Browsing by Subject "Department of Biomedical Engineering"

Now showing 1 - 20 of 24
  • Thumbnail Image
    Item
    Activation of the Inferior Olive
    (2011-04-13) Walter, Camille
    The inferior olive (IO) is a group of nuclei in the brainstem and is the sole origin of climbing fibers to the cerebellar cortex. While complete functions of the IO are unknown, it is believed to contribute to temporal processing. Functional magnetic resonance imaging (fMRI) studies have shown activation of the inferior olive by unexpected sensory stimuli. In this study, we tested the IO’s sensitivity to stimulus timing change to determine the time-change that is most efficient in activating the IO. We scanned normal human subjects while viewing sequences of visual stimuli and recognizing stimuli that deviated from isochronous stimuli by fifty to eight hundred milliseconds. The behavioral results showed that the subjects’ performance increased with timing change. The fMRI data were analyzed using event-related statistical parametric mapping of the hemodynamic responses; then we could see the activation of the inferior olive during all of the different stimulus timing changes. The 300 millisecond stimulus timing change produced the most activation of the IO, with time-changes of 200 to 600 (but not 50, 100, 700 or 800 ms) producing significant but less robust activation than 300 ms. These results were consistent with classical conditioning animal studies and indicate that reliable and robust activation of the inferior olive can be achieved in humans; they also can potentially be used to study diseases in which the IO is implicated.
  • Thumbnail Image
    Item
    Assessment of Tissue Damage from Ultrasonic, Pneumatic and Combination Lithotripsy
    (2011-04-13) Cui, Yuqing; Sarkissian, Carl; Mohsenian, Kevin; Monga, Manoj
    Objective: To conduct a comparative evaluation of ultrasonic, pneumatic, and dual ultrasonic lithotripsy to predict the safety of probes on urinary tract tissue. Methods: Lithotriptors (medical device used to breakup kidney stones) tested were the Swiss Lithoclast Ultra (ultrasonic only - US, and ultrasonic-pneumatic combination US+P), and the Gyrus ACMI Cyberwand (dual ultrasonic). Fresh porcine ureters, bladders, and renal pelvis tissues were used for testing. A hands-free set up was used with each probe to vertically apply no pressure, 400 g, or 700 g of pressure for a duration of 3 seconds, 5 seconds or 180 seconds. Repetitive testing of each tissue/pressure/time combination was performed, for a total of 351 trials. Conclusion: All devices afforded a level of safety at tissue durations typical of inadvertent intraoperative contact (3-5 seconds), though the Lithoclast US-only was superior with regard to perforation for all tissue types. Overall, very similar results were observed between the Lithoclast US+P and Cyberwand.
  • Thumbnail Image
    Item
    Biaxial Testing of Cadaveric and Decellularized Rat Heart Ventricles
    (2011-08-11) Vanderheiden, Sarah
    Whole organ decellularization is a promising technique to create 3D scaffolds necessary to generate bioartificial organs. However, due to the vital role of tissue mechanics in the contraction of the heart [3], it is necessary to assess the changes to the myocardium caused by decellularization. Previous studies have demonstrated that heart tissue is anisotropic [2]. Ventricle tissue fibers are aligned in the circumferential direction, and that orientation is preserved after decellularization [1]. The circumferential orientation of fibers is responsible for a higher stiffness in that direction than the longitudinal direction [1]. It has also been proved that decellularized tissues have a higher tangential modulus than cadaveric tissues [1].
  • Thumbnail Image
    Item
    Binding Residues of Intergrase (IN) and Its Host Cofactor Ini1
    (2011-08-11) Wang, Nayi
    Purpose Integration of viral DNA into its host chromosome is an important step in the HIV replication process (7). HIV integrase is an important enzyme which plays an essential role in inserting the vital DNA into the host chromosome and replicating HIV (6). It is one of the three enzyme will complement the therapeutic use of HIV protease and reverse transcriptase inhibitors. Though combining antiviral therapy with protease and reverse transcriptase inhibitors has proved the improvement of antiviral therapy for treatment of AIDS. However, because there are still some problems for drug resistance and toxicity, we still need to do some additional researches on the antiviral drugs. Integrase is a good target for antivirals due to its necessity for HIV replication. In addition, integrase can only use a single active site to accommodate two different configurations of DNA substrates, which will constrain the process of HIV to develop drug resistance to integrase inhibitors (7). To achieve the goal of crystallizing IN, our lab has been focusing much attention on the proteins that are binding partners of IN or host cofactors known to alter the biochemical characteristics of HIV-IN. One such host cofactor is SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 or also known as Ini1/SNF5. The goal of my research will be to express, purify, and characterize various Ini1 fragments as a potential chaperone in the crystallization of IN. And to find Ini1’s correct residues which binds to IN. Methods We cloned three different Ini1 constructs into the Sumo-Pro expression vector. We used PCR to get three lengths of fragments and inserted our construct into the SUMO vector which encodes a SUMO expression chaperone as well as a 6-Hisitidine affinity tag for IMAC purification. We tested for expression of the Sumo-Ini1 fragments through common methods utilizing the T7 based expression systems engineered into the Sumo-Pro vector. After small scale expression (5ml or 100ml cultures) and lysis via sonication, Ini1 was affinity purified with Ni-NTA and then by size-exclusion chromatography. Once the best behaved Ini1 construct was identified, we produced the protein in multiple 1L scale and purified to >90% purity. The SUMO tag includes an N-terminal recognition site that is recognized by the SUMO protease and will be removed. The purified protein then will be screened for crystal conditions. Results Size exclusion chromatography showed us a single, homogeneous, peak when Ini1 protein fragment from residue 170 to residue 250 was dialyzed with IN. In addition, after purification, both IN and Ini1 was contained in this single peak. This confirmed that we had a Ini1 fragment that was selectively binding to IN and forming a complex upon mixing and dialyzing. The discovery of this stable complex is the first step in our attempts to stabilize IN for our crystallographic pursuits.
  • Thumbnail Image
    Item
    The Biomechanical Puncture Study of the Fossa Ovalis in Human and Porcine Hearts
    (2011-04-13) Balto, Daniel
    About 1 in every 4 adults here in the U.S. has some sort of congenital heart defect, the majority of these defects is caused by a Patent Fossa Ovalis (PFO). It occurs when the hole between the left and right atria (Foramen Ovale) does not close completely at the moment of birth. The study involved designing and then constructing an apparatus to hold an excised heart in proper anatomical position so that the Fossa Ovalis was accessible from both atria of the heart. Once that was accomplished, a catheter type device was designed and then used to measure the force required to puncture the fossa membrane and the data was recorded. Many different factors were analyzed with this data such as fossa morphology and anatomy. The reason for creating such a device for testing fossa strength was to observe if the fixation of the tissue with formalin would change the properties of the fossa in a variety of human and pig hearts that have been preserved in formalin and used as in vivo equivalents. The data gained will allow me to compare how current PFO’s (heart defects) are fixed and what new surgical procedures or biomedical devices can be created based on the strength of the average Fossa Ovalis of a human.
  • Thumbnail Image
    Item
    Cardiac Voltage Analysis Software for Interpretation of Transmembrane Voltage Movies Obtained via the Langendorff Perfusion Setup
    (2021) Callaway, Trenton; Talkachova, Alena; Ravikumar, Vasanth
    Using the Langendorff perfusion setup to study and compare healthy and arrhythmic heart conditions is an increasingly common practice. This technique requires the ex-vivo perfusion of the heart, wherein cardiac tissue is injected with a voltage sensitive fluorescent dye, allowing for video analysis of electrical activity in the heart under normal and arrhythmic conditions. When conducted in this study, this technique resulted in recorded movies of cardiac tissue interpretable as 3D matrices whereby the spatial dimensions are defined by the movie resolution of 80 by 80 pixels, and the temporal dimension is based on the length of the movie in frames. The goal of this project was to further develop and investigate the efficiency of a data analysis application, CVAS (Cardiac Voltage Analysis Software), which is capable of analyzing these matrices in a user-friendly, intuitive way. This MATLAB based software is designed to be capable of creating highly modular plots, calculations, and optical maps for analysis on both paced and arrhythmic data. This task is one that would heavily benefit contemporary electrophysiological cardiology, and provide easy assessment of electrophysiological properties of the heart during normal and abnormal cardiac rhythms. By collecting new data for this software to analyze, CVAS was critiqued and improved to optimize its ease of use and interaction with researchers. Additionally, its ability to generate high quality and immediately presentable optical maps, plots, and calculations for both paced and arrhythmic data was strengthened. CVAS’s current capabilities include loading in and masking optical movie data sets, visualizing the electrical activity of the heart with fluorescence movies and action potential traces, and allowing for visualization and analysis of both paced and arrhythmic data sets through the use of action potential duration, activation time, conduction velocity, dominant frequency, and multiscale frequency maps.
  • Thumbnail Image
    Item
    Comparison of Tissue Remodeling in Engineered Vascular Grafts made from Adult and Neonatal Human Dermal Fibroblasts
    (2011-04-13) Chen, Minna; Syedain, Zeeshan; Tranquillo, Robert
    Tissue engineering provides a means for creating functional biological vascular grafts. A viable, strong, yet compliant, tissue-engineered vascular graft can be used as an alternative to native arteries in vascular surgeries and increase the quality of life for adults with heart disease, a leading cause of death in the United States. Previous work in the Tranquillo lab has shown that vascular grafts seeded with neonatal human dermal fibroblasts (nHDFs) can be engineered with burst pressures of up to 1600 mmHg. However, for the development of autologous vascular grafts for implantation, grafts seeded with adult human dermal fibroblasts (aHDFs) are more relevant. Previous work in the Tranquillo lab has shown that we can engineer grafts seeded with aHDFs to achieve burst pressures of up to 2200 mmHg, but that the remodeling of the fibrin scaffold and collagen production is significantly different between grafts seeded with aHDFs and those seeded with nHDFs. In this study, we analyzed methods to modify fibrin degradation by adult fibroblasts. In an earlier study, changing the initial fibrin concentration was shown to have a strong effect on the remodeling of engineered tissue. Further testing was performed by incubating aHDF grafts in conditioned media from nHDF grafts. Results showed differences from both changing the initial fibrin concentration and from adding conditioned media on tissue remodeling and collagen production.
  • Thumbnail Image
    Item
    Computational Modeling of Deep Brain Stimulation in the Globus Pallidus Internus
    (2012-04-18) Malaga, Karlo
    Deep brain stimulation (DBS) is a neural interface technology developed to improve the quality of life for people with movement disorders (e.g., Parkinson’s disease, dystonia, essential tremor). The general procedure involves placing small electrodes in regions of the brain exhibiting pathological activity and then stimulating those regions with continuous pulses of electricity. Treatment outcome is strongly dependent on the precise placement of the electrodes in the brain and subsequent adjustment of the stimulation settings to fine-tune the therapy. Stimulation of the globus pallidus internus (GPi) has yielded promising results for people with dystonia, a neurological movement disorder in which sustained muscle contractions cause twisting and repetitive movements or abnormal postures. However, specific stimulation settings that provide maximum GPi modulation and have minimal side-effects have yet to be determined. Here we use computational models to show how altering the DBS lead electrode configuration affects GPi modulation and activation of the cortical spinal tract (CST) (i.e., the side-effect pathway). GPi DBS simulations yielded a combination of cell activation and inhibition. Activation was found to be greatest around the cathode of the DBS lead. Modulated cells were localized relative to the lead and the degree of modulation decreased farther away. These results can provide a framework for neurosurgeons and neurologists to improve current techniques that will optimize treatment outcome.
  • Thumbnail Image
    Item
  • Thumbnail Image
    Item
  • Thumbnail Image
    Item
    Development of Brain-Computer Interface for Common Applications: Stage I Developement
    (2009-04-08) Doud, Alexander
    Brain-Computer interfaces are devices that can be used to connect the thoughts of a user to the output of a machine. These devices have the potential to act as a bridge of communication for fully or partially locked in individuals, and may serve as a way for these individuals to interact with their environment. Users can be trained to modulate the synchronization and desynchronization of elements of the EEG signal by employing learned motor imaginations. By interpreting these patterns of voltage potentials recorded on the scalp, sophisticated control systems can be created. It has been the goal of my project to use existing two-dimensional cursor control paradigms as a platform from which to develop a system capable of moving a cursor in three dimensions that is robust and easy to learn. This system could have useful applications in patient communication, rehabilitation, and even mental recreation.
  • Thumbnail Image
    Item
    The Dynamics of Epilepsy in Relation to the Application of Anti-Epileptic Drugs
    (2010-04-21) Huus, Aaron; Rodenkirch, Rebecca M.
    The general purpose of this project is to understand how neurons in a network interact during a seizure. This knowledge would allow for a better comprehension of seizures, as well as the improvement of current treatment options. To accomplish this, Phase Response Curves (PRCs) are used to measure how a periodically firing neuron is perturbed by synaptic inputs. By understanding how a single neuron responds to these inputs, it can be predicted whether a network of neurons will synchronize or not. Currently in the medical field it is accepted that anti-epileptic drugs work, but no one understand why they work the way they do. The preliminary results for this project indicate that some anti-epileptic drugs increase synchrony. This finding is contrary to the general belief that epilepsy is caused by hyper-synchrony, in which case increasing synchrony should cause more seizures. This project examines how the anti-epileptic drug, Phenytoin affects the PRC and thusly the synchrony of the neuronal network. Once it is known whether Phenytoin increases or decreases synchrony, people can use this knowledge to increase the efficiency of anti-epileptic drugs which will be beneficial for individuals with epilepsy.
  • Thumbnail Image
    Item
    The Effect of Anti-Epileptic Drugs on 4- AP Induced Seizures in Rat Brain Slices
    (2011-04-13) Podritz, Courney; Rodenkirch, Rebecca
    Epilepsy is a neurological disorder that affects an estimated 50 million people, nearly one-third of whom do not have sufficient control over its symptoms. It is characterized by the onset of hypersynchronous neuronal activity known as seizures. The Netoff lab is focused on understanding the dynamics of epilepsy at the cellular and neural network levels. Our project focuses on how certain antiepileptic drugs alter the connections between neurons to prevent seizures. In this project, we performed extracellular recordings in rat hippocampal brain slices using a microscope and micropipette electrode setup. The brain slices rested in low-magnesium artificial cerebrospinal fluid containing 4-aminopyridine, a potassium ion channel blocker that causes seizures. Once seizures began, we introduced the anti-epileptic drug ethosuximide to the fluid and observed the effect on the seizures. We have seen that the amplitude of the seizure activity is much lower overall after the drug is applied. Often the drug also reduces the length and/or frequency of the seizures. When we stop adding the drug, the original seizures resume, creating a “wash-out” effect as the drug is no longer present. If we can discover the precise cause of seizure onset and the mechanisms by which anti-epileptic drugs affect it, we can develop more effective treatments for epileptic patients.
  • Thumbnail Image
    Item
    Effect of Variation in Speed on Target Interception
    (2009-04-08) Rao, Hrishikesh
    In day to day life, we make use of hand eye coordination to perform everyday tasks such as reaching out our hand to grab a glass of water or moving a finger over a keyboard to push a button. But we rarely think about the complex processes that occur inside our brains in the very short time span between when we think about moving our hand to actually making contact with the target. With this experiment, we wish to extend our knowledge of how sensory information is utilized to predict the motion of objects targeted by the hand and the extent of hand and eye coordination during this task. We also wish to examine how the speed and acceleration of a moving target affects the decision making process prior to the onset of motion of the subject's hand. To create variation in the speed and acceleration, the motion of the target was governed by one of three speed laws for each trial. With the first law, the target's motion was constructed from a sum of sines in the x and y directions; with the second law, the target's instantaneous velocity was inversely proportional to the curvature of the path at that point; and lastly, as per the third law, the target moved at a constant speed. Based on these three laws, the corresponding targets traveled quite differently around curves and straight paths due to the dissimilar acceleration or even the lack of tangential acceleration. Defining how subjects incorporate information about changes in direction, speed and acceleration provides insight into how the brain processes sensory information.
  • Thumbnail Image
    Item
    Elasticity of the Mouse Ocular Lens Capsule as Measured by Osmotic Swelling
    (2009-04-08) Powell, Tracy
    Animal basement membranes are networks of laminin, type IV collagen and other proteins essential for physiological functions. Deficiencies or abnormalities in the proteins can lead to muscular dystrophy, kidney disease, hearing loss, and, in the extreme, embryonic demise. In an effort to determine how the complex structure determines the functional properties of the basement membrane, the change in mechanical behavior is being investigated on samples with defective or absent associative proteins as compared to those with intact matrix components. A test was developed using the mouse model to take advantage of the genetic control possible in the mouse. The ocular lens capsule is a basement membrane which is large and thick, relative to others in the body, and which can be studied without major disruption. The lens is extracted from the eye and subjected to osmotic swelling, requiring minimal dissection and manipulation. The change in radius over time is evaluated with a mathematical model recently developed using porcine lenses to determine the elasticity of the capsule. Currently, data are being collected and analyzed to determine the elasticity of the normal mouse ocular lens capsule, which will serve as the control for future studies on mice with genetically-determined basement membrane modifications.
  • Thumbnail Image
    Item
    Enlargement of an Aligned Microvascular Tissue
    (2014-04-16) Mattia, Donald
  • Thumbnail Image
    Item
    In vitro Characterization of Mesenchymal Stem Cells
    (2012-04-18) Chen, Minna
    The leading cause of death in the United States is coronary heart disease, which is characterized by the narrowing of blood vessels that deliver blood and oxygen to the heart. A possible way to treat this condition is to bypass the blocked arteries, using an artery or vein taken from elsewhere in the patient’s body to go around the blocked region. However, many candidates for these surgeries lack adequate blood vessels that can be used for such purposes. For this reason, it is important to develop a tissue engineered vascular graft (TEVG) that can be used in place of a native vessel. In the Tranquillo Lab, the method for creating TEVGs involves a cell-seeded fibrin gel that is remodeled over time. Initial animal studies have shown that TEVGs created in this way contain proteins that promote clotting. In native vessels, the surface exposed to blood flow is covered by a monolayer of endothelial cells, which prevent clotting. Endothelial cells are also highly immunogenic, so TEVGs created using endothelial cells would have to be made using each patient’s own cells. In this study, we propose to use a monolayer of mesenchymal stem cells (MSCs), which are non-immunogenic, on this surface instead. We have shown that, when exposed to shear stress, MSCs exhibit decreased levels of platelet adhesion. Staining for endothelial cell markers suggests that we may be able to differentiate MSCs to a functional endothelial cell phenotype. If MSCs can be used as an alternative to endothelial cells in TEVGs, this therapy can potentially be available “off-the-shelf” to a large number of patients in the future.
  • Thumbnail Image
    Item
    Isolation of Low Frequency Cells in Bronchoalveolar Lavage (BAL)
    (2012-04-18) Albares, Luke
    The fourth leading cause of death today in the United States is lung disease which is quite often treated by lung transplantation. Lung transplant recipients seem to carry a greater risk of developing obliterative bronchiolitis (OB) which has been linked to chronic rejection of the transplanted lungs. Some recent studies have produced data that suggests the number of fibroblast and epithelial cells present in bronchoalveolar lavage (BAL) correlates to the severity of OB. Establishing a biomarker that can be used in the diagnosis of OB is important, because no clinical test exists that can be used to directly diagnose the disease. In these studies we show the populations of low frequency cells (fibroblast and epithelial) within different BAL samples. Cells are counted and sorted by type via a panning method and work has been done to prove their phenotype with immunostaining. This is an important step as no other research has documented the relative frequencies of cell populations within BAL samples, and provides a foundation to develop a clinical assay for detection of those subpopulations.
  • Thumbnail Image
    Item
    Mapping Electrode Paths in the Inferior Colliculus
    (2011-08-11) Ryan, Kellie
    Sound surrounds us in everyday life, but to those with a hearing deficit the world seems quiet. Understanding how the auditory system works is essential to creating new devices that will help the percent of the population living in a silent world. Experiments will simulate different regions of the Inferior Colliculus, a section of the brain, and obtain frequency maps. By playing different stimuli and comparing the maps obtained, we hope to better understand the plasticity of the brain. From here we can then further look into what areas are most effective at eliciting the wanted frequency shifts. This is one main are where my part of the research helps, as I create 3D reconstructions of the brains with all the electrode placements that were in place during the experiment. This will then give the anatomical location of the placements, so one can see the exact location where the changes are occurring.
  • Thumbnail Image
    Item
    Mechanism of Disease-Causing Missense Mutations in Dystrophin
    (2009-04-08) Lee, Ann
    Duchenne muscular dystrophy (DMD) is a fatal, x-linked disease that affects 1 in every 3,500 live born males. DMD is caused by the loss of the protein dystrophin due to genetic mutation. Dystrophin is abundant at the cell membrane of muscle cells, where its function is to stabilize the plasma membrane against contraction-induced membrane damage by binding to cytoskeletal f-actin filaments and the transmembrane protein dystroglycan. A small percentage of DMD cases are caused by missense mutations where the change in a single amino acid can cause severe disease. This disease can be caused by dystrophin not being able to bind its intracellular partners or by misfolding of the dystrophin protein, which can lead to degradation or insoluble aggregates. I investigated this aggregation as a possible mechanism for the pathogenesis of DMD missense mutations. I specifically worked with five missense mutations: K18N, L54R, L172H, Y231N, and T279A. These particular mutations are located in the actin-binding domain on the N-terminus of dystrophin. Of the fifteen known missense mutations in DMD patients, nine of them are found in this region. The missense mutations in this area can cause disease in one of two ways. The mutations can cause the protein to fold improperly, which leads to the aggregation and the loss of its localization to the membrane. The mutations can also render the protein unable to bind actin properly, despite normal folding and transportation of the protein to the membrane. For this project, I compared the levels of insoluble protein for various types of mutant dystrophin to the levels of wild type (WT) dystrophin (data provided by D.M. Henderson) to determine whether the mutations cause misfolding. I hypothesized that disease-causing missense mutations in the N-terminal actin binding domain of dystrophin cause misfolding and increase the level of insoluble dystrophin in vivo.