| Interfaces Research Symposium |
| Crossing Disciplinary Lines in Biomedical Research |
| June 15, 2007, 9am - 2pm Weaver Center, Institute of the Americas University of California, San Diego |
Sponsored by the UCSD Interfaces Graduate Program |
| |
| "Cerebral Perfusion Territory Imaging using Vessel Encoded Arterial Spin Labeling" | |||
| Akash Kansagra, UCSD School of Medicine | |||
| with Eric C. Wong | |||
| | |||
| | Purpose Vessel encoded arterial spin labeling (ASL) MRI allows for quantitative, non-invasive imaging of perfusion territories of arteries supplying the brain. Here, we demonstrate the ability of vessel encoded ASL to separately image the perfusion territories of major brain-feeding arteries and discuss the clinical information that one can gather from these data. Materials and Methods Vessel encoded ASL uses a pseudo-continuous ASL sequence to invert arterial water as it traverses a spatially-encoded tagging plane. The spatial encoding allows simultaneous application of unique tags to multiple vessels. Tagging of vessels is performed in one of several locations, depending on the perfusion territories being imaged. With this technique, we can distinguish perfusion from two different arteries on nine 8 mm thick, 64-by-64 slices with 22 cm FOV with one 4:39 minute scan. Additional perfusion territories are determined with additional scans. Results Vessel encoded ASL enables quantitative imaging of perfusion territories of the internal carotid, basilar, vertebral, anterior cerebral, and middle cerebral arteries. Our results are consistent with known cerebrovascular anatomy, but do reveal substantial anatomical variations in the population. Further analysis of the perfusion territory images reveals border zones that occur at the interface of adjacent territories and mixing that occurs through arterial anastomoses such as the circle of Willis or the vertebrobasilar junction. Conclusion Vessel encoded ASL can non-invasively image cerebral perfusion territories and readily reveal anomalies of blood flow. Knowledge of these territories in clinical patients is likely to be of value in the management of cerebrovascular disease and the planning of chemotherapy. In addition, perfusion territory imaging may provide novel insights into functional activation of the brain. | ||
| | |||
| "Finite Element Analysis of the Time-Dependent Smoluchowski Equation for Acetylcholinesterase Reaction Rate Calculations" | |||
| Yuhui Cheng, UCSD Department of Chemistry and Biochemistry | |||
| with Jason K. Suen, Deqiang Zhang, Stephen D. Bond, Yongjie Zhang, Yuhua Song, Nathan A. Baker, Chandrajit L. Bajaj, Michael J. Holst, and J. Andrew McCammon | |||
| | |||
| | This presentation describes the numerical solution of the time-dependent Smoluchowski equation to study diffusion in biomolecular systems. Specifically, finite element methods have been developed to calculate ligand binding rate constants for large biomolecules. The resulting software has been validated and applied to the mouse acetylcholinesterase (mAChE) monomer and several tetramers. Rates for inhibitor binding to mAChE were calculated at various ionic strengths with several different time steps. Calculated rates show very good agreement with experimental and theoretical steady-state studies. Furthermore, these finite element methods require significantly fewer computational resources than existing particle-based Brownian dynamics methods and are robust for complicated geometries. The key finding of biological importance is that the rate accelerations of the monomeric and tetrameric mAChE that result from electrostatic steering are preserved under the non-steady-state conditions that are expected to occur in physiological circumstances. | ||
| | |||
| "A study of affiliative touch: mechanoreceptive C-fiber stimulation activates interoceptive brain areas" | |||
| Jennifer Aron, UCSD Department of Neurosciences | |||
| with A. N. Simmons, I. A. Strigo, K. L. Lovero, and M. P. Paulus | |||
| | |||
| | Background Previous investigations have shown that stimulation of highly sensitive C-mechanoreceptive fibers via slow, low pressure cutaneous stroking of receptive fields activates brain areas important for mood regulation. The aim of this study was to examine individual differences and the degree of anticipatory processing involved in this network. Methods Eighteen healthy volunteers received cutaneuous stimulation either to the forearm (which contains many mechanoreceptive C-fibers) or palm (which contains no mechanoreceptive C-fibers) of the left hand prior to and during blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI) while performing a continuous performance task. Visual analog scales (N=12) were used to assess pleasantness, unpleasantness, tickle, temperature, and softness. Results Slow touch on either palm or forearm activated primary and secondary somatosensory areas. C-fiber activation via forearm stroking revealed significant increased activation in bilateral amygdala, contralateral (right) anterior and mid insular cortex, and medial frontal cortex. Discussion We found greater activation in limbic and paralimbic areas during stimulation of skin areas containing mechanoreceptive C-fibers versus those that do not. The fact that C-fiber stimulation also elicited greater activation in emotionally salient regions, such as the amygdala, is consistent with their role in mediating interoceptive-related emotion processing. Thus, mechanoreceptive C-fiber stimulation may be important for mood regulation and for social interactions. Future investigation will need to examine the functionality of this system in individuals with mood and anxiety disorders. | ||
| | |||
| 1. | Profiling the Fitness Landscape of an Escherichia coli adaptation process using Head-to-Head Competitions with Allelic Frequency Measurements | ||
| | Kenyon Applebee, Tom Conrad, Markus Herrgard, Bernhard Palsson | ||
| | Department of Chemistry and Biochemistry | ||
| | We have compared the fitness of four strains of Escherichia coli independently evolved to growth on glycerol minimal media in the laboratory. Whole genome re-sequencing was previously used to identify all of the adaptive mutation acquired1, which revealed that all four strains had acquired a different mutation to glycerol kinase (glpK) gene, and three had acquired a mutation to one of two RNA polymerase subunit genes (rpoB/C). To determine the relative fitness relationships among adaptively-evolved endpoint strains and the adaptive mutations, we performed head-to-head competition experiments. These experiments entail growing two cell-types in the same vessel to compete directly for resources, and monitoring the rate of population frequency change as one strain selectively out-competes the other2. Results show that the fitness gain by each endpoint strain is distinct. Four sets of strains were competed, including the endpoints and sets of strains constructed to carry the glpK and rpoB/C mutations individually. Results demonstrate that the fitness relationship of each set is internally consistent, and that fitness directly correlates to growth-rate. Additionally, the last mutations acquired by two strains are shown to only have adaptive value in the presence of previously-acquired mutations, even though no functional relationship between the mutated genes is known. Finally, this study also demonstrates that allele-frequency estimation is highly-sensitive method for measuring selection rates during competitions, appropriate for investigating non-additive mutation effects on fitness. 1. Herring, C.D., et al., Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet, 2006. 38(12): p. 1406-1412. 2. Rose, M.R., et al., Long-Term Experimental Evolution in Escherichia Coli. I. Adaptation and Divergence During 2,000 Generations. American Naturalist, 1991. 138(6): p. 1315-1341. | ||
| 2. | Multi-Scale Modeling of the Mouse Heart: From Genotype to Phenotype | ||
| | Stuart Campbell, Andrew D. McCulloch, Robert L. Price, Thomas K. Borg, Anushka Michailova, Sarah N. Flaim, and Roy C. P. Kerckhoffs | ||
| | Department of Bioengineering | ||
| | We propose to develop new multi-scale computational models of the physiology of the mouse heart that integrate functionally and structurally across multiple scales of biological organization from molecular networks to organ systems. Specifically we will develop new models of the electromechanical function of the normal and genetically modified mouse heart that integrate across all five of the following biological scales and classes of mathematical model: 1. Mechanistic biochemical models of molecular regulatory networks, including: (a) Cell signaling pathways; (b) The effects of genetic alterations. 2. Biophysical common pool models of whole myocyte excitation-contraction coupling, including: (a) Sarcolemmal ionic currents; (b) Intracellular calcium handling; (c) Myofilament activation; (d) Crossbridge interactions. 3. Microstructurally-based constitutive models of anisotropic tissue electrical and mechanical properties that incorporate: (a) Regional muscle fiber and sheet architecture and their statistical dispersions; (b) Extracellular matrix structure; (c) Gap junction distributions. 4. Three-dimensional continuum models of whole heart electromechanics that include: (a) Mouse right and left ventricular geometry; (b) Regional muscle fiber and sheet orientations; (c)Conducting system anatomy. 5. Systems models of circulatory dynamics, including: (a) Pulmonary and systemic arterial impedances; (b) Venous capacitance and return. (c) Autonomic responses | ||
| 3. | NMR studies of the transcriptional repressor IκBα | ||
| | Carla Cervantes, Carla F. Cervantes, S. C. Sue, G. Kroon, H. Jane Dyson, Elizabeth A. Komives | ||
| | Department of Chemistry and Biochemistry | ||
| | Although the structure of the transcription factor Nuclear Factor Kappa B (NF-κB) bound to its inhibitor, the ankyrin repeat protein IκBα, has been solved by x-ray crystallography, no structure of the free state of IκBα is available. Native state H/D exchange experiments showed that its ankyrin repeat domain possesses significant structural flexibility in the first, fifth and sixth ankyrin repeats. While the secondary structure of IκBα remains the same in the free and NF-κB-bound states as shown by CD, the β-hairpin regions in the fifth and sixth ankyrin repeats, which are highly solvent accessible, become more structured upon binding NF-κB. This goal of this project, which is a collaboration between the Komives and Dyson labs, is to use NMR dynamics experiments to investigate the backbone dynamics of free IκBα and also to probe the relevance of these motions for the stability and function of IκBα by site-directed mutagenesis. Full NMR backbone assignments for the C-terminally truncated IκBα (67-206) will be presented. We have made various stabilized mutants in which residues are replaced with those corresponding to the consensus sequence for stable ankyrin repeat proteins in order to aid in the assignment of residues 207-287, corresponding to the fifth and sixth repeats. Results of NMR studies on the binding of the NLS of NF-κB to IκBα will also be presented. | ||
| 4. | Generation of an accurate 3D computational model of the mouse heart from MR images | ||
| | Joyce Chuang, Andrew McCulloch, Jeff Omens, Larry Frank | ||
| | Department of Bioengineering | ||
| | Due to the development of genetically engineered strains, the mouse model has become an important tool in cardiovascular disease research. Several techniques have been used to quantify global geometry and function in the mouse heart however, to determine regional cardiac functional parameters such as internal wall stress, computational modeling is necessary. An important component of these models is the incorporation of accurate cardiac geometries since diseased hearts are typically abnormal in shape and size. Due to its high spatial and temporal resolution, MRI is commonly used to obtain reliable in vivo geometric data for modeling of human or large animal hearts and may be particularly useful in characterizing smaller hearts. However, a straightforward approach to generate a 3D anatomical model of a mouse heart from MRI data has not been developed. We have developed a technique for creating 3D finite element models of the mouse heart from high-resolution, temporally resolved high field MR data. With our image acquisition protocol, we can collect detailed spatial data in both the short and long-axis directions. The geometries generated with our technique are applicable to a wide variety of computational experiments. The anatomical models are built in a finite element package that is capable of biomechanical and electrophysiological simulations. We are currently in the process of incorporating material properties and fiber angle data to our model. By coupling the completed model to a circulatory model, it will be possible to study regional mechanics and myocardial activation of a beating mouse heart in silico. | ||
| 5. | Shaped, Scaffold-free Cartilaginous Graft for Large Articular Cartilage Defects | ||
| | Eun Hee Han, Won C. Bae, Van W. Wong, Nancy D. Hsieh-Bonassera, Simon G¶rtz, *Koichi Masuda, William D. Bugbee, Robert L. Sah | ||
| | Department of Bioengineering *Rush University Medical Center, Chicago, IL | ||
| | For treatment of large articular cartilage defects, tissue-engineered constructs, many of which have been flat to date, may not adequately fit with highly contoured surfaces. Prior studies on creating contoured, cartilaginous constructs have all utilized scaffolds. Scaffold-free tissue engineering may reduce possible untoward effects from scaffolds and degradation products, and has been achieved using immature chondrocytes and alginate pre-culture of adult chondrocytes. Therefore, the objective was to establish a platform molding technology for fabrication of scaffold-free cartilaginous constructs that are shaped on one or two surfaces, targeting spherically-shaped hip joint. Isolated chondrocytes from bovine calf knees were cultured in alginate beads for 7 days, released from alginate with their cell-associated matrix, and seeded into culture chambers with molds on one (cup), two (shell), or no (disk) sides. After 10 days, the surface contours of the constructs were measured with a non-contact laser sensor and processed with MATLAB. The radius of curvature and roughness of fitted flat plane (for disk) or spherical surface (for cup and shell) were computed. The constructs were assayed for biochemical content and processed for histology with Safranin O. Scaffold-free constructs with distinct surface contours, in disk, cup, and shell geometries, were fabricated consistently. Analysis of surface contour showed that cup and shell constructs had significantly different sphericities from each other as assessed by radius of curvature from fitted spherical curve. Chondrocytes and their matrix were distributed evenly throughout the constructs as seen by histology. All types of constructs had matrix compositions that were similar, as indicated by DNA, GAG, and collagen per wet weight. These results demonstrate that molding fabrication can generate constructs that are contoured and fabricated only from chondrocytes and their matrix products, which accumulate similarly, independent of shape. This technology has the potential create shaped cartilaginous constructs for surface recreation of large defects. | ||
| 6. | Spontaneous CSF Leak Secondary to a Calcified Disk in the Thoracic Spine: Successful Treatment with an Epidural Blood Patch | ||
| | Dustin Hayward, Scott C. Berta, MD, Howard Tung, MD, Kevin Yoo, MD | ||
| | School of Medicine | ||
| | Reason for study This is a case report of a 41 year-old woman with a history of severe, acute, orthostatic headaches as a result of a spontaneous CSF leak (SCL). CSF hypotension occurred from a spontaneous, ventral sided meningeal tear created by a calcified T11-T12 disc impinging on and eroding into the dural sac. This study's intention is to further our understanding of the pathology, detection, and management of this rare and unusual phenomenon. Methods used to obtain the data Single case report - data was collected from various imaging studies including, but not limited to, CT myelogram, MRI, cysternogram and CT head. Summary of the results A SCL was visualized on CT myelogram supposedly secondary to a T10-T11 calcified disk herniation impinging on the spinal meninges. This phenomenon likely created micro-tears in the ventral dura that ultimately resulted in a rupture through the thecal sac. The rupture was successfully treated with a thoracolumbar epidural blood patch. Conclusion/Discussion The etiology of SCLs in the majority of patients remains elusive. Most SCLs are believed to occur by an underlying structural weakness of the spinal meninges acting alone or in combination with a trivial traumatic event. SCLs usually do not cause local symptoms, but instead manifest with postural headaches, the prototypical symptom of intracranial hypotension. This study demonstrates a SCL that occurred without evidence of meningeal diverticula, generalized connective tissue disorder, bone spur, osteophyte complex, or trauma, the more commonly reported causes of SCLs. Instead, a calcified, herniated thoracic disc that attenuated and ultimately ruptured the dural sac was the culprit responsible for the patient's unprompted CSF egress. The consideration of this rare cause of SCL in the differential diagnosis of any new, acute-onset orthostatic headache may expedite the detection and ultimate correction of the compromised dura via blood patch or surgery | ||
| 7. | Visualization of calcium signaling in rat Mueller retina cells and astrocytes during normal and pathological conditions | ||
| | Dustin Hayward, Marie C. Davidson, Gabriel A. Silva | ||
| | School of Medicine, Department of Bioengineering, Department of Ophthalmology, Department of Neurosciences | ||
| | Glial cells have traditionally been considered to play a substantially supportive role to neurons in the central nervous system. However, recent evidence suggests that glial cells actively contribute to the modulation and execution of several neural processes, such as synaptic transmission, neural plasticity, and the final result of brain damage following trauma and several CNS diseases, reactive gliosis. Glial cells exert their effects via an elaborate network which employs intra and extracellular signaling pathways to communicate between one another and the construct of neurons they are a part of. Most prominent among these signaling pathways is the propagation of intracellular calcium in response to stimulation with glutamate, adenosine triphosphate (ATP) and mechanical excitation. This study attempted to visualize the mechanismas of glial cell communication through the a novel approach that utilized an ATP agonist to elicit a calcium wave in rodent Mueller glial cells (RMC1) and astrocytes. This technique can be applied in future studies to advance our understanding of glial cells and their important contribution to the physiologic functioning of the central nervous system as well as pathologic processes including, but not limited to, the formation of a glial scar following reactive gliosis. | ||
| 8. | Volunteer Visits & Denial of Prognosis: Interacting to Predict Survival Time for Terminally Ill | ||
| | Kathryn Herbst-Damm | ||
| | Department of Psychology | ||
| | A study recently completed by Herbst-Damm and Kulik (2005) found that patients who received support visits from hospice volunteers lived significantly longer than those who were not visited. Exploratory analyses were conducted in an effort to better understand how those who request volunteers may differ from those who do not. One variable of interest is the social workers' perceptions of a patient's denial of prognosis. Volunteer requesters were significantly more likely than non-requesters to be in denial (70.2% versus 29.6%, p = .006) Those who received visits and were in denial lived longer than those who received visits but were not in denial (p = .017), whereas denial was unrelated to longevity in those who did not request visits. Volunteer request status and denial were both unrelated to initial illness status. These exploratory results imply denial may predict who requests a volunteer and may interact with volunteer visits to predict longevity. Future work should include more in-depth measurement of denial in order to better understand patient characteristics that may differ for volunteer requesters and non-requesters as they relate to the earlier reported survival difference. | ||
| 9. | Full Length Zinc Selective Inhibitors of Matrix Metalloproteinase | ||
| | Faith Jacobsen, Cesar Oliveira, J. Andrew McCammon and Seth M. Cohen | ||
| | Department of Chemistry and Biochemistry | ||
| | Matrix metalloproteinases (MMPs) are a class of metalloenzymes implicated in illnesses such as arthritis, heart disease, and inflammatory disease. Full length inhibitors for these enzymes have been synthesized using the zinc-binding group (ZBG) 2,2'-dipicolylamine (J. Am. Chem. Soc., 128(10), 3156 -3157). Computational analysis has helped determine which backbones would yield the optimal inhibitor. These inhibitors have been synthesized and tested for inhibition in a variety of MMPs to give selectivity profiles. A structure activity relationship (SAR) has been performed to identify the optimal linker and backbone. These inhibitors are selective for zinc(II) enzymes over iron enzymes and provide insight into a new class of molecules that can be used for selective inhibition of a variety of zinc(II)-metalloenzymes including histone deacetylase and anthrax lethal factor. | ||
| 10. | A Flexible Polymer Lens Reduces Spherical Aberration in Two-Photon Microscopy and Optical Perturbation with Ultrashort Laser Pulses | ||
| | Benjamin Migliori, B. Migliori, P. S. Tsai, K. Campbell, T. N. Kim, Z. Kam, A. Groisman and D. Kleinfeld | ||
| | Department of Physics | ||
| | We fabricate a flexible membrane lens from polydimethyl siloxane (PDMS) and demonstrate its application to spherical aberration correction. This provides an economical means to restore beam focus when a standard water-immersion objective is used for two-photon laser scanning microscopy (TPLSM) to image deep within a higher-index sample, such as brain tissue. We demonstrate improved imaging of sub-resolution structures (including CFP-labeled mitochondria within fixed brain tissue), as well as enhanced production of optically-induced damage deep within a sample using plasma-mediated laser ablation with amplified ultrashort laser pulses. TPLSM is typically performed with a dipping objective corrected for objects at the surface of the immersed tissue. Refraction at the saline-tissue interface results in spherical aberration, wherein the marginal rays focus deeper than the paraxial rays. This results in degradation of both the resolution and the excitation efficiency. The insertion of a PDMS lens before the objective compensates for the interface-induced aberration, and restores the quality of the focus. Variable inflation of the lens, achieved by adjusting vacuum pressure, provides continuous compensation over a wide range of imaging depths. We used the PDMS lens with a 40X, 0.8 NA dipping objective to image high-index tissue phantoms and cleared histological brain tissues. Imaging at depths greater than 600 µm into high-index media (n = 1.42) induces degradation of the axial resolution from approximately 2 µm to greater than 5 µm. The use of the PDMS lens restores the axial resolution to less than 2.5 µm over a central field of 25 µm. We demonstrate similar compensation of plasma-mediated laser ablation, and achieve a factor of 2 improvement in the axial confinement of the ablated region at depths of 700 µm in glass. Application of the PDMS lens could improve many fluorescence imaging procedures, and extend the usefulness of optical histology, optoporation, and optoaxonomy. | ||
| 11. | Information Propagation and Gain Control in the Drosophila Olfactory system | ||
| | Cory Root, Julia L. Semmelhack and Jing W. Wang | ||
| | Division of Biological Sciences | ||
| | Sensory systems have the difficult task of encoding the identity and intensity of behaviorally relevant stimuli in the environment. The question of how stimuli are encoded and propagated from the periphery to higher brain centers is central to systems neuroscience and the olfactory system is an attractive model system to study information propagation. Investigating how information flows between layers in the olfactory system is an important step towards understanding the olfactory code. In the first olfactory relay station in the Drosophila brain, each glomerular output projection neuron receives two sources of input: the olfactory receptor neurons of the same glomerulus, and lateral excitatory and inhibitory interneurons that innervate many glomeruli. We therefore asked how these inputs interact to produce projection neuron output. We used receptor gene mutations to silence the receptor neurons innervating a specific glomerulus, and recorded projection neuron activity with two-photon calcium imaging and electrophysiology. We observed little or no response in the absence of direct receptor neuron input and found little or no effect on neighboring glomeruli when input to one glomerulus is removed. Furthermore, we recorded projection neuron activity across a range of odor concentrations and saw evidence of balanced excitatory and inhibitory synaptic inputs. Our results suggest that the cognate receptor neurons are the main drivers of projection neuron firing while interneurons are the modulators. Balanced excitatory and inhibitory interneuron input may provide a mechanism to globally enhance or suppress olfactory responses to reflect the behavioral state of the animal. Supported by the Beckman Foundation, Searle Family Trust, and the Whitehall Foundation, and NIH training grant GM08107. | ||
| 12. | The Anatomical Basis of Cognition and Confabulation Theory | ||
| | Soren Solari, Robert Hecht-Nielsen | ||
| | Center for control systems and dynamic, Department of Mechanical and Aerospace Engineering | ||
| | The Anatomical Basis of Cognition and Confabulation Theory (ABCCT) represents the synthesized knowledge of over 200 carefully selected and relevant neuroanatomical papers. The comprehensive neuroanatomical information is presented in a detailed diagrammatic view of the connections between 6-layered cerebral cortex, 20 thalamic nuclei, basal ganglia, and subcortical structures. The primary ABCCT rationale is that a necessary approach to understanding the complexity of cognition is to lay out the entire set of neuroanatomical facts, and guided by concrete theory, develop anatomically realistic neuronal models in order to fundamentally understand the detailed mechanisms of cognition. Confabulation theory offers a detailed framework with which the neuroanatomical facts presented have been translated into function. Confabulation theory proposes that cognition (seeing, hearing, reasoning, etc.) is a phylogenetic outgrowth of movement. We postulate that human cerebral cortex is organized into a few thousand discrete, largely mutually disjoint, thalamocortical modules which function as the "muscles of thought". Each such thalamocortical module is designed to be "contracted" using the same circuitry that evolutionarily had been used to contract muscles. By controlling the contraction of thalmocortical modules in properly coordinated 'movements' (thought processes), valuable information processing (cognition) can be carried out. This deliberate, controlled, "neural contraction" of a thalamocortical module in the brain is postulated by confabulation theory to be the single universal information processing operation of cognition in all mammals. The neural contraction of a module causes progression of a winner-take-all competition among cell assemblies (symbols) that reside within the module, the outcome of which is dependent upon the state of all the other modules with which it is connected by cortical knowledge links, axonal connections. Each conclusion, winning cell assembly, reached by a confabulation operation causes immediate launch of associated action command axonal outputs to subcortical nuclei, that are the cause of behavior (movement and thought processes). | ||
| 13. | Adaptive Memory in the Unfolded Protein Response Pathway in Saccharomyces Cerevisiae | ||
| | Jeffrey Sperling | ||
| | Department of Biology | ||
| | Several cellular stress response pathways, like the heat shock response, can "remember" events of the past in order to better prepare for future; this notion is called "adaptive memory." I discovered a novel version of this memory in the Unfolded Protein Response (UPR) and its response to Endoplasmic Reticulum (ER) stress. Using HAC1 mRNA splicing to measure UPR activity, I "preconditioned" cells with dithiothreitol (DTT) or tunicamycin (Tm) (UPR-inducing drugs) and evaluated whether or not there was a difference in the kinetics of HAC1 mRNA splicing upon a secondary induction. I found that there was indeed a decrease in the speed and robustness of HAC1 mRNA splicing during the secondary induction. Increased time between inductions diminished this phenomenon, while longer induction times intensified this phenotype. If cells were "preconditioned" with a different drug during the primary induction than during the secondary induction, the cells still displayed a decrease in the kinetics and maximum level of HAC1 mRNA splicing; however, there is evidence to suggest that the responses to DTT and Tm are different and that these drugs may not be activating the same UPR pathway. I also found that KAR2 mRNA levels directly follow the splicing of HAC1 mRNA during both the primary and secondary inductions regardless of the recovery length, suggesting that the adaptive phenotype observed is not mediated at the level of KAR2 transcription. This study shows a unique phenomenon of the ER in response to stress and describes a unique mechanism of epigenetic memory. | ||
| 14. | Investigating the effects of blood hematocrit on mean arterial blood pressure using a mathematical model | ||
| | Phi Trannguyen, Daniel Tartakovsky, Diogo Bolster, Marcos Intaglietta | ||
| | Department of Mechanical and Aerospace Engineering | ||
| | It is generally accepted that increased blood viscosity is a factor in hypertension. In fact, several clinical studies report a significant relationship between hypertension and high hematocrit levels. Hypertension is a direct result of increased mean arterial blood pressure (MAP), which is elevated when high whole blood viscosity causes the vasculature to become more resistant. However, a recent study observed that acute changes in hematocrit are not necessarily associated with an increase in MAP. The results showed that increasing hematocrit 7-13% of baseline decreased MAP by 13 mmHg, while increasing hematocrit above 19% reversed this trend and caused MAP to rise above baseline. It is hypothesized that increased blood viscosity could lead to increased shear stress at the endothelium and production of nitric oxide (NO), a vasodilator generated from the conversion of L-arginine to L-citrulline by the enzyme NO synthase. With the initial increase in production of NO, smooth muscle cells within the media relax, allowing MAP to decrease from baseline values. However, larger increases of hematocrit overwhelm the NO effect through the increases in vascular resistance, causing MAP to rise above baseline values. We wish to investigate this effect further with a mathematical model of the blood vessels under physiological conditions. Within the blood vessels in the microcirculation, Stokes flow exists. Furthermore, we assume the blood vessel to be a thin-walled cylindrical shell made of nonlinear pseudo-elastic, anisotropic and incompressible material that has a strain energy density function expressible in terms of Green-St. Venant strains. Coupling the analysis of blood flow with the pseudo-elasticity analysis of blood vessel wall, we are able to explain the functional relationship between MAP and the hematocrit of blood in mathematical expressions. The work could easily be extended to include analysis involving the diffusion-reaction of NO in the microcirculation. | ||
| 15. | Rethinking proteasome evolution: 2 novel bacterial proteasomes | ||
| | Ruben Valas, Phil Bourne | ||
| | Department of Bioinformatics | ||
| | The proteasome is a multi subunit structure that degrades proteins. Protein degradation is an essential level of regulation because proteins can become misfolded, damaged, or simply unnecessary depending on environmental conditions. Proteasomes and their homologs vary greatly in complexity from Hslv which is encoded by 1 gene in bacteria to the eukaryotic proteasome which can be encoded by over 20 genes. Despite this variation in complexity all the proteasomes are composed of homologous subunits that form a barrel with the active sites on the inside. This self compartmentalization ensures only proteins that are targeted to the proteasome are degraded. The actinobacteria have the most complex known bacterial proteasome: a 20s proteasome which is encoded by 2 genes. It has been argued that the 20s proteasome evolved from the simpler homolog Hslv. We searched 238 complete bacterial genomes for structures related to the proteasome, and found evidence of 2 novel groups of bacterial proteasomes. The first, which we name Anbu, is sparsely distributed among several groups of bacteria. Anbu must be very ancient because of its distribution, and it has been lost in many species. We also present evidence for a fourth type of bacterial proteasome found in a few β-proteobacteria, which we name BPH. These families have been missed until now because of their sparse distribution. Sequence and structural analysis both show Anbu and BPH are distinct from known bacterial proteasomes, and but are homologous structures. Anbu is encoded by 1 gene, so we postulate a duplication of Anbu created the 20s proteasome. It appeared bacteria could have either the 20s proteasome or Hslv, but never both in combination. However, we have found different combinations of Anbu, BPH, and Hslv within these genomes which raises questions about specialized protein degradation systems. | ||
| 16. | Biotransport Modeling: Enzyme membrane design for implantable lactate sensors | ||
| | Will Wang, Dale A. Baker | ||
| | Department of Bioengineering | ||
| | Implantable biosensors for continuous monitoring of lactate concentrations in both blood and tissue can provide important information on disease development, severity and possible treatments. Currently, we are designing optimized micro-scale biosensors that satisfy today's clinical demands. However, our design can be modified to deliver nano-scale biosensing that will address the needs of doctors and surgeons in the future as more sophisticated monitoring is used with clinical/surgical (e.g. robotic) machines. One attractive way to optimize sensor performance is by employing an integrated approach of systematic engineering analysis and physiological techniques to study the transport and reactive processes in our bioengineering systems. Such an approach requires the bridging between engineering and medicine: mathematics, physical sciences, chemical engineering and physiology. In this study, mathematical models are used to predict the transient and steady state responses of enzyme electrode sensors. This approach for biosensor design can provide details about the biosensor behavior that is difficult to obtain through other methods. The effects of two possible enzyme membrane compositions were investigated for a 2-dimensional "disk" electrode design: 1) an oxidase enzyme for lactate co-immobilized with catalase, and 2) simply the oxidase enzyme alone. The reaction and diffusion coupled mass conservation equations for oxygen and lactate in the sensor were solved simultaneously using finite element method. The lactate dependent currents were calculated based on the differential oxygen fluxes at the working disk electrode surface. Two trends were observed: 1) decreasing the aspect ratio (the ratio between enzyme membrane radius to length, thus increasing the length with fixed radius) can increase the detection range, but will also increase the response time, and 2) membranes containing these co-immobilized enzymes increased the detection range while decreasing its response time. Further investigations are underway to delineate the effects of scale/size of different enzyme membrane design on sensor responses. | ||
| 17. | Hydrothermal Conversion of Marine Calcium Carbonate Skeletons to Calcium Phosphate as Bone Substitutes | ||
| | Xing Zhang, Kenneth S. Vecchio, Jennifer B. Massie, Mark Wang, Choll W. Kim | ||
| | Department of Materials Science and Engineering | ||
| | Marine CaCO3 skeletons have the hierarchical and optimally designed architectures created by nature. For example, the mollusc shells are microlaminate composite of mineral and biopolymers, exhibiting exceptional nanoscale regularity and a strength ~3000 times greater than that of CaCO3 crystals themselves. Cuttlebone, coral and sea urchin spines have three-dimensional interconnected porous structures, which can be used as the scaffolds for bone tissue engineering. In this investigation, seashells, cuttlebone, coral and sea urchin spines were hydrothermally converted to calcium phosphates as bone substitutes. Conch and clam seashells were converted to dense hydroxyapatite [HAP, Ca0(PO4)6(OH)2] around 200ºC, while cuttlebone and coral were converted to interconnected macroporous HAP. Urchin spines were converted to bioresorbable porous Mg-substituted tricalcium phosphate [β-TCMP, (Ca,Mg)3(PO4)2] around 180ºC. Evaluation of the suitability of the converted shell and spine samples for bio-implant materials was evaluated in terms of their mechanical properties as well as their biocompatibility via in-vivo tests. Partially converted shell samples have the compressive strength similar to compact human bone, which can be used as load-bearing implants. On the other hand, converted coral, cuttlebone and urchin spines have relatively low strength and can be used in non-load bearing cases, such as, bone defect filling. In-vivo results show good biocompatibility and bioactivity of converted shell and spine samples after implantation in rat femoral defects for 6 weeks, indicating these materials can be used as bone substitutes. | ||
| 18. | Involvement of Shp2 in the regulation of pancreatic beta-cell function and glucose homeostasis | ||
| | Sha Zhang | ||
| | Molecular Pathology Graduate Program | ||
| | The pancreatic beta cell plays a central role in glucose homeostasis by secretion of the hormone insulin in response to increased blood glucose concentration. Previous study demonstrated that the insulin receptor (IR)-signaling pathway is active in the pancreatic beta-cells. Shp2 is a ubiquitously expressed protein tyrosine phophatase (PTP) that possesses two Src-homology 2 (SH2) domains at the N-terminus. This phosphatase is demonstrated to mediate the insulin signaling through interaction with IR and IRS in insulin responsive tissues. However, the function of Shp2 in pancreatic beta cells remains to be determined. Accordingly, we have generated conditional knockout mice in which the shp2 gene is selectively deleted in pancreas. The mutant mice exhibited defective glucose-stimulated insulin secretion and impaired glucose tolerance. The major glucose transport isoform Glut2 and Pdx-1 expression are decreased in islets of mutant mice. Knockdown of Shp2 in INS-1 cells decreases insulin secretion in both basal and high glucose condition, but mitochondrial ATP generation is increased conversely. We found that insulin content is significantly decreased and gene profile of several beta cells specific genes are disrupted in Shp2KD cells. Further studies demonstrate that insulin signaling components PI3K/Akt/Foxo1 and Erk1/2 are altered by shp2 deletion. Therefore, the defective insulin secretion and production result from the defective insulin signaling and Erk1/2 activation. These findings provide direct evidence of an important role of Shp2 in the regulation of glucose-stimulated insulin secretion from pancreatic beta cells and glucose homeostasis. | ||
| | |||
| 19. | Modeling action potential of ventricular myocyte and Purkinje fibers |
| | Behrad Azimi, Anusha Mehta, Hoda Feizi, Erin McElfish |
| | Department of Bioengineering |
| | We propose the modeling of myocyte electrophysiology with an emphasis on the comparison of action potential in the Purkinje and ventricular myocytes. The first aim of the study will be to model the electrophysiology of these cells. We intend to investigate how the action potential differs between these two types of myocytes. We will attempt to find out if the known information is sufficient to account for these differences. Next, we will investigate the effects of a known drug (e.g. Class I antiarrhythmic) on the generated action potential. Finally, we will construct a simple tissue model combining Purkinje cells and simple ventricular myocytes and will model the signal propagation across the tissue. The action potentials will be found on the cellular level. We will then proceed to investigating the nature of signal propagation in tissue level. We intend to use Virtual Cell for modeling of the action potential and Continuity for tissue-level studies. |
| 20. | Computational Modeling of the Effects of L-type Ca2+ Channel Blockers (Verapamil) on Atrioventricular (AV) Nodal Reentrant Tachycardia |
| | Elliot Howard, Chris MacDonald, Kevin Chung |
| | Department of Bioengineering |
| | The focus of this study was to investigate the pathological events at the molecular, cellular, and tissue levels that ultimately result in atrioventricular (AV) nodal reentrant tachycardia. Additionally, the effects of L-type Ca2+ channel blockers, such as the drug Verapamil, on regulating AV nodal reentrant tachycardia was simulated. At the molecular level, drug-receptor interactions are modeled, which allows for an assessment on the efficacy of the drug in blocking L-type calcium channels. Specifically, the effect of ion channel transport inhibition on the propagation of the action potential was modeled, and the information on the propagation of these waves was then used to simulate the propagation of the action potential on the tissue/organ scale. The effect of the action potential propagation under different drugs was then studied at the whole tissue level, in particular our simulations predicted the electrophysical changes that can minimize the occurrence of an arrhythmic event. |
| 21. | Dynamic Effects of Caveolae Unfolding and Effects of Compartmentalization in Cardiomyocytes |
| | Amy Hsieh, Corbin Clawson |
| | Department of Bioengineering |
| | Caveolae are invaginations found within the plasma membranes of mammalian cells. These invaginations have lipid compositions that are similar to those of lipid rafts and they contain an organelle-specific structural protein, caveolin. Caveolae are able to fuse to the cellular lipid membrane, opening a pore and exposing key proteins and receptors to the extracellular environment. The cellular and biochemical activities regulated by caveolae include nutrient transport, endocytosis, exocytosis, and signaling activation and desensitization. It has been noted that certain signaling components have been localized to the caveolae and this may provide a means for rapidly activating signaling cascades. In the case of cardiomyocytes, adenylyl cyclase type V/VI is widely expressed in the caveolar lipid domain, whereas adenylyl cyclase type IV/VII is located within the extracaveolar domains. Adenylyl cyclase is a key protein involved in the production of cAMP. Cyclic AMP, subsequently, is involved in the regulation of electrical, mechanical, and metabolic activity of cardiomyocytes. Currently, the dynamics of caveolae unfolding and the resulting effects on signaling pathways has not been fully explored in computational simulations. Two software packages, MCell/Dreamm and Virtual Cell, are powerful tools useful in studying the dynamics of signaling cascades. MCell/Dreamm is a Monte Carlo simulator of microphysiology at the molecular, subcellular, and cellular level using discrete molecules. Virtual Cell utilizes continuum models to simulate cellular and subcellular signaling, electrophysiology, and metabolism. These two programs were used to study the dynamics of caveolae unfolding and effects of compartmentalization on cAMP signaling in cardiomyocytes. |
| 22. | Molecular Changes from Insulin Resistance Affects Vascular Dynamics |
| | Joy Liau, Joseph Godoy, Phillip Cheng |
| | Department of Bioengineering |
| | No abstract available. |
| 23. | Does Function Follow Form in the TMJ Disc? A Metabolic and Structural Evaluation |
| | William McCarty, Andrea Pallante |
| | Department of Bioengineering |
| | No abstract available. |
| 24. | Assesment of Dynamic Properties of Human Glucosamine Metabolism |
| | Vasiliy A Portnoy, John Lee |
| | Department of Bioengineering |
| | No abstract available. |
| 25. | The Effects of Ca2+ Diffusion on Force Generation in Cardiac Muscle |
| | Joanna So, Hazreen Harith, Yessenia Lopez |
| | Department of Bioengineering |
| | No abstract available. |
