigin null mice and that the blindness is attributed to faulty photoreceptor metabolism. Therefore, the purpose of this study was to …

Quantifying Agonist Activity At G Protein-Coupled Receptors, Frederick J. Ehlert, Hinako Suga, Michael T. Griffin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

When an agonist activates a population of G protein-coupled receptors (GPCRs), it elicits a signaling pathway that culminates in the response of the cell or tissue. This process can be analyzed at the level of a single receptor, a population of receptors, or a downstream response. Here we describe how to analyze the downstream response to obtain an estimate of the agonist affinity constant for the active state of single receptors.

Receptors behave as quantal switches that alternate between active and inactive states (Figure 1). The active state interacts with specific G proteins or other signaling partners. In the absence …

Stress-Induced Proteolysis Of Fkbp10: Mutational Analysis And Functional Implications, Lindsey A. Murphy

Featured Research

Cellular signaling is a complex system of communication that regulates cell function through a variety of molecular messengers. When cell survival is threatened by changes in environment or by malfunction of internal regulatory pathways, signals are initiated to restore homeostasis. Deficient protein processing within the endoplasmic reticulum (ER) causes an accumulation of misfolded proteins and stress signaling. The resulting stress signaling includes both adaptive signals (unfolded protein response) and in cases of severe ER stress apoptotic signals induced via the mitochondria. FKBP10 is a key ER luminal peptidy-prolyl isomerase (rotamase) that mediates protein folding. The production of chaperone proteins and …

Analysis Of Biological Features Associated With Meiotic Recombination Hot And Cold Spots In Saccharomyces Cerevisiae, Loren Hansen, Nak-Kyeong Kim, Leonardo Mariño-Ramírez, David Landsman

Mathematics & Statistics Faculty Publications

Meiotic recombination is not distributed uniformly throughout the genome. There are regions of high and low recombination rates called hot and cold spots, respectively. The recombination rate parallels the frequency of DNA double-strand breaks (DSBs) that initiate meiotic recombination. The aim is to identify biological features associated with DSB frequency. We constructed vectors representing various chromatin and sequence-based features for 1179 DSB hot spots and 1028 DSB cold spots. Using a feature selection approach, we have identified five features that distinguish hot from cold spots in Saccharomyces cerevisiae with high accuracy, namely the histone marks H3K4me3, H3K14ac, H3K36me3, and H3K79me3; …

Escherichia Coli Fpg Glycosylase Is Nonrendundant And Required For The Rapid Global Repair Of Oxidized Purine And Pyrimidine Damage In Vivo, Brandy J. Schalow, Charmain T. Courcelle, Justin Courcelle

Biology Faculty Publications and Presentations

Endonuclease (Endo) III and formamidopyrimidine-N-glycosylase (Fpg) are two of the predominant DNA glycosylases in Escherichia coli that remove oxidative base damage. In cell extracts and purified form, Endo III is generally more active toward oxidized pyrimidines, while Fpg is more active towards oxidized purines. However, the substrate specificities of these enzymes partially overlap in vitro. Less is known about the relative contribution of these enzymes in restoring the genomic template following oxidative damage. In this study, we examined how efficiently Endo III and Fpg repair their oxidative substrates in vivo following treatment with hydrogen peroxide. We found …

The Characterization Of Genes Involved In Response To The Phenol Derivative And Xenoestrogen Bisphenol-A In Saccharomyces Cerevisiae, Sasha N. Farina

CMC Senior Theses

Bisphenol A is an estrogenic compound that is found in polycarbonate plastics and epoxy resins; humans are continuously exposed to the compound and it is believed to possess the same carcinogenic effects as estrogen (Iso, 2006). In this study, I used Saccharomyces cerevisiae as a model organism to identify mechanisms by which BPA acts based on the genomic profiling of kinase genes from a Mat-α haploid deletion library. Kinases regulate many other proteins, so the identification of a single mutant could identify an entire affected pathway of genes. I conducted a systematic screen of these mutants using the phenotype of …

Rho Kinase Regulates Basement Membrane Dynamics To Coordinate Salivary Gland Branching Morphogenesis And Tissue Organization, William Patrick Daley

Legacy Theses & Dissertations (2009 - 2024)

Branching morphogenesis is a developmental mechanism utilized by many organs, including the salivary gland, lung, kidney, and mammary gland, to increase the epithelial surface area for secretion or absorption. The embryonic submandibular salivary gland (SMG) is a classic model for studying tissue morphogenesis in three dimensions ex vivo. Salivary gland development requires distinct but overlapping processes: morphogenesis, the actual physical rearrangement of cells into complex three dimensional structures, and cytodifferentiation, the process by which these cells begin to take on their own specialized function. Polarization, or the organization of cells into a cohesive tissue structure, also occurs concurrently during organ …