Cell and Developmental Biology Commons^™

Dynamic Nucleosome Organization At Hox Promoters During Zebrafish Embryogenesis, Steven Weicksel, Jia Xu, Charles G. Sagerstrom

University of Massachusetts Medical School Faculty Publications

Nucleosome organization at promoter regions plays an important role in regulating gene activity. Genome-wide studies in yeast, flies, worms, mammalian embryonic stem cells and transformed cell lines have found well-positioned nucleosomes flanking a nucleosome depleted region (NDR) at transcription start sites. This nucleosome arrangement depends on DNA sequence (cis-elements) as well as DNA binding factors and ATP-dependent chromatin modifiers (trans-factors). However, little is understood about how the nascent embryonic genome positions nucleosomes during development. This is particularly intriguing since the embryonic genome must undergo a broad reprogramming event upon fusion of sperm and oocyte. Using four stages of early embryonic ...

Networking Development By Boolean Logic, Shikui Tu, Thoru Pederson, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

Eric Davidson at Caltech has spent several decades investigating the molecular basis of animal development using the sea urchin embryo as an experimental system ( 1) (,) ( 2) although his scholarship extends to all of embryology as embodied in several editions of his landmark book. ( 3) In recent years his laboratory has become a leading force in constructing gene regulatory networks (GRNs) operating in sea urchin development. ( 4) This axis of his work has its roots in this laboratory's cDNA cloning of an actin mRNA from the sea urchin embryo (for the timeline see ref. 1)-one of the first eukaryotic ...

Metabolizing Challenges, Erica Chin

2013 Grand Challenge Scholars Program

This project reflects upon the author's experiences in the five areas of study requested by the Grand Challenge Scholars program, specifically her research on bacterial metabolism. the focus is on how these experiences shaped her identity and goals.

Is There A Role For Reactive Oxygen Species In Zebrafish Embryonic Development?, Vivek Krishnan

Biology Master's Theses

Reactive oxygen species (ROS) are generated by many exogenous and endogenous sources. They are highly reactive and can attack biomolecules such as proteins, lipids and DNA, causing damage to living cells. DNA is subjected to constant attack by many damage inducing agents including ROS, but constant repair and maintenance by multiple DNA repair pathways helps to maintain genomic stability. The cell is also protected from the effects of ROS by antioxidants. However, ROS are implicated in cell signaling as important primary and secondary messengers. Many critical transcription factors involved in embryonic development are sensitive to the redox condition in the ...

Role Of The Cytoplasmic Polyadenylation Element Binding Proteins In Neuron: A Dissertation, Aparna Oruganty

GSBS Dissertations and Theses

Genome regulation is an extremely complex phenomenon. There are various mechanisms in place to ensure smooth performance of the organism. Post-transcriptional regulation of gene expression is one such mechanism. Many proteins bind to mRNAs and regulate their translation. In this thesis, I have focused on the Cytoplasmic Polyadenylation Element Binding family of proteins (CPEB1-4); a group of sequence specific RNA binding proteins important for cell cycle progression, senescence, neuronal function and plasticity. CPEB protein binds mRNAs containing a short Cytoplasmic Polyadenylation Element (CPE) in 3’ untranslated Region (UTR) and regulates the polyadenylation of these mRNAs and thereby controls translation. In ...

Comparison Of Th1 Cytokines And T Cell Markers Gene Expressions Between Virulent And An Attenuated Eiav Vaccine Strain, Talia R. Henkle

Honors Program Senior Capstone Collection

The equine infectious anemia virus (EIAV) is closely related to HIV and has been used as a model to identify protective mechanisms against lentivirus infection. In horses, EIA infection progresses for about a year before infected horses manage to control virus replication. This naturally-gained protection is absolutely dependent on active immune responses as evidenced by the fact that immunosuppressive drugs can induce the recurrence of disease. As the resolution of initial viremia correlates with the appearance of virus specific cytotoxic T lymphocytes (CTL), we believe that cellular immune responses play a key role in controlling EIAV in the horse. In ...

Endogenous Inhibitor Proteins That Connect Ser/Thr Kinases And Phosphatases In Cell Signaling., Masumi Eto, David L Brautigan

Department of Molecular Physiology and Biophysics Faculty Papers

Protein phosphatase activity acts as a primary determinant of the extent and duration of phosphorylation of cellular proteins in response to physiological stimuli. Ser/Thr protein phosphatase-1 (PP1) belongs to the PPP superfamily, and is associated with regulatory subunits that confer substrate specificity, allosteric regulation, and subcellular compartmentalization. In addition, all eukaryotic cells contain multiple heat-stable proteins that originally were thought to inhibit phosphatase catalytic subunits released from the regulatory subunits, as a fail-safe mechanism. However, discovery of C-kinase-activated PP1 inhibitor, Mr of 17 kDa (CPI-17) required fresh thinking about the endogenous inhibitors as specific regulators of particular phosphatase complexes ...

Nuclear Localization Of Cpi-17, A Protein Phosphatase-1 Inhibitor Protein, Affects Histone H3 Phosphorylation And Corresponds To Proliferation Of Cancer And Smooth Muscle Cells., Masumi Eto, Jason A Kirkbride, Rishika Chugh, Nana Kofi Karikari, Jee In Kim

Department of Molecular Physiology and Biophysics Faculty Papers

CPI-17 (C-kinase-activated protein phosphatase-1 (PP1) inhibitor, 17kDa) is a cytoplasmic protein predominantly expressed in mature smooth muscle (SM) that regulates the myosin-associated PP1 holoenzyme (MLCP). Here, we show CPI-17 expression in proliferating cells, such as pancreatic cancer and hyperplastic SM cells. Immunofluorescence showed that CPI-17 was concentrated in nuclei of human pancreatic cancer (Panc1) cells. Nuclear accumulation of CPI-17 was also detected in the proliferating vascular SM cell culture and cells at neointima of rat vascular injury model. The N-terminal 21-residue tail domain of CPI-17 was necessary for the nuclear localization. Phospho-mimetic Asp-substitution of CPI-17 at Ser12 attenuated the nuclear ...

Evolutionary And Molecular Analysis Of Conserved Vertebrate Immunity To Fungi, Erin Carter

Honors College

The innate immune system is highly conserved amongst all multicellular organisms. Yet a constant battle exists between host cells and pathogens due to the rapid evolution of immune system components. Functional genomics and in silico methods can be employed to elucidate the evolutionary patterns of vertebrate immunity to pathogenic fungi such as Candida albicans, an opportunistic fungal pathogen that can cause lethal candidiasis in the immunocompromised. Mammals such as humans and mice possess conserved C-type lectin receptors that recognize the C. albicans cell wall. However, these receptors have not been identified in fish. Here I describe how we identified potential ...

Diverse Mechanisms Of Trinucleotide Repeat Disorders: An Exploration Of Fragile X Syndrome And Huntington’S Disease, Cara Strobel

Undergraduate Review

Trinucleotide repeat disorders are an umbrella group of genetic diseases that have been well described clinically for a long time; however, the scientific community is only beginning to understand their molecular basis. They are classified in two basic groups depending on the location of the relevant triplet repeats in a coding or a non-coding region of the genome. Repeat expansion past a disease-specific threshold results in molecular and cellular abnormalities that manifest themselves as disease symptoms. Repeat expansion is postulated to occur via slippage during DNA replication and/or transcription-mediated DNA repair. Trinucleotide repeat disorders are characterized by genetic anticipation ...

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 ...