Biophysics Commons^™

Developing Droplet Based 3d Cell Culture Methods To Enable Investigations Of The Chemical Tumor Microenvironment, Jacqueline Alexandria De Lora

Biomedical Sciences ETDs

Adaptation of cancer cells to changes in the biochemical microenvironment in an expanding tumor mass is a crucial aspect of malignant progression, tumor metabolism, and drug efficacy. In vitro, it is challenging to mimic the evolution of biochemical gradients and the cellular heterogeneity that characterizes cancer tissues found in vivo. It is well accepted that more realistic and controllable in vitro 3D model systems are required to improve the overall cancer research paradigm and thus improve on the translation of results, but multidisciplinary approaches are needed for these advances. This work develops such approaches and demonstrates that new droplet-based cell-encapsulation …

Study Of The Visual Adaptation Mechanism In Marine Species With The Change Of Habitation Depth., Demid Osipov, Daniil Moshnikov

The International Student Science Fair 2018

The goal of our work was to determine the principal mechanisms that provide the difference in visual perception of two marine species that live on different depths: T. Pacificus and O. Vulgaris. In nature, visual perception of species that live deeper is shifted towards the blue region. This is related to the fact that red, orange and yellow light is absorbed more strongly by water than the blue light. On the other hand, the visual perception spectrum of an animal is determined by the absorption spectrum of the "light sensor" located in rods and cones of its eye retina. These …

Inference And Control In Regulatory Genomics, Siddharth Sharma

Biology and Medicine Through Mathematics Conference

No abstract provided.

The Role Of Criticality Of Gene Regulatory Networks On Emergent Properties Of Biological Systems, Hyobin Kim

Graduate Dissertations and Theses

The relationship between criticality of gene regulatory networks (GRNs) and dynamics of GRNs at a single cell level has been vigorously studied. However, the relationship between the criticality of GRNs and properties of multicellular organisms at a higher level has not been fully explored. Here we aim at revealing potential roles of the criticality of GRNs at a multicellular and hierarchical level, using a random Boolean network as a GRN. We perform three studies. Firstly, we propose a GRN-based morphogenetic model, and delve into the role of the criticality of GRNs in morphogenesis at a multicellular level. Secondly, we include …

Molecular Mechanism Of Early Amyloid Self-Assembly Revealed By Computational Modeling, Mohtadin Hashemi

Theses & Dissertations

Protein misfolding followed by the formation of aggregates, is an early step in the cascade of conformational changes in a protein that underlie the development of several neurodegenerative diseases, including Alzheimer’s and Parkinson’s diseases. Efforts aimed at understanding this process have produced little clarity and the mechanism remains elusive.

Here, we demonstrate that the hairpin fold, a structure found in the early folding intermediates of amyloid b, induces morphological and stability changes in the aggregates of Aβ(14-23) peptide. We structurally characterized the interactions of monomer and hairpin using extended molecular dynamics (MD) simulations, which revealed a novel intercalated type complex. …

The Beta-Catenin/Muc1.Ct Interaction In Pancreatic Cancer, Edwin Wiest

Theses & Dissertations

MUC1 is overexpressed in over 90% of pancreatic cancer cases, and its interaction with beta-catenin promotes progression of the disease. Various in vitro and in vivo methods show that beta-catenin and MUC1 interact by way of the cytoplasmic tail of MUC1 (MUC1.CT). This interaction occurs in the membrane of pancreatic cancer cells but is found to a smaller extent in the nucleus as well. Biophysical methods suggest that MUC1 interacts with beta-catenin through a sequence of amino acids in the tail of MUC1 that sit very near the transmembrane domain of MUC1. In pancreatic ductal adenocarcinoma cells, it appears that …

State Dependent Function And Dynamics In Cerebral Cortical Networks, Leila Fakhraei

Graduate Theses and Dissertations

Cerebral cortex exhibits vigorous ongoing, internal neural activity even with no sensory input is present or the animal is minimally engaged in a task or behavior. This internal ongoing activity is not static; the ‘cortical state’ varies ranging from synchronous and highly correlated activity to asynchronous and weakly correlated neural activity. The main goal of the work presented here is to understand how changes in cortical states effect several aspects of cortical function and dynamics.

To meet this goal, we did three separate projects. First, we compared the predictability of neuronal network dynamics across cortical states in somatosensory cortex of …

Photonic Tools For Advanced Sensing And Imaging At The Nanoscale., Jafar Hamed Ghithan

Electronic Theses and Dissertations

This dissertation reports a novel bio-sensing strategy based on single-mode, electro-active, integrated optical waveguide (SM-EA-IOW) platforms. It also reports the development of a super-resolved far-field optical imaging tool to enable optical, electronic, and spectroelectrochemical investigations at the nanoscale. SM-EA-IOW platforms with its outstanding sensitivity for spectroelectrochemical interrogation was combined with a sandwich bioassay for the development of a novel immunosensing based strategy for label-free detection of infectious pathogens. The strategy begins with the functionalization of the electroactive waveguide surface with a capturing antibody aimed at a specific target analyte. Once the target analyte is bound to the photonic interface, it …

Nanoscale Organization Of The Small Gtpase Rac1, Kelsey Maxwell

Dissertations and Theses (Open Access)

Rac1 is a small, guanine-nucleotide binding protein that cycles between an inactive GDP-bound and active GTP-bound state to regulate actin-mediated motility, migration, and adhesion. Plasma membrane (PM) localization is essential for its biological activity. Rac1 PM targeting is directed by a C-terminal membrane anchor that encompasses a geranylgeranyl-cysteine-methyl-ester, palmitoyl, and a polybasic domain (PBD) of contiguous lysine and arginine residues. Using high-resolution imaging combined with spatial mapping analysis, I found that Rac1 forms nanoclusters on the PM. Cycling between the GTP- and GDP-bound states, Rac1 forms nanoclusters that are non-overlapping, consequently undergoing guanine nucleotide-dependent spatial segregation. I further found that …

Characterization Of Bacteriorhodopsin And Halorhodopsin Reconstituted In Lipid Bilayer Membranes, Joel Domkam Kamwa

Graduate Theses and Dissertations

Motivated to produce electricity with photon activated ion pumps, the main purpose of this work was to characterize the photosynthetic membrane proteins bacteriorhodopsin (proton pump) and halorhodopsin (chloride pump). The proteins were re-suspended in lipid bilayers. For this work, an experimental set-up was built which included: chambers for lipid bilayer formation and characterization, lasers for ion pump activation, and an AxoPatch electrophysiology system for small photocurrent measurement. Lipid bilayer membranes were formed using mostly folding method: folding two monolayers together. The membranes were characterized by their resistance, capacitance, and generated photocurrent. Photocurrent was generated upon illumination of lipid-protein membranes with …

A Mechanistic Understanding Of Self-Propagating Amyloid-Β Oligomer Conformations In Alzheimer Disease, Dexter Nathanael Dean

Dissertations

Alzheimer disease (AD) is a fatal neurodegenerative disorder characterized by the widespread deposition of proteinaceous plaques abundant in amyloid-β (Aβ) aggregates. Although the plaques mainly contain high molecular weight, insoluble Aβ fibrils, the low molecular weight soluble aggregates called oligomers have been shown as the primary toxic species responsible for synaptic dysfunction and neuronal loss in AD. The process of aggregation is nucleation-dependent, but also highly stochastic and inhomogeneous resulting in biophysically diverse assemblies. Recent advances in the field indicate a potential correlation between the phenotypic diversity observed in AD subtypes and aggregate polymorphism. Therefore, understanding the molecular mechanisms which …

Binding Of Maize Necrotic Streak Virus (Mnesv) 3’ I-Shaped Structure (3’ Iss) To Eukaryotic Translation Factors (Eifs) And Implication In Eif4f Mediated Translation Initiation, Qiao Liu

Dissertations, Theses, and Capstone Projects

5' m⁷GpppN cap and the 3' poly adenosine (A) tail of eukaryotic mRNAs are key elements for recruiting translation initiation machinery in canonical translation initiation. Unlike host mRNAs, many viruses lack these elements and yet they are translated efficiently. Plant viruses, in particular, have complex structures within their untranslated regions (UTR) that allow them to bypass some cellular translation control steps. In Maize necrotic streak virus (MNeSV) 3' UTR, an I-Shaped RNA Structure (ISS) has been reported to mediate the virus translation initiation progress. 3’ ISS binding with eIF4F has been shown to facilitate translation. 5’ -3’ kissing …

Mechanism And Development Of Peptide-Based Inhibitors To Human Islet Amyloid Polypeptide (Hiapp) Self-Assembly, Jayson Vedad

Dissertations, Theses, and Capstone Projects

Amyloid fibrils formed by of hIAPP_1-37 (also known as amylin) has been linked to type-II diabetes mortalities and its formation was found to be related to the three aromatic residues in hIAPP_1-37. In this dissertation, the role of aromatic amino acids, particularly that of Phe-23, and its various interactions to the self-assembly of human islet amyloid polypeptide (hIAPP)_22-29 were investigated. Using a variety of spectroscopic techniques with emphasis to vibrational spectroscopy (FT-IR and Raman spectroscopies) in conjunction with computational methods, different factors leading to aggregation as well as its inhibition were identified. Among the driving forces …

Regulation Of The Tubulin Homolog Ftsz In Escherichia Coli, Monika S. Buczek

Dissertations, Theses, and Capstone Projects

Escherichia coli is a well-known pathogen, and importantly, a widely used model organism in all fields of biological sciences for cloning, protein purification, and as a model for Gram-negative bacterial species. And yet, researchers do not fully understand how this bacterium replicates and divides. Every year additional division proteins are discovered, which adds complexity to how we understand E. coli undergoes cell division. Due to their specific roles in cytokinesis, some of these proteins may be potential targets for development of antibacterials or bacteriostatics, which are much needed for fighting the current global antibacterial deficit. My thesis work focuses on …

Dna Binding Kinetics Of Large Antiviral Hairpin Polyamides, Jacquelyn Niederschulte

Dissertations

While vaccines exist for the some of the most problematic strains of human papillomavirus (HPV), a double stranded DNA virus, there is currently no cure. HPV remains one of the most commonly sexually transmitted infections and is responsible for virtually all cervical cancers and genital warts. Natural products Distamycin A and netropsin have inspired the hairpin Nmethylpyrrole (Py)/N-methylimidazole (Im) polyamides (PAs) studied here. The larger hairpin PAs, designed to bind to sites of 10 or more DNA bp, have been shown to be effective antivirals against oncogenic HPV strains 16, 18, and 31, while smaller hairpin PAs are not. Despite …

Analyzing The Effects Of Ca2+ Dynamics On Mitochondrial Function In Health And Disease, Patrick Toglia

USF Tampa Graduate Theses and Dissertations

Mitochondria plays a crucial role in cells by maintaining energy metabolism and directing cell death mechanisms by buffering calcium (Ca²⁺ )from cytosol. Therefore, the Ca²⁺ overload of mitochondria due to the upregulated cytosolic Ca²⁺ , observed in many neurological disorders is hypothesized to be a key pathway leading to mitochondrial dysfunction and cell death. In particular, Ca²⁺ homeostasis disruptions due to Alzheimer’ s disease (AD)-causing presenilins (PS1/PS2) and oligomeric forms of β-amyloid peptides Aβ commonly found in AD patients are presumed to cause detrimental effects on the mitochondria and its ability to function properly. We begin …

Cloning, Purification, And Preliminary Dna-Binding And Unfolding Results For The Dna Polymerase I From The Psychrophile Psychromonas Ingrahamii, John Tod Baker

LSU Master's Theses

Psychromonas ingrahamii is a psychrophilic bacterium that lives in Arctic polar sea ice and grows at a temperature range of -12 to 10º C. This bacterium resides within veins inside the ice where the salinity is high, resulting in a freezing point depression and liquid water. The large fragment of DNA polymerase I from Psychromonas ingrahamii, called Klenpin, has been cloned, expressed, and purified in our laboratory. Although enzyme kinetic studies have been performed on a few psychrophilic enzymes, the thermodynamics of ligand binding and of protein stability have not been well studied for this class of extremophilic proteins. …

Experiences Of The Breast Cancer Patients Undergoing Radiotherapy At A Public Hospital Peshawar Pakistan, Gulzar Habibullah, Raisa Raisa, Shanaz Hussein Cassum, Rehana Elahi

School of Nursing & Midwifery

Objective: This study aimed to explore the experiences of female breast cancer patients undergoing radiotherapy (RT) in a public hospital in Peshawar, Pakistan.
Methods: This study employed a descriptive exploratory method. A purposive sample of 14 breast cancer women undergoing RT was selected for this study. Data were collected over the period of 5 months, using a semi-structured interview guide and conducting in-depth face-to-face interviews. These interviews were audio taped and transcribed by a bilingual transcriber. The translated version of the interview was coded, and the analysis was done manually.
Results: Four main categories emerged from data analysis, which were: …

Maternal Protein Restriction (Mpr): A Risk Factor For Acute Respiratory Distress Syndrome (Ards), Reza Khazaee

Western Research Forum

Background: Acute respiratory distress syndrome (ARDS) is defined as severe lung dysfunction. The lung impairments in ARDS result from alterations to pulmonary surfactant; a lipid-protein mixture coating the inside of the lung and maintains the lungs’ ability to expand easily. Due to a lack of effective pharmacological therapies mortality associated with ARDS is over 30%. Our research focuses on risk factors that indicate a susceptibility to the disease, which could provide new and early therapeutic options. One such potential risk factor is Maternal Protein Restriction (MPR). MPR is defined by low birth weight and contributes to a variety of adult-onset …

Thermodynamics In Large Hairpin Polyamide-Dna Interactions, Yang Song

Dissertations

Human papillomavirus (HPV) is a common sexually transmitted virus responsible for cervical cancers, and its infection is currently incurable. Only a few vaccines against high-risk HPV strains are available. Hairpin polyamides (PAs) in different sizes (8-20 units long) bind DNA in different lengths. They have been shown to have different anti-HPV activities in cell culture.

The interaction between PA and DNA is stabilized by two types of molecular forces: attractive and repulsive forces. Attractive forces include hydrogen bonds, van der Waals contacts and electrostatic forces between PA and DNA. Repulsive forces include the hydrophobic effect, which forces the PA out …