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Exploring The Mechanism Of Shp2 And Egfr/Her2 Cooperation In Breast Cancer Cell Signaling, Zachary Raymond Hartman

Graduate Theses, Dissertations, and Problem Reports

The Src homology 2-containing protein tyrosine phosphatase 2 (SHP2) has been established as a critical mediator of cancer-related cell signaling downstream of receptor tyrosine kinases like EGFR and HER2. As such, targeting of SHP2 is being recognized as a potentially viable therapeutic option in HER2-positive and triple-negative breast cancers. In this report, I employed molecular and cellular biology techniques to further elucidate the role of SHP2 downstream of receptor tyrosine kinases in breast cancer cell lines. In this way, I was able to contribute knowledge to how SHP2 controls triple-negative cell motility. In addition, the mechanism of SHP2 control of …

Gene Expression Studies For The Analysis Of Domoic Acid Production In The Marine Diatom Pseudo-Nitzschia Multiseries, Katie Boissonneault, Brooks M. Henningsen, Stephen S. Bates, Deborah L. Robertson, Sean Milton, Jerry Pelletier, Deborah A. Hogan, David E. Housman

Dartmouth Scholarship

Pseudo-nitzschia multiseries Hasle (Hasle) (Ps-n) is distinctive among the ecologically important marine diatoms because it produces the neurotoxin domoic acid. Although the biology of Ps-n has been investigated intensely, the characterization of the genes and biochemical pathways leading to domoic acid biosynthesis has been limited. To identify transcripts whose levels correlate with domoic acid production, we analyzed Ps-n under conditions of high and low domoic acid production by cDNA microarray technology and reverse-transcription quantitative PCR (RT-qPCR) methods. Our goals included identifying and validating robust reference genes for Ps-n RNA expression analysis under these conditions.

Srs2 Prevents Rad51 Filament Formation By Repetitive Motion On Dna, Yupeng Qiu, Edwin Antony, Sultan Doganay, Hye Ran Koh, Timothy M. Lohman, Sua Myong

Biological Sciences Faculty Research and Publications

Srs2 dismantles presynaptic Rad51 filaments and prevents its re-formation as an anti-recombinase. However, the molecular mechanism by which Srs2 accomplishes these tasks remains unclear. Here we report a single-molecule fluorescence study of the dynamics of Rad51 filament formation and its disruption by Srs2. Rad51 forms filaments on single-stranded DNA by sequential binding of primarily monomers and dimers in a 5′–3′ direction. One Rad51 molecule binds to three nucleotides, and six monomers are required to achieve a stable nucleation cluster. Srs2 exhibits ATP-dependent repetitive motion on single-stranded DNA and this activity prevents re-formation of the Rad51 filament. The same activity of …

Absorption Of Marine Vs Non-Marine Sources Of Epa And Dha, John S. Ketz

Graduate Theses, Dissertations, and Problem Reports

Docosahexaenoic acid (DHA) from algae oil has been incorporated into tissues at a lower level and has been less effective than fish oil (FO) at reducing body fat. Our objective was to determine fecal excretion of eicosapentaenoic acid (EPA) and DHA from different dietary sources. Male mice (n=100) were fed a 12% lipid diet containing soy oil (SO), FO, yeast oil (YO) algae oil (AO), or AO+YO. The AO diet was fed to contain amounts of DHA equal to the FO diet, and the YO diet was fed to contain amounts of EPA equal to the FO diet. To measure …

Biochemistry As A Liberal Art, David M. Morgan

The Western Conference on Science Education

One now routinely learns of a university theatre department closed here, a philosophy department closed there, of budget pressure that has forced the cancellation of this language program, or how funding cutbacks have permitted that fine arts department to continue to function, but only with sessional faculty. The sciences (of course?) have been largely spared. But how ought science faculty to respond to the philosophical questions involved in the cultural squeeze on their colleagues? Herein I argue that science faculty ought to be as outraged as they are: what is at stake is the cultural understanding of the meaning and …

An Ethnobotanical Approach To Finding Antimicrobial Compounds In Wooly Blue Curls (Trichostema Lanatum) Using A Kirby-Bauer Disc Diffusion Assay, Matthew C. Fleming, P. Matthew Joyner

Featured Research

Plants can be an important source of creativity and production of new drugs. In this study, extracts of wooly blue curls (Trichostema lanatum) were made using DMSO and tested for antimicrobial activity on a panel of bacteria commonly found in separate ecological niches. Wooly blue curls (WBC) was chosen due to its being recorded as a strong disinfectant by the Chumash people. It was found that WBC does exhibit antimicrobial activity against gram positive bacteria and not against gram negative bacteria. However, gram negative bacteria with reduced drug efflux function became susceptible to the WBC extract.

Development And Application Of Mass Spectrometry-Based Proteomics To Generate And Navigate The Proteomes Of The Genus Populus, Paul Edward Abraham

Doctoral Dissertations

Historically, there has been tremendous synergy between biology and analytical technology, such that one drives the development of the other. Over the past two decades, their interrelatedness has catalyzed entirely new experimental approaches and unlocked new types of biological questions, as exemplified by the advancements of the field of mass spectrometry (MS)-based proteomics. MS-based proteomics, which provides a more complete measurement of all the proteins in a cell, has revolutionized a variety of scientific fields, ranging from characterizing proteins expressed by a microorganism to tracking cancer-related biomarkers. Though MS technology has advanced significantly, the analysis of complicated proteomes, such as …

Disulfide Bridging The Gap Between Src And Cortactin: A New Paradigm In Sh2 Domain-Mediated Signaling, Jason Vanburen Evans

Graduate Theses, Dissertations, and Problem Reports

Src and cortactin are cytoplasmic proteins that are implicated in cancer progression and metastasis. Src is a non-receptor tyrosine kinase that also regulates normal cell homeostasis through phosphorylation of multiple downstream substrates. Cortactin is an actin binding protein and nucleation promoting factor that promotes the formation of stable branching networks within the actin cytoskeleton. Together, these proteins work in concert to promote the invasive and metastatic potential of tumor cells due to tyrosine phosphorylation of cortactin by Src. However, the mechanistic details of the interaction between Src and cortactin have never been elucidated. Collectively, this work aims to define how …

Diagnosis And Prevention Of Metabolic Diseases In Drosophila Melanogaster, Claire Marie Coogan

Collection of Engaged Learning

No abstract provided.

Integrating Art And Science In Undergraduate Education, Daniel Gurnon

Chemistry & Biochemistry Faculty Publications

The prevailing vision for undergraduate science education includes increased collaboration among teachers of science, technology, engineering and math (STEM) and an overhaul of introductory courses [1]–[4]. But by staying within the borders of STEM, are we overlooking connections between the arts and innovative science? Likewise, are we missing an important opportunity to inspire and inform nonscientists? Here we explore how weaving the visual arts into a science curriculum can both help develop scientific imagination and engage nonscientists. As an example, we describe a recent collaboration between artists and scientists to create a series of science-inspired sculptures.

Helix Turn Helix Domain, David J. Hall

Protein Domains

Helix turn helix domain #3V1A. The helix-turn helix is a DNA-binding domain. The two alpha helices are the reading or recognition helices, which bind in a groove in the DNA and recognize specific gene regulatory sequences in the DNA.

Ring Domain, David J. Hall

Protein Domains

Ring domain #1CHC. The RING finger is a specialized type of Zn finger consisting of 40–60 residues that binds two atoms of zinc, and is involved in mediating protein—protein interactions. Many zinc fingers bind nucleic acids. The presence of a RING finger domain is a characteristic of RING-class E3 ubiquitin protein ligases capable of transferring ubiquitin from an E2 enzyme to a substrate protein.

Sh2 Domain, David J. Hall

Protein Domains

SH2 domain #1BFJ. Src-homology 2 (SH2) domains are modules of ~100 amino acids that bind to specific phospho tyrosine (pY) containing peptide motifs. Conventional SH2 domains have a conserved pocket that recognizes pY, and a more variable pocket that binds 3-6 residues C-terminal to the pY and confers specificity.

Sh3 Domain, David J. Hall

Protein Domains

SH3 domain #1NEB. Src-homology 3 (SH3) domains bind to Pro-rich peptides that form a left-handed poly-Pro type II helix, with the minimal consensus Pro-X-X-Pro. Each Pro is usually preceeded by an aliphatic residue. Each in the aliphatic-Pro pair binds to a hydrophobic pocket on the SH3 domain.

Ig Domain, David J. Hall

Protein Domains

Ig domain #2CKN. This particular domain is named for the first protein in which it was found, the immunoglobulin. An immunoglobulin is a antibody. Antibodies are generated by our immune system to recognize the specific size, shape and charge of pathogens. This domain is also found on the extracellular portion of many receptors including the interleukin-1 family of receptors.

Beta Barrel, David J. Hall

Protein Domains

Beta barrel (cyan fluorescent protein) #4AR7. This fluorescent protein is a variation of green fluorescent protein from a jellyfish and is the only domain that is a complete protein. The protein is routinely used to visualize a variety of biological processes. The beta barrel domain is a beta sheet wrapped around the fluorescent active site to provide structure.

Phi X 174, David J. Hall

Infectious Pathogens

Phi X 174 database number # 1CD3. Phi X 174 is a virus that infects bacteria and was the first DNA-based genome to be sequenced in 1977. This bacteriophage has a [+] circular single-stranded DNA genome. The assembly of the capsid has been successfully done in vitro and is the focus of many studies on self-assembly, drug delivery and nanotechnology.

Human Papilloma Virus 16, David J. Hall

Infectious Pathogens

Human Papilloma virus 16, database# 1DZL Infection by most papillomaviruses is either asymptomatic or causes small benign tumors, known as papillomas or warts (e.g. human papillomavirus HPV6 or HPV11). Papillomas caused by some types, however, such as human papillomaviruses 16 and 18, carry a risk of becoming cancerous. Human papilloma virus is a non-enveloped, double stranded, circular DNA virus.

Dengue Virus, David J. Hall

Infectious Pathogens

Dengue virus, database # 1THD Dengue fever, is an infectious tropical disease caused by the dengue virus and transmitted by mosquito. Symptoms include fever, headache, muscle and joint pains, and a characteristic skin rash that is similar to measles. In a small proportion of cases the disease develops into the life-threatening dengue hemorrhagic fever. Dengue is a positive strand RNA virus that is part of the flavivirus family. Dengue is an enveloped virus meaning it has a nucleocapsid protecting the RNA and the nucleocapsid is surrounded by lipids (hence the name enveloped).

Hepatitis B, David J. Hall

Infectious Pathogens

Hepatitis B, database # 2g33. Hepatitis B is an infectious inflammatory illness of the liver caused by the hepatitis B virus (HBV). Hepatitis B virus (HBV) is a member of the Hepadnavirus family.The virus particle, (virion) consists of an outer lipid envelope and an icosahedral nucleocapsid core composed of protein. These virions are 42 nM in diameter. The nucleocapsid encloses the viral DNA and a DNA polymerase that has reverse transcriptase activity.

Physiological Effects Of Tourism And Associated Food Provisioning In An Endangered Iguana, Charles R. Knapp, Kirsten N. Hines, Trevor T. Zachariah, Caro Perez-Heydrich, John B. Iverson, Sandra D. Buckner, Shelley C. Halach, Christine R. Lattin, L. Michael Romero

Faculty Publications

© The Author 2013. Deliberately feeding wildlife is an increasingly popular tourism-related activity despite a limited understanding of long-term impacts on the species being fed. As a result, tourist behaviours that may have adverse impacts on imperiled species have often been encouraged without the necessary evaluation or oversight. Here, we report the responses of Northern Bahamian Rock Iguanas (Cyclura cychlura) to human-visitation pressure and associated food provisioning. We compared a variety of blood chemistry parameters of iguanas subjected to supplemental feeding at popular tourist destinations with iguanas occurring on islands where supplemental feeding does not take place. We demonstrate that …

Using Computational Molecular Docking Methods To Further Understand The Structure And Function Of The Mala Protein Through Binding Of Different Sugars, Dinah Draluk

Summer Research

No abstract provided.

Identification And Stoichiometric Analysis Of The Monosomal Translational Complex, Xin Wang

Doctoral Dissertations

The identification of the components involved in translational complexes has relied primarily on in vitro studies. Determining which proteins associate together in these complexes, under what conditions they do so, and how the composition of the complexes change under different conditions have became the key issues of in vivo studies. After a one-step affinity purification, using a novel technique of analytical ultracentrifugation with a fluorescence detection system (AU-FDS) I have identified a 77S monosomal translational complex in the yeast Saccharomyces cerevisiae. Major components of the 77S complex include the 80S ribosome, mRNA, and components of the closed-loop structure, eIF4E, eIF4G1/eIF4G2 …

The Identification And Characterization Of The Interaction Between Upf1 And Pab1 During Nonsense-Mediated Decay & The Identification Of Novel Protein Complexes Associated With Translation Termination Factor Erf1, Roy Richardson

Doctoral Dissertations

There are still many protein interactions that occur during translation termination that are poorly understood. One of the important termination pathways still under investigation is nonsense-mediated decay (NMD), which rapidly degrades mRNAs that contain a premature stop codon (PTC). I identified that the interaction between Upfl, which is required for NMD, and PAB1 occurs via the RRM1 domain of PAB1 in the yeast Saccharomyces cerevisiae. Determining the role of this interaction during NMD was performed with pulse-chase assays using a PGKlpG mRNA. These assays revealed that the interaction between Upfl and PAB1 is required for a shift from distributive to …

Regulation Of The Catalytic And Allosteric Properties Of Photoreceptor Phosphodiesterase (Pde6) By The Glutamic Acid-Rich Protein-2 (Garp2), Wei Yao

Doctoral Dissertations

The photoreceptor phosphodiesterase (PDE6) must be precisely regulated to control the sensitivity, amplitude, and kinetics of the photoresponse during excitation, termination and adaptation to light stimulation in rod and cone photoreceptors. The central hypothesis of this thesis is that one PDE6 binding partner, the glutamic acid-rich protein (GARP2), may regulate PDE6 to reduce its "dark noise", enhance its sensitivity and conserve metabolic energy during rod photoresponse saturation.

The first aim of this research is to better understand the unique biochemical and biophysical characteristics of GARP2 in order to reveal its functional attributes for regulating PDE6 during phototransduction in rod photoreceptors. …

Patterns Of Cytosine Methylation In The Genome Of Caenorhabditis Elegans, Kazufusa Okamoto

Doctoral Dissertations

Recent large-scale comparative analysis of cytosine DNA methylation across diverse eukaryotes suggest that early features of DNA methylation present in the last common ancestor of all eukaryotes some 1.6 to 1.8 billion years ago included the methylation of gene bodies and transposable elements (Zemach, McDaniel et al. 2010; Parfrey, Lahr et al. 2011). These potentially ancient patterns may reflect a primitive role of methylation in transcriptional fidelity and as a mechanism to protect the germ line from transposon, or repeat, mediated mutation. Because spurious transcription and mutation are hypothesized to be among the critical limiting factors to genome size, an …

Design, Synthesis And Characterization Of Chain-End Functionalized Glyco-Polymer For Efficient Proteomic Analysis, Satya Nandana Narla

ETD Archive

No abstract provided.

Broadly Applicable Methodology For The Rapid And Dosable Small Molecule-Mediated Regulation Of Transcription Factors In Human Cells, M. D. Shoulders, L. M. Ryno, Christina B. Cooley, J. W. Kelly, R. L. Wiseman

Chemistry Faculty Research

Direct and selective small molecule control of transcription factor activity is an appealing avenue for elucidating the cell biology mediated by transcriptional programs. However, pharmacologic tools to modulate transcription factor activity are scarce because transcription factors are not readily amenable to small molecule-mediated regulation. Moreover, existing genetic approaches to regulate transcription factors often lead to high nonphysiologic levels of transcriptional activation that significantly impair our ability to understand the functional implications of transcription factor activity. Herein, we demonstrate that small molecule-mediated conformational control of protein degradation is a generally applicable, chemical biological methodology to obtain small molecule-regulated transcription factors that …

Decoding Prmt1: Studies On The Catalytic Mechanism, Regulation, Inhibition, And Crosstalk Of Prmt1-Dependent Methylation, Heather L. Rust

Theses and Dissertations

Arginine methylation is catalyzed by the protein arginine methyltransferase (PRMT) family of enzymes, which transfer a methyl group from S-adenosylmethionine (SAM) to the guanidinium group of an arginine residue. This reaction first produces monomethylated arginine (MMA) that can then be further methylated to produce either asymmetrically dimethylated arginine (ADMA) or symmetrically dimethylated arginine (SDMA). There are nine PRMT family members described to date, with PRMT1 as the predominant member, suggested to be responsible for ~85% of asymmetric dimethylation. In addition, PRMT1-dependent methylation likely plays a significant role in a plethora of diseases (e.g., cancer, heart disease, and ALS). These observations …

Investigating The Interaction Of Zinc-Finger Peptides And Nicked Dna Using Phage Display, Rachel Maria Guerra

Honors Theses

Recognition of structural features of DNA such as gaps, nicks and abasic sites is critical for many DNA-binding proteins, such as those involved in DNA damage repair. This study explores a novel strategy to model these protein-DNA interactions using phage display. Phage display has been commonly used to identity zinc fingers that bind to DNA sequences, but selection of peptides that binding to specific DNA structures has not been reported in the literature. A phage library of 109 variants was created based on one of three zinc finger domains of the DNA repair protein poly (ADP-ribose) polymerase I. The library, …