Cell and Developmental Biology Commons^™

Analysis Of The Chondroitinase Operon Of Flavobacterium Columnare, Erin L. Sorlien

Senior Honors Projects

Analysis of the chondroitinase operon of Flavobacterium columnare

Erin Sorlien

Major

Cell and Molecular Biology, Chemistry

Advisor

Dr. David R. Nelson

Date

May 2, 2013

Keywords

Flavobacterium columnare, columnaris disease, chondroitin AC lyase, complementation, csl operon

Abstract
Flavobacterium columnare, an opportunistic bacterial pathogen of fish, is the causative agent of columnaris disease (CD). The bacterium is a Gram-negative rod that exhibits gliding motility and avidly forms biofilms. CD affects both wild and cultured freshwater fish, and continues to cause large economic losses to the fish farming industry. According to an investigation conducted by the National Animal Health Monitoring System, CD ...

Herv-H Rna Is Abundant In Human Embryonic Stem Cells And A Precise Marker For Pluripotency, Federico A. Santoni, Jessica Guerra, Jeremy Luban

Open Access Articles

BACKGROUND: Certain post-translational modifications to histones, including H3K4me3, as well as binding sites for the transcription factor STAT1, predict the site of integration of exogenous gamma-retroviruses with great accuracy and cell-type specificity. Statistical methods that were used to identify chromatin features that predict exogenous gamma-retrovirus integration site selection were exploited here to determine whether cell type-specific chromatin markers are enriched in the vicinity of endogenous retroviruses (ERVs).

RESULTS: Among retro-elements in the human genome, the gamma-retrovirus HERV-H was highly associated with H3K4me3, though this association was only observed in embryonic stem (ES) cells (p < 10-300) and, to a lesser extent, in induced pluripotent stem (iPS) cells. No significant association was observed in nearly 40 differentiated cell types, nor was any association observed with other retro-elements. Similar strong association was observed between HERV-H and the binding sites within ES cells for the pluripotency transcription factors NANOG, OCT4, and SOX2. NANOG binding sites were located within the HERV-H 5'LTR itself. OCT4 and SOX2 binding sites were within 1 kB and 2 kB of the 5'LTR, respectively. In keeping with these observations, HERV-H RNA constituted 2% of all poly A RNA in ES cells. As ES cells progressed down a differentiation pathway, the levels of HERV-H RNA decreased progressively. RNA-Seq datasets showed HERV-H transcripts to be over 5 kB in length and to have the structure 5'LTR-gag-pro-3'LTR, with no evidence of splicing and no intact open reading frames.

CONCLUSION: The developmental regulation of HERV-H ...

A Specific Family Of Interspersed Repeats (Sines) Facilitates Meiotic Synapsis In Mammals, Matthew E. Johnson, Ross A. Rowsey, Sofia Shirley, Catherine Vandevoort, Jeffrey A. Bailey, Terry Hassold

Open Access Articles

BACKGROUND: Errors during meiosis that affect synapsis and recombination between homologous chromosomes contribute to aneuploidy and infertility in humans. Despite the clinical relevance of these defects, we know very little about the mechanisms by which homologous chromosomes interact with one another during mammalian meiotic prophase. Further, we remain ignorant of the way in which chromosomal DNA complexes with the meiosis-specific structure that tethers homologs, the synaptonemal complex (SC), and whether specific DNA elements are necessary for this interaction.

RESULTS: In the present study we utilized chromatin immunoprecipitation (ChIP) and DNA sequencing to demonstrate that the axial elements of the mammalian ...

Isolation And Characterization Of Active Elderberry Fractions That Inhibit Melanoma Growth In Vitro And In Vivo, Alexandra M. Okihiro

Master's Theses

The incidence rates of melanoma continue to rise annually despite recent progression in cancer treatments. Cancer is the most prevalent amongst elderly individuals, where immunosenescence has compromised some immune function, and therefore decreased certain tumor detection abilities. Current tumor removal strategies include radiation, chemotherapy and surgical excision: treatments that aim to lower cancer cells, but may also affect normal cells in the process. In the case of chemotherapy, which targets and kills rapidly dividing cells, many immune cells are lowered as a side effect, leaving many patients immune-suppressed and more susceptible to infection. There is a need for naturopathic treatments ...

A Search For Light-Detecting Proteins In The Free-Living Protist, Tetrahymena Thermophila: Does Tetrahymena Have Opsin-Like Or Bacteriorhodopsin-Like Proteins?, Jillian Marie Rainville

Senior Honors Projects

Tetrahymena is a genus of ciliated protozoans, a diversified lineage of unicellular eukaryotes. They are freshwater organisms, and generally inhabit streams, lakes, and ponds. Tetrahymena thermophila is commonly studied as a model cell because of its unique variety of complex and specialized cell structures and processes, which are similar to those of higher animals.

G-protein-coupled receptors (GPCRs) are transmembrane proteins that transduce stimuli from outside of the cell into intracellular signals, through the interaction of their intracellular domains with heterotrimeric G proteins. GPCRs make up a vast protein family that includes a variety of subfamilies with distinct functions. They are ...

Characterization Of Differentiation And Prognostic Biomarkers On Cd8+ Tumor-Infiltrating Lymphocytes In Metastatic Melanoma, Richard C. Wu

UT GSBS Dissertations and Theses (Open Access)

CD8⁺ cytotoxic T lymphocytes (CTL) frequently infiltrate tumors, yet most melanoma patients fail to undergo tumor regression. We studied the differentiation of the CD8⁺ tumor-infiltrating lymphocytes (TIL) from 44 metastatic melanoma patients using known T-cell differentiation markers. We also compared CD8⁺ TIL against the T cells from matched melanoma patients’ peripheral blood. We discovered a novel subset of CD8⁺ TIL co-expressing early-differentiation markers, CD27, CD28, and a late/senescent CTL differentiation marker, CD57. This CD8⁺CD57⁺ TIL expressed a cytolytic enzyme, granzyme B (GB), yet did not express another cytolytic pore-forming molecule, perforin (Perf). In contrast, the CD8⁺CD57⁺ T ...

Drosophila Prl-1 Is A Growth Inhibitor That Counteracts The Function Of The Src Oncogene, Krystle T. Pagarigan, Bryce Bunn, Jake Goodchild, Travis K. Rahe, Julie F. Weiss, Leslie J. Saucedo

All Faculty Scholarship

Abstract

Phosphatase of Regenerating Liver (PRL) family members have emerged as molecular markers that significantly correlate to the ability of many cancers to metastasize. However, contradictory cellular responses to PRL expression have been reported, including the inhibition of cell cycle progression. An obvious culprit for the discrepancy is the use of dozens of different cell lines, including many isolated from tumors or cultured cells selected for immortalization which may have missing or mutated modulators of PRL function. We created transgenic Drosophila to study the effects of PRL overexpression in a genetically controlled, organismal model. Our data support the paradigm that ...

Salinomycin: A Notch Signaling Antagonist - A Novel Way Of Targeting Cancer Stem Cells, Carlos U. Muzlera

The Meducator

Dr. Hassell’s research team aims to investigate the roles of therapeutically-relevant genes or gene signatures in the development of “tumour-initiating cells” or breast cancer stem cells. His research team also explores the effects of antagonistic compounds on certain regulatory receptor pathways using in vitro breast cancer cultures and transgenic mouse models. The following research focuses on validating the inhibitory effects of an anti-breast cancer stem cell agent, salinomycin, on downstream Notch signaling. It suggests the possibility of targeting cancer stem cells, the primary culprit in tumour initiation, chemoresistance, and metastasis, by inhibiting key regulatory pathways - such as Notch signaling ...

Carbonic Anhydrase 9 And Radiation Resistance In Rcc, Daniel R. Gallino

Open Access Dissertations and Theses

Renal cell carcinoma (RCC) is the most frequently lethal of urological cancers. It arises in the lining of the proximal convoluted tubule of the kidney and is most common in men ages 50–70. Often, partial or radical nephrectomy is needed to effectively treat the disease, leaving patients with reduced kidney function. RCC frequently displays significant radiation resistance, limiting the usefulness of traditional radiation therapy which might spare patients’ normal tissue. The enzyme carbonic anhydrase 9 (CA9), a product of the hypoxia pathway, is found upregulated in the majority of RCC, particularly the clear cell type. It catalyses the dissolution ...

Galectin-3 Enhances The Malignant Melanoma Phenotype By Regulating Autotaxin, Russell R. Braeuer

UT GSBS Dissertations and Theses (Open Access)

In melanoma patient specimens and cell lines, the over expression of galectin-3 is associated with disease progression and metastatic potential. Herein, we have sought out to determine whether galectin-3 affects the malignant melanoma phenotype by regulating downstream target genes. To that end, galectin-3 was stably silenced by utilizing the lentivirus-incorporated small hairpin RNA in two metastatic melanoma cell lines, WM2664 and A375SM, and subjected to gene expression microarray analysis. We identified and validated the lysophospholipase D enzyme, autotaxin, a promoter of migration, invasion, and tumorigenesis, to be down regulated after silencing galectin-3. Silencing galectin-3 significantly reduced the promoter activity of ...

The Role Of Retrograde Intraflagellar Transport In Flagellar Assembly, Maintenance, And Function, Benjamin D. Engel, Hiroaki Ishikawa, Kimberly A. Wemmer, Stefan Geimer, Ken-Ichi Wakabayashi, Masafumi Hirono, Branch Craige, Gregory J. Pazour, George B. Witman, Ritsu Kamiya, Wallace F. Marshall

Cell and Developmental Biology Publications and Presentations

The maintenance of flagellar length is believed to require both anterograde and retrograde intraflagellar transport (IFT). However, it is difficult to uncouple the functions of retrograde transport from anterograde, as null mutants in dynein heavy chain 1b (DHC1b) have stumpy flagella, demonstrating solely that retrograde IFT is required for flagellar assembly. We isolated a Chlamydomonas reinhardtii mutant (dhc1b-3) with a temperature-sensitive defect in DHC1b, enabling inducible inhibition of retrograde IFT in full-length flagella. Although dhc1b-3 flagella at the nonpermissive temperature (34 degrees C) showed a dramatic reduction of retrograde IFT, they remained nearly full-length for many hours. However, dhc1b-3 cells ...

Avalanche-Like Behavior In Ciliary Import, William B. Ludington, Kimberly A. Wemmer, Karl-Ferdinand Lechtreck, George B. Witman, Wallace F. Marshall

Cell and Developmental Biology Publications and Presentations

Cilia and flagella are microtubule-based organelles that protrude from the cell body. Ciliary assembly requires intraflagellar transport (IFT), a motile system that delivers cargo from the cell body to the flagellar tip for assembly. The process controlling injections of IFT proteins into the flagellar compartment is, therefore, crucial to ciliogenesis. Extensive biochemical and genetic analyses have determined the molecular machinery of IFT, but these studies do not explain what regulates IFT injection rate. Here, we provide evidence that IFT injections result from avalanche-like releases of accumulated IFT material at the flagellar base and that the key regulated feature of length ...

The Interrelationship Between Apc/C And Plk1 Activities In Centriole Disengagement, Toshiyuki Hatano, Greenfield Sluder

Cell and Developmental Biology Publications and Presentations

Mother-daughter centriole disengagement, the necessary first step in centriole duplication, involves Plk1 activity in early mitosis and separase activity after APC/C activity mediates securin degradation. Plk1 activity is thought to be essential and sufficient for centriole disengagement with separase activity playing a supporting but non-essential role. In separase null cells, however, centriole disengagement is substantially delayed. The ability of APC/C activity alone to mediate centriole disengagement has not been directly tested. We investigate the interrelationship between Plk1 and APC/C activities in disengaging centrioles in S or G2 HeLa and RPE1 cells, cell types that do not reduplicate ...

Regulation Of Mrna Export By The Pi3 Kinase / Akt Signal Transduction Pathway, Alexandre Jose Christino Quaresma, Rachel Sievert, Jeffrey A. Nickerson

Cell and Developmental Biology Publications and Presentations

UAP56, ALY/REF, and NXF1 are mRNA export factors that sequentially bind at the 5' end of a nuclear mRNA, but are also reported to associate with the Exon Junction Complex (EJC). To screen for signal transduction pathways regulating mRNA export complex assembly we used Fluorescence Recovery after Photobleaching (FRAP) to measure the binding of mRNA export and EJC core proteins in nuclear complexes. The fraction of UAP56, ALY/REF, and NXF1 tightly bound in complexes was reduced by drug inhibition of the PI3 kinase / AKT pathway, as was the tightly bound fraction of the core EJC proteins eIF4A3, MAGOH ...

Nuclear Shape Changes Are Induced By Knockdown Of The Swi/Snf Atpase Brg1 And Are Independent Of Cytoskeletal Connections, Karen M. Imbalzano, Nathalie Cohet, Qiong Wu, Jean M. Underwood, Anthony N. Imbalzano, Jeffrey A. Nickerson

Cell and Developmental Biology Publications and Presentations

Changes in nuclear morphology occur during normal development and have been observed during the progression of several diseases. The shape of a nucleus is governed by the balance of forces exerted by nuclear-cytoskeletal contacts and internal forces created by the structure of the chromatin and nuclear envelope. However, factors that regulate the balance of these forces and determine nuclear shape are poorly understood. The SWI/SNF chromatin remodeling enzyme ATPase, BRG1, has been shown to contribute to the regulation of overall cell size and shape. Here we document that immortalized mammary epithelial cells show BRG1-dependent nuclear shape changes. Specifically, knockdown ...

Activation Of Fgfr1 In Adult Cardiomyocytes Leads To Development Of A Hypertrophic Cardiomyopathy, Joy I. Wang

Undergraduate Research Symposium

In both humans and mice, Fibroblast Growth Factor (FGF) is upregulated following injury to the heart, and published studies have shown that FGF2 serves as a mediator in cardioprotection following cardiac stress or injury. Although FGF2 plays an important role following injury, mice that lack or overexpress FGF2 develop normally and do not have a phenotype under homeostatic conditions. It is currently unknown how FGF signaling is regulated in the adult heart and why the effects are only observed following injury. We hypothesized that FGF signaling may be repressed in the adult heart under homeostatic conditions and becomes reactivated following ...

Intrinsic Apoptotic Pathway: Effects Of Calcium On Murine Cytochrome C Release In Brain And Liver Mitochondria, Dane M. Edwards

Senior Honors Papers

A cell may use one of three main apoptotic pathways leading to programmed cell death: the extrinsic pathway, the perforin/granzyme pathway and the intrinsic pathway. The most pertinent to this discussion is the intrinsic pathway, which utilizes the mitochondria as an essential intermediary. Mitochondria’s primary function in relation to this pathway is the subsequent release of pro-apoptotic factors including cytochrome c, which activate a caspase cascade leading to the death of the cell. Cytochrome c is released partly due to an increase in cytosolic calcium levels. Two methods of the release of cytochrome c have been proposed. The ...

Flash4 Dark Reference Images, George Mcnamara

George McNamara

Hamamatsu FLASH4.0 dark reference images, acquired with 10 second exposure times, no light to camera. Camera offset (set by Hamamatsu( is ~100 (the average intensity of the first image is always ~1 intensity level higher - an odd feature, but trivial in practice for a 16-bit camera).

George McNamara, Ph.D.

Single Cells Analyst at L.J.N. Cooper Lab

University of Texas M.D. Anderson Cancer Center

Mechanisms Underlying The Heterogeneous Sensitivities Of Cancer Cells To Proteasome Inhibitors, Matthew C. White

UT GSBS Dissertations and Theses (Open Access)

The mechanisms underlying cellular response to proteasome inhibitors have not been clearly elucidated in solid tumor models. Evidence suggests that the ability of a cell to manage the amount of proteotoxic stress following proteasome inhibition dictates survival. In this study using the FDA-approved proteasome inhibitor bortezomib (Velcade®) in solid tumor cells, we demonstrated that perhaps the most critical response to proteasome inhibition is repression of global protein synthesis by phosphorylation of the eukaryotic initiation factor 2-α subunit (eIF2α). In a panel of 10 distinct human pancreatic cancer cells, we showed marked heterogeneity in the ability of cancer cells to induce ...

The P63 Isoform ∆Np63Α Inhibits Epithelial – Mesenchymal Transition By Promoting The Expression Of Mir-205 In Human Bladder Cancer Cells, Mai Tran

UT GSBS Dissertations and Theses (Open Access)

p63, a p53 family member, is a transcription factor that has complex roles in cancer. This study focuses on the role of the ∆Np63α isoform in bladder cancer (BC). Epithelial – mesenchymal transition (EMT) is a physiological process that plays an important part in metastasis and drug resistance. At the molecular level, EMT is characterized by the loss of the epithelial marker E-cadherin, and the acquisition of the transcriptional repressors of E-cadherin (ZEB1, ZEB2, TWIST, SNAI1 and SNAI2). Recent publications highlight the role of microRNAs belonging to the miR-200 family and miR-205 in preventing EMT through suppression of ZEB1 and ZEB2 ...