Bulletin of the American Physical Society
Joint Meeting of the Four Corners and Texas Sections of the American Physical Society
Volume 61, Number 15
Friday–Saturday, October 21–22, 2016; Las Cruces, New Mexico
Session C5: Biophysics |
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Chair: Nicole Herbots, Arizona State University Room: Meeting Room 1 |
Friday, October 21, 2016 1:00PM - 1:24PM |
C5.00001: Label-free Optical Detection of Bioanalytes for Cancer and Neurodisease Monitoring Invited Speaker: Felicia Manciu Although not yet ready for clinical application, methods based on Raman spectroscopy have shown significant potential in identifying, characterizing, and discriminating between bioanalytes responsible for cancer and neurodiseases. Real-time and accurate diagnosis achievable through this vibrational optical method largely benefits from improvements in current technological and software capabilities. Not only is the acquisition of spectra now possible in milliseconds and high throughput data analysis in minutes, but Raman spectroscopy also allows simultaneous detection and monitoring of all biological components. Besides demonstrating a significant Raman signature distinction between cancerous and noncancerous breast epithelial cells, we demonstrate that Raman can be used as a label-free method to evaluate epidermal growth factor (EGF) activity in tumor cells. Comparative Raman profiles and images of specimens in the presence or absence of EGF show important differences in regions attributed to protein and nucleic acid vibrations. Parallel Western blotting analysis reveals EGF induction of phosphorylated Akt protein, corroborating the Raman results of signal transduction from membrane to nucleus, with concomitant modification of DNA/RNA structural characteristics. We also demonstrate that confocal Raman mapping provides rapid, detailed, and accurate neurotransmitter monitoring, enabling analysis of biochemical dynamics. As a prototypical demonstration of the power of the method, we present real-time \textit{in vitro} serotonin, adenosine, and dopamine detection, and dopamine diffusion in an inhomogeneous organic gel, which was used as a substitute for neurologic tissue. With the ultimate goal of clinically implementing Raman-guided techniques for diagnosis of tumors and neurodiseases, the current results lay foundations for developing label-free optical tools. [Preview Abstract] |
Friday, October 21, 2016 1:24PM - 1:36PM |
C5.00002: Boron-Doped Diamond Signal Processing John Ciubuc, Kendall Lee, Kip Ludwig, Jonathan Tomshine, Shinho Cho, Josh Jacobs, Seth Hara, Felicia Manciu, Kevin Bennet Recent advances in closed loop deep brain stimulation (DBS) technologies lean in favor of enhanced sensitivity and increased stimulation electrode detection limits. There are two primary methods of improvement: hardware and software. This work focuses on the software approach for increasing the sensitivity of the electrodes. The signal processing technique employed consists of three primary approaches: background subtraction, noise reduction, and analyte specification. Background subtraction is used to maximize the signal-to-noise ratio without degrading the signal in the process. Noise reduction is then applied to clean the resulting voltammogram series, further enhancing the signal response for the analyte. Lastly, analyte specification is applied allowing the algorithm to isolate and extract as much of the processed signal as possible. The final result is an order of magnitude increase in the limit of detection for fast scan cyclic voltammetry deep brain stimulation electrodes. [Preview Abstract] |
Friday, October 21, 2016 1:36PM - 1:48PM |
C5.00003: Simulating conformational transitions of the transmembrane symporter Taylor Colburn, Sean Seyler, Oliver Beckstein The function of many proteins depends on large-scale conformational changes. Because these conformational transitions are rare events, it is very difficult to investigate them with equilibrium molecular dynamics (MD) simulations, which have otherwise become an important tool to study the molecular mechanisms of macromolecular systems. A variety of techniques --- such as the Dynamic IMportance Sampling (DIMS) method and various elastic network-based approaches --- have been developed to overcome timescale limitations and produce physically plausible trajectories between putative metastable states. We sought to characterize a number of different path generating and sampling methods, including DIMS with and without an implicit membrane model, by producing multidirectional trajectories of the transmembrane nucleobase symporter Mhp1$^{[1]}$. All trajectories were compared to one another using Root-Mean-Square Distances (RMSDs), structural order-parameters and Path Similarity Analysis (PSA)$^{[2]}$. In particular, PSA showed that while trajectory generating methods were broadly similar, paths from each method were also clearly distinguishable. \\ 1. Shimamura, T. et al. Science 328, 470473 (2010). 2. Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) PLoS Comput Biol 11(10) [Preview Abstract] |
Friday, October 21, 2016 1:48PM - 2:00PM |
C5.00004: Reverse-Engineering Gene Networks That Can Remember Using the Manifold Boundary Approximation Method Andrew White, Mark Transtrum Observable behaviors in biology result from the collective interactions of many microscopic elements. These microscopic elements make up complex biological systems that we can model mathematically. Ideally, mechanistic models should predict the system's behavior without misrepresenting the system's biochemistry. The computational method of model reduction known as the Manifold Boundary Approximation Method (MBAM) can help us identify which parts of a model are relevant for explaining a particular behavior. This project attempts to apply MBAM to gene transcription networks that are responsible for ensuring the permanence of cellular decisions to activate or silence genes. This behavior is known as ``memory,'' and our goal is to use MBAM to reverse-engineer genetic design motifs that could produce memory in developmental transcription networks. [Preview Abstract] |
Friday, October 21, 2016 2:00PM - 2:12PM |
C5.00005: Parameter Reduction of the Hodgkin-Huxley model of Action Potential Propagation Tyler Bahr In 1952 Hodgkin and Huxley formulated the fundamental biophysical model of how neurons integrate voltage input and fire electric spikes. Like most biological models, it is very complex, both in terms of its dynamics and number of parameters. A Hodgkin-Huxley model of a single neuron with two ion channels has 25 parameters. Using information theory and model reduction methods, we explore the extent to which all of these parameters are necessary. The manifold boundary approximation method (MBAM), is a powerful approach to parameter reduction based on a geometric interpretation of statistics. Using MBAM, we have derived a simpler model of spike firing (14 parameters). We present preliminary data in evaluating the behavior of the reduced model compared to original for different experimental conditions, including a network from the literature. [Preview Abstract] |
Friday, October 21, 2016 2:12PM - 2:24PM |
C5.00006: Working toward a de novo structure of the hypothetical zinc binding protein, AztD Hridindu Roychowdhury, Erik Yukl ATP-binding cassette transporters (ABC transporters) are essential for pathogenic scavenging of transition metals in the often metal-starved environments of host-pathogen interfaces. ABC transporters canonically consist of three proteins: a membrane bound permease, an ATPase, and a periplasmic solute-binding protein (SBP). A fourth protein on the operon has been found to be highly conserved across a number of pathogenic bacteria. In this study, we aim to understand the structure of this hypothetical protein, AztD, native to the soil bacteria Paracoccus denitrificans, of which there are a number of virulent homologs. Because wild-type AztD binds only 0.6 Zn per protein, an insufficient number to obtain phases necessary to solve structure via x-ray crystallography, innocuous mutations changing leucine residues to seleno-methionine have been made as well as soaking the crystals in bromide salts. We hope to solve the crystal structure using anomalous scattering off the selenium and bromine atoms covalently incorporated into the protein. [Preview Abstract] |
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