Biomedical Engineering and Bioengineering Commons^™

Tissue Engineering: Applications In Developmental Toxicology, Stephanie N. Thiede, Nimisha Bajaj, Kevin Buno, Sherry L. Voytik-Harbin

The Summer Undergraduate Research Fellowship (SURF) Symposium

In vivo toxicology assays are expensive, low-throughput, and often not predictive of a human response. Three-dimensional in vitro human cell-based tissue systems incorporating cell-cell and cell-matrix interactions have promise to provide high-throughput, physiologically-relevant information on the mechanism of the toxin and a more accurate assessment of the toxicity of a chemical before progression to human trials. Quantification of the disruption of vasculogenesis, the de novo formation of blood vessels from endothelial progenitor cells, can serve as an appropriate indicator of developmental toxicity since vasculogenesis is critical to the early development of the circulatory system. The current routinely used in vitro …

Impedance Biosensors For The Rapid Detection Of Viral And Bacterial Pathogens Using Avian Influenza Virus Subtypes H5n1 And H7n2 And Escherichia Coli O157:H7 As Model Targets, Jacob David Lum

Graduate Theses and Dissertations

This research investigated impedance biosensors for the rapid detection of viral and bacterial pathogens using avian influenza virus (AIV) subtypes H5N1 and H7N2 and Escherichia coli O157:H7 as the model targets, which were chosen due to their impact on the agricultural and food industries. For the detection of AIV H7N2, a single stranded DNA aptamer was selected using systematic evolution of ligands by exponential enrichment (SELEX). The selected aptamer and a previously selected aptamer against AIV H5N1 were used in a microfluidics chip with an embedded interdigitated array microelectrode to fabricate an impedance biosensor for specific detection of AIV H7N2 …

Construction Of 3d Biomimetic Tissue Niches For Directing Pancreatic Lineage Differentiation Of Human Embryonic Stem Cells, Weiwei Wang

Graduate Theses and Dissertations

The potential of human embryonic stem cells (hESCs) to differentiate into insulin producing beta cells offers great hope for cell-based therapy for diabetes treatment. However, in vitro pancreatic differentiation of hESCs remains challenging. In the past decade, most protocols for differentiating pancreatic cells have been focused on the use of signaling molecule cocktails on 2D substrates. Studies on embryonic development biology strongly suggest that extracellular matrix (ECM) plays a critical role on hESCs behavior. In this work, we first established a 3D collagen scaffold culture system for hESCs differentiating into definitive endoderm (DE), which is the first and most important …

Development Of An Efficient Human Hepatocyte Culture Platform For Assessing Novel Therapeutic Efficacy Against Plasmodium Liver Parasites, Steven Patrick Maher

USF Tampa Graduate Theses and Dissertations

Malaria is a critical and global public health problem, affecting over 200 million people every year, resulting in over 500,000 deaths. A vaccine is not currently available and only one drug, primaquine, is effective against the dormant stages of Plasmodium vivax. Preclinical assessment of novel therapeutic drugs and vaccines is hampered by the lack of an in vitro liver model for P. falciparum and P. vivax. To provide a stable human hepatocyte-based culture platform for parasite development, we engineered a microfluidic bilayer device capable of both simple and complex culture methods, including perfusion and co-culture, to better understand the requirements …

Particle Swarm Optimization Using Multiple Neighborhood Connectivity And Winner Take All Activation Applied To Biophysical Models Of Inferior Colliculus Neurons, Brandon S. Coventry

Open Access Theses

Age-related hearing loss is a prevalent neurological disorder, affecting as many as 63% of adults over the age of 70. The inability to hear and understand speech is a cause of much distress in aged individuals and is becoming a major public health concern as age-related hearing loss has also been correlated with other neurological disorders such as Alzheimer's dementia. The Inferior Colliculus (IC) is a major integrative auditory center, receiving excitatory and inhibitory inputs from several brainstem nuclei. This complex balance of excitation and inhibition gives rise to complex neural responses, which are measured in terms of firing rate …

Developent Of A Phospholipid Encapsulation Process For Quantum Dots To Be Used In Biologic Applications, Logan Grimes

Master's Theses

The American Cancer Society predicts that 1,665,540 people will be diagnosed with cancer, and 585,720 people will die from cancer in 2014. One of the most common types of cancer in the United States is skin cancer. Melanoma alone is predicted to account for 10,000 of the cancer related deaths in 2014. As a highly mobile and aggressive form of cancer, melanoma is difficult to fight once it has metastasized through the body. Early detection in such varieties of cancer is critical in improving survival rates in afflicted patients. Present methods of detection rely on visual examination of suspicious regions …

Smooth Muscle Cell Organization In The Stem Region Of The Gracilis Collateral Circulation, Amanda Krall

Biomedical Engineering

Many patients who suffer from the ischemic Peripheral Arterial Occlusive Disease (PAOD) experience intermittent claudication, which can be attributed to impaired vasodilation. Collateral vessels are the primary site of resistance to blood flow downstream; therefore maximizing vasodilation in collaterals is crucial for efficient circulation. Collaterals function as natural bypasses around the occluded arteries and the increase in flow into these vessels causes them to outwardly remodel into conduit vessels. However, functional vasodilation in the stem region of collateral vessels is impaired at day 7 following femoral ligation, which can be attributed to smooth muscle cell malfunction. However, the increase in …

Modeling The Adaptive Immune Response To Mutation-Generated Antigens, Rory J. Geyer

University Scholar Projects

Somatic mutations may drive tumorigenesis or lead to new, immunogenic epitopes (neoantigens). The immune system is thought to represses neoplastic growths through the recognition of neoantigens presented only by tumor cells. To study mutations as well as the immune response to mutation-generated antigens, we have created a conditional knockin mouse line with a gene encoding, 5’ to 3’, yellow fluorescent protein (YFP), ovalbumin (which is processed to the immunologically recognizable peptide, SIINFEKL), and cyan fluorescent protein (CFP), or, YFP-ovalbumin-CFP. A frame shift mutation has been created at the 5’ end of the ovalbumin gene, hence YFP should always be expressed, …

Cryoprotectant Loading In A Microchannel, Shelby Pursley

Honors Capstones

No abstract provided.

In Vivo Evaluation Of An Automated Pressure Sore Reducer, Linda J. Cross

Honors Capstones

No abstract provided.

Computational Modeling Of Drug Release From Bone Scaffolds, Corey Landry

Honors Capstones

No abstract provided.

Tht And Capillary Electrophoresis To Monitor The Effects Of Solutions Conditions On Amylin Aggregation, Michael May

Graduate Theses and Dissertations

Amylin (hIAPP) aggregates have been found in 90% of patients with type II diabetes at autopsy, and are suspected to play a role in the death of islet &beta-cells¹. However, this aggregation process is not well understood. Here, we explore methods that utilize capillary electrophoresis (CE) as a means to better understand amylin's aggregation process.

We examined the effects of solutions conditions: agitation, pH, salt, and temperature on amylin aggregation using Thioflavin T, dot blots, and capillary electrophoresis. Thiofalvin T was used to predict the lag time to &beta-sheet formation. Our results indicated all variables with the exception …

Modeling The Adaptive Immune Response To Mutation-Generated Antigens, Rory J. Geyer

Honors Scholar Theses

Somatic mutations may drive tumorigenesis or lead to new, immunogenic epitopes (neoantigens). The immune system is thought to represses neoplastic growths through the recognition of neoantigens presented only by tumor cells. To study mutations as well as the immune response to mutation-generated antigens, we have created a conditional knockin mouse line with a gene encoding, 5’ to 3’, yellow fluorescent protein (YFP), ovalbumin (which is processed to the immunologically recognizable peptide, SIINFEKL), and cyan fluorescent protein (CFP), or, YFP-ovalbumin-CFP. A frame shift mutation has been created at the 5’ end of the ovalbumin gene, hence YFP should always be expressed, …

Comparing Virus Ultrafiltration Of Bacteriophages With Filtration Of Minute Virus Of Mice, Kent Smith

Graduate Theses and Dissertations

Industrial production of protein therapeutics demand rigorous testing and clearance of viruses. The U.S. Food and Drug Administration dictate the purity of pharmaceuticals with regards to viral contamination. As this testing is time consuming and expensive using mammalian cells and viruses, bacteriophages may provide a faster and cheaper alternative for membrane filtration processes. We used ultrafiltration membranes to filter protein solutions with viruses. Two bacteriophages were tested against membranes with two different pore sizes. These membranes were then tested by inverting the membrane's orientation. Flux measurements and log virus removal data were taken. Flux and log virus removal were seen …

Progress Of Mesenchymal Stem Cell Therapy For Neural And Retinal Diseases, Tsz Kin Ng, Veronica R. Fortino, Daniel Pelaez, Herman S. Cheung

Biology Faculty Articles

Complex circuitry and limited regenerative power make central nervous system (CNS) disorders the most challenging and difficult for functional repair. With elusive disease mechanisms, traditional surgical and medical interventions merely slow down the progression of the neurodegenerative diseases. However, the number of neurons still diminishes in many patients. Recently, stem cell therapy has been proposed as a viable option. Mesenchymal stem cells (MSCs), a widely-studied human adult stem cell population, have been discovered for more than 20 years. MSCs have been found all over the body and can be conveniently obtained from different accessible tissues: bone marrow, blood, and adipose …

Combined Metal-Enhanced Fluorescence-Surface Acoustic Wave (Mef-Saw) Biosensor, Samuel Morrill

USF Tampa Graduate Theses and Dissertations

Immunofluorescence assays are capable of both detecting the amount of a protein and the location of the protein within a cell or tissue section. Unfortunately, the traditional technique is not capable of detecting concentrations on the nanoscale. Also, the technique suffers from non-specific attachment, which can cause false-positives, as well as photobleaching when detecting lower concentrations is attempted. There is also a time constraint problem since the technique can take from many hours to a few days in some cases.

In this work, metal-enhanced fluorescence (MEF) is used to lower the detection limit and reduce photobleaching. Unfortunately, MEF also increases …

An Imaging-Based Platform For High-Content, Quantitative Evaluation Of Therapeutic Response In 3d Tumour Models, Jonathan P. Celli, Imran Rizvi, Adam R. Blanden, Iqbal Massodi, Iqbal Massodi, Michael D. Glidden, Brian Pogue, Tayyaba Hasan

Dartmouth Scholarship

While it is increasingly recognized that three-dimensional (3D) cell culture models recapitulate drug responses of human cancers with more fidelity than monolayer cultures, a lack of quantitative analysis methods limit their implementation for reliable and routine assessment of emerging therapies. Here, we introduce an approach based on computational analysis of fluorescence image data to provide high-content readouts of dose-dependent cytotoxicity, growth inhibition, treatment-induced architectural changes and size-dependent response in 3D tumour models. We demonstrate this approach in adherent 3D ovarian and pancreatic multiwell extracellular matrix tumour overlays subjected to a panel of clinically relevant cytotoxic modalities and appropriately designed controls …

Physiological And Transcriptional Memory In Guard Cells During Repetitive Dehydration Stress, Laetitia Virlouvet, Michael E. Fromm

Nebraska Center for Biotechnology: Faculty and Staff Publications

Arabidopsis plants subjected to a daily dehydration stress and watered recovery cycle display physiological and transcriptional stress memory. Previously stressed plants have stomatal apertures that remain partially closed during a watered recovery period, facilitating reduced transpiration during a subsequent dehydration stress. Guard cells (GCs) display transcriptional memory that is similar to that in leaf tissues for some genes, but display GC-specific transcriptional memory for other genes. The rate-limiting abscisic acid (ABA) biosynthetic genes NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) and ALDEHYDE OXIDASE 3 (AAO3) are expressed at much higher levels in GCs, particularly during the watered recovery interval, relative to their low …

Investigation Of Cardiac Electrophysiology In Human Ventricular Tissue, Kathleen Brownson

Theses and Dissertations--Biomedical Engineering

Individuals with cardiomyopathy are at higher risk to die from sudden cardiac arrest than those with non-failing (NF) hearts. This study examined the differences in electrical properties of failing and NF human hearts in terms of cardiac memory through explicit control of diastolic intervals in a sinusoidal fashion, restitution of action potential duration (APD) through standard and dynamic pacing protocols, maximum rate of depolarization and APD alternans. Recordings of transmembrane potentials were made in tissues extracted from patients with heart failure and one donor NF heart. Computational simulations were performed using the O’Hara Rudy model for generating surrogates of control …

Dielectric Characterization Of Coastal Cartilage Chondrocytes, Michael W. Stacey, Ahmet C. Sabuncu, Ali Beskok

Bioelectrics Publications

BACKGROUND: Chondrocytes respond to biomechanical and bioelectrochemical stimuli by secreting appropriate extracellular matrix proteins that enable the tissue to withstand the large forces it experiences. Although biomechanical aspects of cartilage are well described, little is known of the bioelectrochemical responses. The focus of this study is to identify bioelectrical characteristics of human costal cartilage cells using dielectric spectroscopy.

METHODS: Dielectric spectroscopy allows non-invasive probing of biological cells. An in house computer program is developed to extract dielectric properties of human costal cartilage cells from raw cell suspension impedance data measured by a microfluidic device. The dielectric properties of chondrocytes are …

Design And Study Of The Efflux Function Of The Egfp Fused Mexab-Oprm Membrane Transporter In Pseudomonas Aeruginosa Using Spectroscopy, Feng Ding, Kerry J. Lee, Ardeschir Vahedi-Faridi, Hiroshi Yoneyama, Christopher J. Osgood, Xiao-Hong Nancy Xu

Biological Sciences Faculty Publications

Multidrug membrane transporters (efflux pumps) can selectively extrude a variety of structurally and functionally diverse substrates (e.g., chemotoxics, antibiotics), leading to multidrug resistance (MDR) and ineffective treatment of a wide variety of diseases. In this study, we have designed and constructed a fusion gene (egfp-mexB) of N-terminal mexB with C-terminal egfp, inserted it into a plasmid vector (pMMB67EH), and successfully expressed it in the Δ MexB (MexB deletion) strain of Pseudomonas aeruginosato create a new strain that expresses MexA-(EGFP-MexB)-OprM. We characterized the fusion gene using gel electrophoresis and DNA sequencing, and determined its expression in live …

Ph Regulation And The Assessment Of Renal Injury Biomarkers In A Warm Perfusion Renal Allograft Preservation System, Aaron Meyer

Legacy Theses & Dissertations (2009 - 2024)

A shortage of viable kidneys available for transplantation exists today, as the number of individuals waiting for a kidney transplant continues to grow while the number of kidneys available each year for transplantation has remained stagnant. The development of technology that will allow for transplantation of organs that currently may be considered too damaged for transplant will provide access to a large number of donors who have experienced traumatic injury deaths resulting in loss of cardiac function. These potential donors account for the majority of all traumatic injury deaths in intensive care units, however their organs have experienced a degree …

The Pseudomonas Syringae Type Iii Effector Hopd1 Suppresses Effector-Triggered Immunity, Localizes To The Endoplasmic Reticulum, And Targets The Arabidopsis Transcription Factor Ntl9, Anna Block, Tania Y. Toruno, Christian G. Elowsky, Chi Zhang, Jens Steinbrenner, Jim Beynon, James R. Alfano

Nebraska Center for Biotechnology: Faculty and Staff Publications

Pseudomonas syringae type III effectors are known to suppress plant immunity to promote bacterial virulence. However, the activities and targets of these effectors are not well understood. We used genetic, molecular, and cell biology methods to characterize the activities, localization, and target of the HopD1 type III effector in Arabidopsis. HopD1 contributes to P. syringae virulence in Arabidopsis and reduces effector-triggered immunity (ETI) responses but not pathogen-associated molecular pattern-triggered immunity (PTI) responses. Plants expressing HopD1 supported increased growth of ETI-inducing P. syringae strains compared with wild-type Arabidopsis. We show that HopD1 interacts with the membrane-tethered Arabidopsis transcription factor NTL9 and …

Raman Spectroscopic Investigation Of Chondroitinase Abc Treatment After Spinal Cord Injury In An Organotypic Model, Shane Ruberto

Theses - ALL

This study investigated (1) the ability of an organotypic model of spinal cord injury (SCI) to recapitulate significant pathobiological events of in vivo SCI from a Raman spectroscopic perspective, and (2) the Raman spectroscopic effects of chondroitinase ABC (cABC) treatment on said model of SCI. Tissue from mouse spinal cords was excised, sectioned, and placed into culture, before being systematically injured to induce trauma. Cultures with and without cABC treatment were assessed using Raman spectroscopy at varying times post-injury. We demonstrate that Raman spectral phenomena characteristic of SCI can be observed using an organotypic model. By comparing these phenomena with …

Electrotransfer Of Single-Stranded Or Double-Stranded Dna Induces Complete Regression Of Palpable B16.F10 Mouse Melanomas, Loree Heller, Vesba Todorovic, Maja Cemazar

Bioelectrics Publications

Enhanced tumor delivery of plasmid DNA with electric pulses in vivo has been confirmed in many preclinical models. Intratumor electrotransfer of plasmids encoding therapeutic molecules has reached Phase II clinical trials. In multiple preclinical studies, a reduction in tumor growth, increased survival or complete tumor regression have been observed in control groups in which vector or backbone plasmid DNA electrotransfer was performed. This study explores factors that could produce this antitumor effect. The specific electrotransfer pulse protocol employed significantly potentiated the regression. Tumor regression was observed after delivery of single-stranded or double-stranded DNA with or without CpG motifs in both …

Near-Infrared Surface-Enhanced Fluorescence Using Silver Nanoparticles In Solution, Michael D. Furtaw

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Fluorescence spectroscopy is a widely used detection technology in many research and clinical assays. Further improvement to assay sensitivity may enable earlier diagnosis of disease, novel biomarker discovery, and ultimately, improved outcomes of clinical care along with reduction in costs. Near-infrared, surface-enhanced fluorescence (NIR-SEF) is a promising approach to improve assay sensitivity via simultaneous increase in signal with a reduction in background. This dissertation describes research conducted with the overall goal to determine the extent to which fluorescence in solution may be enhanced by altering specific variables involved in the formation of plasmonactive nanostructures of dye-labeled protein and silver nanoparticles …

The Development Of A Traumatic Brain Injury Bioreactor, Zachery Heller

Graduate Theses and Dissertations

Approximately 1.7 million Americans experience a traumatic brain injury (TBI) each year. Concussive injuries are a subset of TBI in which blows to the head cause the brain to collide against the interior of the skull. Damage to the neurons, supporting cells, and surrounding extra cellular matrix resulting from these collisions can lead to permanent physical, cognitive, and psychological impairment. We believe the prevalence and clinical significance of concussive injures warrants research investment. To study brain injury following TBI, in vivo models have been the gold standard for TBI experiments. Although a valuable research alternative, animals are expensive, raise ethical …

Skeletal Muscle Contraction Simulation: A Comparison In Modeling, Jonathan M. Ford

USF Tampa Graduate Theses and Dissertations

Computer generated three-dimensional (3-D) models are being used at increasing rates in the fields of entertainment, education, research, and engineering. One of the aspects of interest includes the behavior and function of the musculoskeletal system. One such tool used by engineers is the finite element method (FEM) to simulate the physics behind muscle mechanics. There are several ways to represent 3-D muscle geometry, namely a bulk, a central line of action and a spline model. The purpose of this study is to exmine how these three representations affect the overall outcome of muscle movement. This is examined in a series …

Synthesis And Characterization Of Nucleic Acid-Functionalized Nanomaterials, Brianna S. Carroll, Jong Hyun Choi

The Summer Undergraduate Research Fellowship (SURF) Symposium

Motor proteins such as kinesin move along microtubules in order to transport cellular cargos throughout the cell by obtaining energy from RNA hydrolysis which allows the cell to complete the tasks needed to stay alive. In this work, we developed synthetic molecular motors using DNA enzymes (DNAzyme) and fluorescent nanomaterials which mimic the functions and structures of motor proteins. A DNAzyme-capped CdS nanoparticle and a RNA-functionalized single-walled carbon nanotube (SWCNT) were used as a walker and a track in the motor platform, respectively. As a walking mechanism, the DNAzyme cleaved the RNA substrates in the presence of metal cations. The …

Bicistronic Design For Precise And Reliable Gene Expression, Nidhi N. Menon, Jenna Rickus

The Summer Undergraduate Research Fellowship (SURF) Symposium

Despite having progressed extensively in the field of synthetic biology in terms of DNA synthesis, analysis and transplanting, we still cannot reliably, quantitatively measure expression of new genetic constructs. We engineered a biobrick compatible expression cassette to control transcription and translation initiation which can be reused in new genetic contexts. Previous research has shown that the Bicistronic design have much lesser variations in expression with varying genes of interest as compared to the regular monocistronic design.(Mutalik, Endy, Guimaraes, Cambray, Lam, Juul, Tran & Paull, 2013) The Bicistronic design(BCD) consists of two Shine-Dalgarno sequences in its translation element which when combined …