- Browse by Date Submitted
Biomedical Engineering Department Theses and Dissertations
Permanent URI for this collection
Information about the Purdue School of Engineering and Technology Graduate Degree Programs available at IUPUI can be found at: http://www.engr.iupui.edu/academics.shtml
Browse
Browsing Biomedical Engineering Department Theses and Dissertations by browse.metadata.dateaccessioned
Now showing 1 - 10 of 66
Results Per Page
Sort Options
Item THE ROLE OF DAP-KINASE IN MODULATING VASCULAR ENDOTHELIAL CELL FUNCTION UNDER FLUID SHEAR STRESS(2010-05-05T15:00:50Z) Rennier, Keith; Ji, Julie Ying Hui; Yokota, Hiroki, 1955-; Li, JiliangAtherosclerosis preferentially develops in vascular regions of low or disturbed flow and high spatial gradients. Endothelial cells that line the vessel walls actively participate in translating mechanical stimuli, shear stress due to fluid flow, into intracellular signals to regulate cellular activities. Atherosclerosis is a chronic disease. During its development, a cascade of inflammatory signals alters the arterial endothelial homeostatic functions. Death-associated protein (DAP) kinase and its correlated pathway have been associated with cell apoptosis, turnover, and cytoskeleton remodeling in cellular networks, ultimately leading to changes in cell motility and vascular wall permeability. DAP-kinase is also highly regulated by inflammatory triggers such as TNF-α. This thesis investigates DAP-kinase modulation due to shear stress, and the role of DAP-kinase activity in endothelial responses toward applied shear stress. Using bovine aortic endothelial cells (BAEC), DAP-kinase expression is demonstrated in both sheared (10 dynes/cm2) and static conditions. Overall DAPK expression increased with extended shearing, while the presence of phosphorylated DAPK decreased with applied shear stress, as demonstrated in Western blot analysis. In correlation, DAPK RNA expression profiles were explored to understand pre-translational behavior and to understand just how shear stress influences DAPK expression over time. There is a temporal increase in DAPK mRNA, occurring at earlier time points when compared to DAPK protein expression, displaying the precedence of mRNA expression leading to increased translation into protein. From our apoptosis assay results, shear stress reduces apoptotic and late stage/necrotic cell fractions. The exposure of shear stress potentially plays a role in inhibiting apoptosis activation and TNF-α induced death cascade. Overall, the apoptosis activity influenced by shear further exhibits a possible connection between shear stress and apoptosis inhibition. The shear stress ultimately decreases overall apoptosis, while DAPK expression is increased. Therefore, DAPK may have a function in other possible mechano-transduction cascades, when endothelial cells are exposed to constant shear. Our data suggests shear stress modulation of DAP-kinase expression and activity, and the potential crosstalk of mechano-transduction and DAPK/apoptosis pathway, may lead to further understanding the responsibility of DAPK in endothelial cell function.Item Signaling Pathways Involved in Mechanical Stimulation and ECM Geometry in Bone Cells(2010-07-27T20:24:41Z) Jiang, Chang; Yokota, Hiroki, 1955-; Liu, Yunlong; Ji, JulieThe proliferation and differentiation of osteoblasts are influenced by mechanical and geometrical growth environments. A specific aim of my thesis was the elucidation of signaling pathways involved in mechanical stimulation and geometric alterations of the extracellular matrix (ECM). A pair of questions addressed herein was (a) Does mechanical stimulation modulate translational regulation through the phosphorylation of eukaryotic initiation factor 2 (eIF2)? (b) Do geometric alterations affect the phosphorylation patterns of mitogen-activated protein kinase (MAPK) signaling? My hypothesis was mechanical stress enhances the proliferation and survival of osteoblasts through the reduction in phosphorylation of eIF2, while 3-dimensional (3D) ECM stimulates differentiation of osteoblasts through the elevation of phosphorylation of p38 MAPK. First, mechanical stimulation reduced the phosphorylation of eIF2. Furthermore, flow pre-treatment reduced thapsigargin-induced cell mortality through suppression of phosphorylation of protein kinase RNA-like ER kinase (Perk). However, H2O2-driven cell mortality, which is not mediated by Perk, was not suppressed by mechanical stimulation. Second, in the ECM geometry study, the expression of the active (phosphorylated) form of p130Cas, focal adhesion kinase (FAK) and extracellular signal-regulated protein kinase (ERK) was reduced in cells grown in the 3D matrix. Conversely, phosphorylation of p38 MAPK was elevated in the 3D matrix and its up-regulation was linked to an increase in mRNA levels of dentin matrix protein 1 and bone sialoprotein. In summary, our observations suggest the pro-survival role of mechanical stimulation and the modulation of osteoblastic fates by ECM geometry.Item Preparation and Evaluation of Antibacterial Dental Glass-ionomer Cements(2010-10-22) Guo, Xia; Xie, Dong; Na, Sungsoo; Song, FengyuThe functional quaternary ammonium salts (QAS) and their constructed polyQAS or PQAS were synthesized, characterized and formulated into a novel antibacterial glass-ionomer cement. Compressive strength (CS) and Streptococcus mutans (S. mutans) viability were used to evaluate the mechanical strength and antibacterial activity of the cements. Fuji II LC cement was used as control. The specimens were conditioned in distilled water at 37 oC for 24 h prior to testing. The effects of the substitute chain length, loading as well as grafting ratio of the QAS and aging on CS and S. mutans viability were investigated. Chapter 2 describes how we studied and evaluated the formulated antibacterial glass-ionomer cement by incorporating QAS chloride-containing polymer into the formulation. The results show that with PQAS addition, the studied cements showed a reduction in CS with 25-95% for Fuji II LC and 13-78% for the experimental cement and a reduction in S. mutans viability with 40-79% for Fuji II LC and 40-91% for the experimental cement. The experimental cement showed less CS reduction and higher antibacterial activity as compared to Fuji II LC. The long-term aging study indicates that the cements are permanently antibacterial with no PQAS leaching. Chapter 3 describes how we studied and evaluated the formulated antibacterial cements by changing chain length, type of halide, loading, grafting ratio and aging time. The results show that the effects of the chain length, loading and grafting ratio of the QAS were significant. Increasing chain length, loading, grafting ratio significantly enhanced antibacterial activity but reduced CS. The experimental cement showed less CS reduction and higher antibacterial activity as compared to Fuji II LC. The long-term aging study indicates that the cements are permanently antibacterial with no PQAS leaching. There was no significant difference between QAS bromide and QAS chloride, suggesting that we can use QAS bromide directly without converting bromide to chloride. In summary, we have developed a novel PQAS-containing antibacterial glass-ionomer cement. The cement has demonstrated significant antibacterial activities. Our experimental cement is a promising system because the reduced strength of the cement with addition of PQAS is still above those demonstrated by original commercial cement Fuji II LC without any PQAS addition. It appears that the experimental cement is a clinically attractive dental restorative that can be potentially used for long-lasting restorations due to its high mechanical strength and permanent antibacterial function.Item A NOVEL FURANONE-CONTAINING ANTIBACTERIAL SYSTEM FOR IMPROVED DENTAL RESTORATIVES(2012-05-02) Howard, Leah Ann; Xie, Dong; Yokota, Hiroki; Gregory, Richard L.The furanone derivatives and their constructed polymers were synthesized, characterized and formulated into dental glass-ionomer cement (GIC) and resin composite for improved antibacterial properties. Compressive strength (CS) and S. mutans viability were used to evaluate the mechanical strength and antibacterial activity of the restoratives. Fuji II LC cement and P60 were used as control. The specimens were conditioned in distilled water at 37 oC for 24 h prior to testing. The effects of loading, saliva and aging on CS and S. mutans viability were investigated. The antibacterial effect of the furanone derivative on other bacteria was also studied. Chapter 2 describes how we studied and evaluated the formulated antibacterial glass-ionomer cement by incorporating the synthesized furanone derivative-containing polymer into the formulation. The results show that all the formulated furanone-containing cements showed a significant antibacterial activity, accompanying with an initial CS reduction. Increasing loading significantly enhanced antibacterial activity but reduced the initial CS of the formed cements. The derivative showed a broad antibacterial spectrum on bacteria including S. mutans, lactobacillus, S. aureus and S. epidermidis. Human saliva did not affect the antibacterial activity of the cement. The long-term aging study indicates that the cements may have a long-lasting antibacterial function. Chapter 3 describes how we studied and evaluated the formulated antibacterial resin composite by incorporating the synthesized furanone derivative into the basic resin formulations. The results show that the modified resin composites showed a significant antibacterial activity without substantially decreasing the mechanical strengths. With 5 to 30% addition of the furanone derivative, the composite kept its original CS unchanged but showed a significant antibacterial activity with a 16-68% reduction in the S. mutans viability. Further, the antibacterial function of the new composite was not affected by human saliva. The aging study indicates that the composite may have a long-lasting antibacterial function. In summary, we have developed a novel furanone-containing antibacterial system for dental restoratives. Both glass-ionomer cement and resin composite have demonstrated significant antibacterial activities. The modified experimental glass-ionomer cement is a promising system because the reduced strength of the cement with addition of the furanone-containing polymer is still above those demonstrated by original commercial cement Fuji II LC. The modified resin composite shows nearly no reduction in mechanical strength after incorporation of the antibacterial furanone derivative. It appears that both experimental cement and resin composite are clinically attractive dental restoratives that can be potentially used for long-lasting restorations due to their high mechanical strength and permanent antibacterial function.Item Monte Carlo Simulation to Study Propagation of Light through Biological Tissues(2012-09-20) Prabhu Verleker, Akshay; Berbari, Edward J.; Stantz, Keith; Yoshida, KenPhotoacoustic Imaging is a non-invasive optical imaging modality used to image biological tissues. In this method, a pulsating laser illuminates a region of tissues to be imaged, which then generates an acoustic wave due to thermal volume expansion. This wave is then sensed using an acoustic sensor such as a piezoelectric transducer and the resultant signal is converted into an imaging using the back projection algorithm. Since different types of tissues have different photo-acoustic properties, this imaging modality can be used for imaging different types of tissues and bodily organ systems. This study aims at quantifying the process of light conversion into the acoustic signal. Light travels through tissues and gets attenuated (scattered or absorbed) or reflected depending on the optical properties of the tissues. The process of light propagation through tissues is studied using Monte Carlo simulation software which predicts the propagation of light through tissues of various shapes and with different optical properties. This simulation gives the resultant energy distribution due to light absorption and scattering on a voxel by voxel basis. The Monte Carlo code alone is not sufficient to validate the photon propagation. The success of the Monte Carlo code depends on accurate prediction of the optical properties of the tissues. It also depends on accurately depicting tissue boundaries and thus the resolution of the imaging space. Hence, a validation algorithm has been designed so as to recover the optical properties of the tissues which are imaged and to successfully validate the simulation results. The accuracy of the validation code is studied for various optical properties and boundary conditions. The results are then compared and validated with real time images obtained from the photoacoustic scanner. The various parameters for the successful validation of Monte Carlo method are studied and presented. This study is then validated using the algorithm to study the conversion of light to sound. Thus it is a significant step in the quantification of the photoacoustic effect so as to accurately predict tissue properties.Item PREPARATION AND EVALUATION OF NOVEL ANTIBACTERIAL DENTAL RESIN COMPOSITES(2013-07-12) Chong, Voon Joe; Xie, Dong; Na, Sungsoo; Li, Jiliang; Berbari, Edward J.Both quaternary ammonium bromide (QAB) and furanone derivatives were synthesized, characterized and formulated into dental resin composites for improved antibacterial properties. Compressive strength (CS) and S. mutans viability were used to evaluate the mechanical strength and antibacterial activity of the restoratives. The effects of chain length, loading, saliva and aging on CS and S. mutans viability were investigated. Chapter 2 describes how we studied and evaluated the formulated antibacterial resin composites by incorporating the synthesized QAB-containing oligomers into the formulation. The results show that all the QAB-modified resin composites showed significant antibacterial activity and mechanical strength reduction. Increasing chain length and loading significantly enhanced the antibacterial activity but dramatically reduced the CS as well. The 30-day aging study showed that the incorporation of the QAB accelerated the degradation of the composite, suggesting that the QAB may not be well suitable for development of antibacterial dental resin composites or at least the QAB loading should be well controlled. Chapter 3 describes how we studied and evaluated the formulated antibacterial resin composite by incorporating the synthesized furanone derivative into the formulation. The results show that the modified resin composites showed a significant antibacterial activity without substantially decreasing the mechanical strengths. With 5 to 30% addition of the furanone derivative, the composite kept its original CS unchanged but showed a significant antibacterial activity with a 16-68% reduction in the S. mutans viability. Further, the antibacterial function of the new composite was found not to be affected by human saliva. The aging study indicates that the composite may have a long-lasting antibacterial function. In summary, we have developed a novel QAB- and furanone-containing antibacterial system for dental restoratives. Both QAB- and furanone-modified resin composites have demonstrated significant antibacterial activities. The QAS-modified experimental resin composite may not be well suitable for development of antibacterial dental resin composites due to its accelerated degradation in water unless the QAB loading is well controlled. The furanone-modified resin composite shows nearly no reduction in mechanical strength after incorporation of the antibacterial furanone derivative. It appears that the furanone-modified resin composite is a clinically attractive dental restorative that can be potentially used for long-lasting restorations due to its high mechanical strength and permanent antibacterial function.Item Effects of Collagen Gel Stiffness on Cdc42 Activities of Endothelial Colony Forming Cells during Early Vacuole Formation(2013-08-14) Kim, Seung Joon; Na, Sungsoo; Xie, Dong; Li, JiliangRecent preclinical reports have provided evidence that endothelial colony forming cells (ECFCs), a subset of endothelial progenitor cells, significantly improve vessel formation, largely due to their robust vasculogenic potential. While it has been known that the Rho family GTPase Cdc42 is involved in this ECFC-driven vessel formation process, the effect of extracellular matrix (ECM) stiffness on its activity during vessel formation is largely unknown. Using a fluorescence resonance energy transfer (FRET)-based Cdc42 biosensor, we examined the spatio-temporal activity of Cdc42 of ECFCs in three-dimensional (3D) collagen matrices with varying stiffness. The result revealed that ECFCs exhibited an increase in Cdc42 activity in a soft (150 Pa) matrix, while they were much less responsive in a rigid (1 kPa) matrix. In both soft and rigid matrices, Cdc42 was highly activated near vacuoles. However, its activity is higher in a soft matrix than that in a rigid matrix. The observed Cdc42 activity was closely associated with vacuole formation. Soft matrices induced higher Cdc42 activity and faster vacuole formation than rigid matrices. However, vacuole area is not dependent on the stiffness of matrices. Time courses of Cdc42 activity and vacuole formation data revealed that Cdc42 activity proceeds vacuole formation. Collectively, these results suggest that matrix stiffness is critical in regulating Cdc42 activity in ECFCs and its activation is an important step in early vacuole formation.Item Exploring Chondrocyte Integrin Regulation of Growth Factor IGF-I Expression from a Transient pAAV Vector(2013-08-20) Ratley, Samantha Kay; Trippel, Stephen B.; Lin, Chien-Chi; Stocum, David L.Insulin-like Growth Factor I (IGF-I) is a growth factor that stimulates both mitogenic and anabolic responses in articular chondrocytes. While it has been shown that exogenous IGF-I can regulate chondrocyte integrins, little is known regarding regulatory effects of IGF-I produced from a transiently expressed plasmid based adeno-associated virus (pAAV) vector. Because chondrocytes are using cellular machinery to overexpress IGF-I, it is of interest to see whether or not pAAV IGF-I will significantly upregulate or downregulate chondrocyte integrins. Additionally, it is of interest to know whether chondrocyte adhesion through integrins will have any regulatory effects on the production of IGF-I from the transgene. Therefore, this study will ascertain if pAAV IGF-I will have similar effects that exogenous IGF-I has on integrin regulation and if integrin silencing mechanisms will affect the production of IGF-I from the transgene. To test these hypotheses, adult articular chondrocytes were doubly transfected with the pAAV vector for IGF-I and short interference ribonucleic acid (siRNA) for integrins beta 1 and alpha V. Gene products were monitored at the transcriptional levels using quantitative real time polymerase chain reactions (qPCR) and IGF-I protein production was monitored at the translational level using enzyme linked immunoabsorbant assays (ELISAs). Adult articular chondrocytes doubly transfected were encapsulated in a three dimensional hydrogel system to simulate an in vivo environment. Samples were collected for analysis at days 2, 4, and 6 post encapsulation. Results show that IGF-I treatment with the pAAV vector does not cause significant changes in the transcriptional regulation of the beta 1 integrin in a three dimensional hydrogel system. The pAAV IGF-I vector did not cause significant regulatory changes on integrin alpha V at any time point during the experiment. Additionally, by knocking down the expression levels of integrins by using siRNA, it was shown that integrin knockdown does not have a significant regulatory effect on transcriptional or translational expression levels of IGF-I from the pAAV vector.Item Developing a Neural Signal Processor Using the Extended Analog Computer(2013-08-21) Soliman, Muller Mark; Yoshida, Ken; Eberhart, Russell C.; Mills, Jonathan W. (Jonathan Wayne); Berbari, Edward J.Neural signal processing to decode neural activity has been an active research area in the last few decades. The next generation of advanced multi-electrode neuroprosthetic devices aim to detect a multiplicity of channels from multiple electrodes, making the relatively time-critical processing problem massively parallel and pushing the computational demands beyond the limits of current embedded digital signal processing (DSP) techniques. To overcome these limitations, a new hybrid computational technique was explored, the Extended Analog Computer (EAC). The EAC is a digitally confgurable analog computer that takes advantage of the intrinsic ability of manifolds to solve partial diferential equations (PDEs). They are extremely fast, require little power, and have great potential for mobile computing applications. In this thesis, the EAC architecture and the mechanism of the formation of potential/current manifolds was derived and analyzed to capture its theoretical mode of operation. A new mode of operation, resistance mode, was developed and a method was devised to sample temporal data and allow their use on the EAC. The method was validated by demonstration of the device solving linear diferential equations and linear functions, and implementing arbitrary finite impulse response (FIR) and infinite impulse response (IIR) linear flters. These results were compared to conventional DSP results. A practical application to the neural computing task was further demonstrated by implementing a matched filter with the EAC simulator and the physical prototype to detect single fiber action potential from multiunit data streams derived from recorded raw electroneurograms. Exclusion error (type 1 error) and inclusion error (type 2 error) were calculated to evaluate the detection rate of the matched filter implemented on the EAC. The detection rates were found to be statistically equivalent to that from DSP simulations with exclusion and inclusion errors at 0% and 1%, respectively.Item Effect of Shear Stress on RhoA Activities and Cytoskeletal Organization in Chondrocytes(2013-09-05) Wan, Qiaoqiao; Na, Sungsoo; Li, Jiliang; Yokota, HirokiMechanical force environment is a major factor that influences cellular homeostasis and remodeling. The prevailing wisdom in this field demonstrated that a threshold of mechanical forces or deformation was required to affect cell signaling. However, by using a fluorescence resonance energy transfer (FRET)-based approach, we found that C28/I2 chondrocytes exhibited an increase in RhoA activities in response to high shear stress (10 or 20 dyn/cm2), while they showed a decrease in their RhoA activities to intermediate shear stress at 5 dyn/cm2. No changes were observed under low shear stress (2 dyn/ cm2). The observed two-level switch of RhoA activities was closely linked to the shear stress-induced alterations in actin cytoskeleton and traction forces. In the presence of constitutively active RhoA (RhoA-V14), intermediate shear stress suppressed RhoA activities, while high shear stress failed to activate them. Collectively, these results herein suggest that intensities of shear stress are critical in differential activation and inhibition of RhoA activities in chondrocytes.