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Teaching Systems Biology Of The Circadian Clock With Journal Articles And Matlab, Stephanie R. Taylor 2016 Colby College

Teaching Systems Biology Of The Circadian Clock With Journal Articles And Matlab, Stephanie R. Taylor

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Extracting Biochemical Parameters From Protein Distributions Of Vascular Cells, Partha Srinivasan 2016 Cleveland State University

Extracting Biochemical Parameters From Protein Distributions Of Vascular Cells, Partha Srinivasan

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Actin-Based Feedback Circuits In Cell Migration And Endocytosis, Xinxin Wang 2016 Washington University in St. Louis

Actin-Based Feedback Circuits In Cell Migration And Endocytosis, Xinxin Wang

Arts & Sciences Electronic Theses and Dissertations

In this thesis, we study the switch and pulse functions of actin during two important cellular processes, cell migration and endocytosis. Actin is an abundant protein that can polymerize to form a dendritic network. The actin network can exert force to push or bend the cell membrane. During cell migration, the actin network behaves like a switch, assembling mostly at one end or at the other end. The end with the majority of the actin network is the leading edge, following which the cell can persistently move in the same direction. The other end, with the minority of the actin ...


Comparative Analysis Of In Situ Fibronectin Using Tof-Sims, Spi-Ms, And Dropdesi-Ms In A Microfluidic Reactor, Shannon Fasing, Xiao-Ying Yu, Juan Yao, Jiachao Yu 2016 Pacific Northwest National Laboratory

Comparative Analysis Of In Situ Fibronectin Using Tof-Sims, Spi-Ms, And Dropdesi-Ms In A Microfluidic Reactor, Shannon Fasing, Xiao-Ying Yu, Juan Yao, Jiachao Yu

STAR (STEM Teacher and Researcher) Program Posters

Fibronectin is an important biomolecule due to its role in cell differentiation, growth, kinesis, and adhesion. Such biological responses are mediated through membrane recognition and signaling; where fibronectin is found. Studying the outer molecular surface of fibronectin allows deeper insight into the microbiological reactions that occur during these processes. In situ mass spectrometry analysis in aqueous solution accurately represents fibronectin’s chemical components, made possible by a vacuum compatible microfluidic reactor, SALVI (System for Analysis at the Liquid Vacuum Interface). SALVI was paired with the analytical tools: time-of-flight secondary ion mass spectrometer (ToF-SIMS), single photon ionization mass spectrometer (SPI-MS) and ...


Pinpointing The Molecular Basis For Metal Ion Effects On Plasminogen Activator Inhibitor-1 (Pai-1), Joel Cullen Bucci 2016 University of Tennessee, Knoxville

Pinpointing The Molecular Basis For Metal Ion Effects On Plasminogen Activator Inhibitor-1 (Pai-1), Joel Cullen Bucci

Doctoral Dissertations

Plasminogen activator inhibitor type-1 (PAI-1) specifically inhibits the proteases tissue type plasminogen activator and urokinase plasminogen activator to control the activation of fibrinolysis. Vitronectin interacts with PAI-1 primarily through the somatomedin B (SMB) domain to stabilize and localize PAI-1 to sites of injury. Our laboratory observed that transition metals such as copper2+ have VN dependent, reciprocal effects on how long PAI-1 remains active. We aim to determine the molecular basis for effects of copper2+ on PAI-1 activity. We employed a computational algorithm (MUG) to predict metal binding clusters, and introduced mutations hypothesized to create metal binding deficiency. We ...


Ribosome*Rela Structures Reveal The Mechanism Of Stringent Response Activation, Anna B. Loveland, Eugene Bah, Rohini Madireddy, Ying Zhang, Axel F. Brilot, Nikolaus Grigorieff, Andrei A. Korostelev 2016 University of Massachusetts Medical School

Ribosome*Rela Structures Reveal The Mechanism Of Stringent Response Activation, Anna B. Loveland, Eugene Bah, Rohini Madireddy, Ying Zhang, Axel F. Brilot, Nikolaus Grigorieff, Andrei A. Korostelev

Open Access Articles

Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 A wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the ...


Assessment Of Post-Treatment Imaging Changes Following Radiotherapy Using Magnetic Susceptibility Techniques, Jean-Guy Belliveau 2016 The University of Western Ontario

Assessment Of Post-Treatment Imaging Changes Following Radiotherapy Using Magnetic Susceptibility Techniques, Jean-Guy Belliveau

Electronic Thesis and Dissertation Repository

Radiation therapy (RT) is a common treatment for brain neoplasms and is used alone or in combination with other therapies. The use of RT has been found to be successful in controlling tumors and extending the overall survival of patients; however, there are many unanswered questions regarding radiotherapy effects in the normal brain surrounding or infiltrated by tumor. Changes to the vascular and parenchyma have been documented, and more recently inflammatory mechanisms have been postulated to play a role in radiation injury. Traditional imaging techniques used within the clinic (CT and MRI) are often lacking in their ability to differentiate ...


Computational Modeling Of Allosteric Stimulation Of Nipah Virus Host Binding Protein, Priyanka Dutta 2016 University of South Florida

Computational Modeling Of Allosteric Stimulation Of Nipah Virus Host Binding Protein, Priyanka Dutta

Graduate Theses and Dissertations

Nipah belongs to the family of paramyxoviruses that cause numerous fatal diseases in humans and farm animals. There are no FDA approved drugs for Nipah or any of the paramyxoviruses. Designing antiviral therapies that are more resistant to viral mutations require understanding of molecular details underlying infection. This dissertation focuses on obtaining molecular insights into the very first step of infection by Nipah. Such details, in fact, remain unknown for all paramyxoviruses. Infection begins with the allosteric stimulation of Nipah virus host binding protein by host cell receptors. Understanding molecular details of this stimulation process have been challenging mainly because ...


Closing The Net On Retroviruses, Jeremy Luban 2016 University of Massachusetts Medical School

Closing The Net On Retroviruses, Jeremy Luban

Open Access Articles

Structural studies reveal how an antiviral factor forms a molecular net to restrict retroviruses including HIV-1.


Differential Association Of Vitronectin And Fibronectin With Glass And Electrospun Fibers Of A Poly (D-Lysine) /Poly (Acrylic Acid), Syed Muhammad Sohaib Zafar Zafar 2016 University of South Florida

Differential Association Of Vitronectin And Fibronectin With Glass And Electrospun Fibers Of A Poly (D-Lysine) /Poly (Acrylic Acid), Syed Muhammad Sohaib Zafar Zafar

Graduate Theses and Dissertations

Proteins represent major constituent of the extracellular matrix which plays an important role in the formation, maintenance and remodeling of tissues, this project focuses on adsorption of two specific serum proteins fibronectin (FN) and vitronectin (VTN) responsible for mediating cell matrix interaction through integrin binding, tripeptide Arg-Gly-Asp (RGD) sequence found in these protein features are recognized by αβV3 integrin which ultimately helps in clot formation.


Inquiry Of Lipid Membranes Interacting With Functional Peptides And Polyphenol Drug Molecules, Chian Sing Ho 2016 University of South Florida

Inquiry Of Lipid Membranes Interacting With Functional Peptides And Polyphenol Drug Molecules, Chian Sing Ho

Graduate Theses and Dissertations

Cellular membranes are important targets for many membrane-active peptides and drug compounds. Here we are interested in deciphering how lipid membranes are perturbed by several membrane-active molecules, including the transmembrane domain of the influenza M2 protein (M2TM), aggregates formed by a synthetic polyglutamine peptide, and three polyphenol compounds (i.e., tamoxifen, genistein, and verapamil). We employ phase-separated ternary lipid model membranes in the form of giant unilamellar vesicles (GUVs) to simulate raft-like structures that have been proposed to govern many important processes in plasma membranes (e.g., intracellular singling and trafficking). Specifically, we use fluorescent microscopy to interrogate how those ...


Conformational Dynamics And Stability Associated With Magnesium Or Calcium Binding To Dream In The Regulation Of Interactions Between Dream And Dna Or Presenilins, Khoa Ngoc Pham 2016 Florida International University

Conformational Dynamics And Stability Associated With Magnesium Or Calcium Binding To Dream In The Regulation Of Interactions Between Dream And Dna Or Presenilins, Khoa Ngoc Pham

FIU Electronic Theses and Dissertations

Downstream regulatory element antagonist modulator (DREAM) is involved in various interactions with targets both inside and outside of the nucleus. In the cytoplasm, DREAM interacts with the C-terminal fragments of presenilins to facilitate the production of β-amyloid plaques in Alzheimer’s disease. In the nucleus, Ca2+ free DREAM directly binds to specific downstream regulatory elements of prodynorphin/c-fos gene to repress the gene transcription in pain modulation. These interactions are regulated by Ca2+ and/or Mg2+ association at the EF-hands in DREAM. Therefore, understanding the conformational dynamics and stability associated with Ca2+ and/or Mg ...


Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas 2016 Graduate Center, City University of New York

Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Newly transcribed precursor messenger RNA (pre-mRNA) molecules contain coding sequences (exons) interspersed with non-coding intervening sequences (introns). These introns must be removed in order to generate a continuous coding sequence prior to translation of the message into protein. The mechanism through which these introns are removed is known as pre-mRNA splicing, a two-step reaction catalyzed be a large macromolecular machine, the spliceosome, located in the nucleus of eukaryotic cells. The spliceosome is a protein-directed ribozyme composed of small nuclear RNAs (snRNA) and hundreds of proteins that assemble in a very dynamic process. One of these snRNAs, the U2 snRNA, is ...


Analysis Of Gompertzian Growth In Aggregating Multicellular Tumor Nodules, Gwendolyn A. Deger 2016 University of Massachusetts Boston

Analysis Of Gompertzian Growth In Aggregating Multicellular Tumor Nodules, Gwendolyn A. Deger

Graduate Masters Theses

Past studies have shown that tumor growth generally follows an exponential growth function or, with a limiting growth constraint, the sigmoid Gompertzian function, where a terminal tumor size is reached at late times. The classical Gompertzian description of tumor growth applies in the case of two-dimensional (2D) in vitro cell studies due to the effect of physical limitations on possible growth area. This project asked whether Gompertzian form applies to the in vitro growth of multifocal 3D tumor nodules, whose size is determined by aggregation events as well as cell proliferation. Previous reports have indicated that these three-dimensional (3D) spheroids ...


Single Molecule Analysis Reveals Reversible And Irreversible Steps During Spliceosome Activation, Aaron A. Hoskins, Margaret L. Rodgers, Larry J. Friedman, Jeff Gelles, Melissa J. Moore 2016 University of Wisconsin-Madison

Single Molecule Analysis Reveals Reversible And Irreversible Steps During Spliceosome Activation, Aaron A. Hoskins, Margaret L. Rodgers, Larry J. Friedman, Jeff Gelles, Melissa J. Moore

Open Access Articles

The spliceosome is a complex machine composed of small nuclear ribonucleoproteins (snRNPs) and accessory proteins that excises introns from pre-mRNAs. After assembly the spliceosome is activated for catalysis by rearrangement of subunits to form an active site. How this rearrangement is coordinated is not well-understood. During activation, U4 must be released to allow U6 conformational change, while Prp19 complex (NTC) recruitment is essential for stabilizing the active site. We used multi-wavelength colocalization single molecule spectroscopy to directly observe the key events in Saccharomyces cerevisiae spliceosome activation. Following binding of the U4/U6.U5 tri-snRNP, the spliceosome either reverses assembly by ...


Protein Adsorption Using A Lattice Toy Model, Ari J. Weiland 2016 Macalester College

Protein Adsorption Using A Lattice Toy Model, Ari J. Weiland

Macalester Journal of Physics and Astronomy

Protein adsorption is an important subfield of Biophysics particularly relevant in medical science. Using a computational simulation with a basic but configurable two-dimensional square lattice model of approximate amino acid interactions, I investigated the entropic effects of protein adsorption on a weakly attractive surface. These simulations allow for a precise calculation of the partition functions of these complex systems, from which I can then analyze other thermodynamic properties.


Force Generation And Contraction Of Random Actomyosin Bundles., Dietmar B. Oelz 2016 Courant Institute (NYU)

Force Generation And Contraction Of Random Actomyosin Bundles., Dietmar B. Oelz

Biology and Medicine Through Mathematics Conference

No abstract provided.


Geometric Control Of Yap-Dependent Mechanotransduction: A Proposed Model, Ngozi A. Eze, Heather A. Cirka, Kristen L. Billiar 2016 Worcester Polytechnic Institute

Geometric Control Of Yap-Dependent Mechanotransduction: A Proposed Model, Ngozi A. Eze, Heather A. Cirka, Kristen L. Billiar

UMass Center for Clinical and Translational Science Research Retreat

The Billiar lab is interested in the interplay between mechanical tension and programmed cell death (namely, apoptosis) in cells growing on micro-contact printed aggregates. The Billiar lab uses a bioinspired hydrogel to develop an in vitro model for mechanosensitive signaling in mammalian cells. The micro-contact printed cell aggregates experience a loss of tensional homeostasis at the center of the aggregates, which results in selective cell death at the center, but not periphery of the aggregates, followed by calcification, similar to excised diseased aortic valves. However, the subcellular mechanisms responsible for transducing the mechanical cues from the loss of tensional homeostasis ...


Id4 Acts As A Tumor Suppressor Via P53: Mechanistic Insight, Derrick J. Morton Jr. 2016 Clark Atlanta University

Id4 Acts As A Tumor Suppressor Via P53: Mechanistic Insight, Derrick J. Morton Jr.

Electronic Theses & Dissertations Collection for Atlanta University & Clark Atlanta University

Overexpression of tumor-derived mutant p53 is a common event in tumorigenesis, suggesting an advantageous selective pressure in cancer initiation and progression. Given that p53 is found to be mutated in 50% of all human cancers, restoration of mutant p53 to its wild type biological function has been a widely sought after avenue for cancer therapy. Most research efforts have largely focused on restoration of mutant p53 by artificial means given that p53 has some degree of conformational flexibility allowing for introduction of short peptides and artificial compounds. Recently, theoretical modeling and studies focused on restoration of mutant p53 by physiological ...


Rna Interference Knock-Down Suggests That Pirl6 Functions In The Male Gametophyte Of Arabidopsis Thaliana, Savannah R. McNichol 2016 Whitman College

Rna Interference Knock-Down Suggests That Pirl6 Functions In The Male Gametophyte Of Arabidopsis Thaliana, Savannah R. Mcnichol

Honors Theses

Signal transduction pathways are critical to the success of multicellular organisms because they direct normal cellular processes and healthy responses to stimuli. Conversely, signaling pathway malfunctions can have large consequences for the survival of an organism and its progeny. Leucine-rich repeat proteins (LRRs) are a superfamily of proteins found in all eukaryotes that are capable of forming specific protein-protein interactions, and thus are well-suited to function in these signal transduction pathways. The Ras-group LRRs are one class of LRRs that interact with Ras or Ras-like small G-proteins. In the plant model system Arabidopsis thaliana, the Plant Intracellular Ras-group Leucine-rich-repeat (PIRL ...


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