Bulletin of the American Physical Society
APS March Meeting 2017
Volume 62, Number 4
Monday–Friday, March 13–17, 2017; New Orleans, Louisiana
Session K29: Physics Leading the Frontier of Genomics and ApplicationsIndustry Invited
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Sponsoring Units: DBIO FIAP Chair: Cha-Mei Tang, Creatv Microtech Room: 292 |
Wednesday, March 15, 2017 8:00AM - 8:36AM |
K29.00001: Quantum sequencing: opportunities and challenges Invited Speaker: Massimiliano Di Ventra Personalized or precision medicine refers to the ability of tailoring drugs to the specific genome and transcriptome of each individual [1,2]. It is however not yet feasible due the high costs and slow speed of present DNA sequencing methods. I will discuss a sequencing protocol that requires the measurement of the distributions of transverse tunneling currents during the translocation of single-stranded DNA into nanochannels [3-6]. I will show that such a quantum sequencing approach can reach unprecedented speeds, without requiring any chemical preparation, amplification or labeling. I will discuss recent experiments that support these theoretical predictions [7], the advantages of this approach over other sequencing methods, and stress the challenges that need to be overcome to render it commercially viable. [1] M. Di Ventra and M. Taniguchi, Nature Nanotechnology, 11, 117 (2016). [2] M. Zwolak, M. Di Ventra, Rev. Mod. Phys. 2008, 80, 141. [3] M. Zwolak and M. Di Ventra, Nano Lett. 5, 421 (2005). [4] J. Lagerqvist, M. Zwolak, and M. Di Ventra, Nano Lett., 2006 6, 779. [5] J. Lagerqvist, M. Zwolak, and M. Di Ventra, Biophys. J. 2007, 93, 2384. [6] M. Krems, M. Zwolak, Y.V. Pershin, and M. Di Ventra, Biophys. J. 2009, 97, 1990. [7] T. Ohshiro, K. Matsubara, M. Tsutsui, M. Furuhashi, M. Taniguchi and T. Kawai, Nature: Scientific Reports, 2012, 2, 501. [Preview Abstract] |
Wednesday, March 15, 2017 8:36AM - 9:12AM |
K29.00002: Nanopore Kinetic Proofreading of DNA Sequences Invited Speaker: Xinsheng Sean Ling The concept of DNA sequencing using the time dependence of the nanopore ionic current was proposed in 1996 by Kasianowicz, Brandin, Branton, and Deamer (KBBD). The KBBD concept has generated tremendous amount interests in recent decade. In this talk, I will review the current understanding of the DNA ``translocation'' dynamics and how it can be described by Schrodinger's 1915 paper on first-passage-time distribution function. Schrodinger's distribution function can be used to give a rigorous criterion for achieving nanopore DNA sequencing which turns out to be identical to that of gel electrophoresis used by Sanger in the first-generation Sanger method. A nanopore DNA sequencing technology also requires discrimination of bases with high accuracies. I will describe a solid-state nanopore sandwich structure that can function as a proofreading device capable of discriminating between correct and incorrect hybridization probes with an accuracy rivaling that of high-fidelity DNA polymerases. The latest results from Nanjing will be presented. This work is supported by China 1000-Talent Program at Southeast University, Nanjing, China. [Preview Abstract] |
Wednesday, March 15, 2017 9:12AM - 9:48AM |
K29.00003: Iso-Flux Tension Propagation Theory and It's Application to Driven Polymer Translocation Invited Speaker: Tapio Ala-Nissila The translocation dynamics of polymers though nanopores driven by external fields is a far-from-equilibrium process, which is described by the tension propagation (TP) theory of Sakaue [1]. In particular, the Brownian Dynamics TP theory within the iso-flux (IFTP) assumption [2] allows a self-consistent derivation of analytic equations of motion for the dynamics, including an explicit form for the chain length dependence of the average translocation time [3]. In this talk I will discuss the application of IFTP theory to the case of a flickering pore and an oscillating external driving force [4], and translocation dynamics of semi-flexible polymer chains [5]. \\ 1. T. Sakaue, Phys. Rev. E 76, 021803 (2007).\\ 2. P. Rowghanian and A. Y. Grosberg, J. Phys. Chem. B 115, 14127 (2011).\\ 3. J. Sarabadani, T. Ikonen and T. Ala-Nissila, J. Chem. Phys. 141, 214907 (2014).\\ 4. J. Sarabadani, T. Ikonen and T. Ala-Nissila, J. Chem. Phys. 143, 074905 (2015).\\ 5. J. Sarabadani et al., submitted (2016). [Preview Abstract] |
Wednesday, March 15, 2017 9:48AM - 10:24AM |
K29.00004: Precision Genome Editing for Treating Single-gene Disorders Invited Speaker: Gang Bao There are an estimated 6,000 human single-gene disorders, most of them have no cure. This imposes a significant burden on human health worldwide. The recent advent in developing engineered nucleases, especially CRISPR/Cas9 (clustered, regularly interspaced, short palindromic repeats and CRISPR-associated protein 9) systems provides a powerful tool for precisely modifying the human genome, thus revolutionizing the treatment of single-gene disorders.\\ \\In this talk, I will present recent work in my lab on developing new tools and methods for the design and optimization of CRISPR/Cas9 systems, and the efforts in developing a clinically applicable gene correction strategy for treating sickle cell disease (SCD), which is the first single-gene disorder with molecular understanding. We optimized CRISPR/Cas9 systems targeting the beta-globin gene, and systematically evaluated their on- and off-target cleavage in different cells. We also quantified the nuclease-induced gene modification rates in CD34+ cells from SCD patients, and demonstrated that CRISPR/Cas9 based genome editing is effective in generating normal hemoglobin (HbA) and reducing sickling hemoglobin (HbS). These studies significantly facilitated our pre-clinical investigation of SCD treatment using CRISPR/Cas9 and donor templates. The opportunities and challenges in developing nuclease-based genome editing strategies for treating single-gene disorders are discussed. [Preview Abstract] |
Wednesday, March 15, 2017 10:24AM - 11:00AM |
K29.00005: Influence of pore charge, pressure, and electric field on protein transport through nanopores Invited Speaker: Meni Wanunu Abstract not available. [Preview Abstract] |
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