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Development of Light‐Activated CRISPR Using Guide RNAs with Photocleavable Protectors

Angewandte Chemie 2016年第40期128卷

作者： Piyush K. Jain Vyas Ramanan Arnout G. Schepers Nisha S. Dalvie Apekshya Panda Heather E. Fleming Sangeeta N. Bhatia Institute for Medical Engineering & Science Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA Department of Biological Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA Department of Electrical Engineering and Computer Science Marble Center for Cancer Nanomedicine Massachusetts Institute of Technology Cambridge MA 02139 USA Department of Medicine Brigham and Women's Hospital Boston MA 02115 USA Broad Institute of MIT and Harvard Cambridge MA 02139 USA Howard Hughes Medical Institute Cambridge MA 02139 USA

The ability to remotely trigger CRISPR/Cas9 activity would enable new strategies to study cellular events with greater precision and complexity. In this work, we have developed a method to photocage the activity of the guide RNA called “CRISPR‐plus” (CRISPR‐precise light‐mediated unveiling of sgRNAs). The photoactivation capability of our CRISPR‐plus method is compatible with the simultaneous targeting of multiple DNA sequences and supports numerous modifications that can enable guide RNA labeling for use in imaging and mechanistic investigations.

关键词： CRISPR DNA-Spaltung Gentechnik Nucleinsäuren Photochemie

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Gene expression imputation across multiple brain regions provides insights into schizophrenia risk (vol 51, pg 659, 2019)

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NATURE GENETICS 2019年第6期51卷 1068-1068页

作者： Huckins, Laura M. Dobbyn, Amanda Ruderfer, Douglas M. Hoffman, Gabriel Wang, Weiqing Pardinas, Antonio F. Rajagopal, Veera M. Als, Thomas D. Nguyen, Hoang T. Girdhar, Kiran Boocock, James Roussos, Panos Fromer, Menachem Kramer, Robin Domenici, Enrico Gamazon, Eric R. Purcell, Shaun Demontis, Ditte Borglum, Anders D. Walters, James T. R. O'Donovan, Michael C. Sullivan, Patrick Owen, Michael J. Devlin, Bernie Sieberts, Solveig K. Cox, Nancy J. Im, Hae Kyung Sklar, Pamela Stahl, Eli A. Pamela Sklar Division of Psychiatric Genomics Icahn School of Medicine at Mount Sinai New York NY USA Department of Genetics and Genomics Icahn School of Medicine at Mount Sinai New York NY USA Department of Psychiatry Icahn School of Medicine at Mount Sinai New York NY USA Icahn Institute for Genomics and Multiscale Biology Icahn School of Medicine at Mount Sinai New York NY USA Vanderbilt University Medical Center Nashville TN USA MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff UK Department of Biomedicine Aarhus University Aarhus Denmark The Lundbeck Foundation Initiative for Integrative Psychiatric Research iPSYCH Denmark Center for Integrative Sequencing Aarhus University Aarhus Denmark Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA Human Brain Collection Core National Institute of Mental Health Bethesda MD USA Laboratory of Neurogenomic Biomarkers Centre for Integrative Biology (CIBIO) University of Trento Trento Italy Clare Hall University of Cambridge Cambridge UK University of North Carolina at Chapel Hill Chapel Hill NC USA Karolinska Institutet Stockholm Sweden Department of Psychiatry University of Pittsburgh Pittsburgh PA USA Systems Biology Sage Bionetworks Seattle WA USA Section of Genetic Medicine Department of Medicine University of Chicago Chicago IL USA Integrated Technology Research Laboratories Pharmaceutical Research Division Takeda Pharmaceutical Company Limited Fujisawa Japan Neuropsychiatry Section Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Neuropsychiatric Signaling Program Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Psychiatry JJ Peters Virginia Medical Center Bronx NY USA Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York NY USA Friedman Brain Institute

Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.

关键词： Gene expression Genome-wide association studies Schizophrenia Transcriptomics

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Inertial microfluidics for multiplexed affinity separation of proteins and cells 18

Inertial microfluidics for multiplexed affinity separation o...

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18th International Conference on Miniaturized Systems for Chemistry and Life sciences, MicroTAS 2014

作者： Sarkar, A. Hou, H.W. Mahan, Alison Han, Jongyoon Alter, Galit Ragon Institute of MGH MIT Harvard United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology United States Department of Biological Engineering Massachusetts Institute of Technology United States

ISBN: (纸本)9780979806476

We present an inertial microfluidic platform for rapid, multiplexed affinity purification of proteins and cells from complex mixtures. Beads of different sizes, coated with different bait molecules bind specific proteins or cells in a single reaction step and the bound targets are then size-sorted by flowing in a spiral microchannel. We use this scheme to simultaneously purify antibodies specific to three different HIV antigens from HIV patient sera. We then demonstrate the simultaneous sorting of various cell types and also the isolation of rare antigen-specific cells such as HIV-specific cells from peripheral blood mononuclear cells (PBMC) from HIV patients. © 14CBMS.

关键词： Cells

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Orthogonal designs optimize achievable dispersion for coherent MISO channels

Orthogonal designs optimize achievable dispersion for cohere...

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IEEE International Symposium on Information Theory

作者： Austin Collins Yury Polyanskiy Department of Electrical Engineering and Computer Science MIT Cambridge MA USA

This work addresses the question of finite block-length fundamental limits of coherently demodulated multi-antenna channels, subject to frequency non-selective isotropic fading. Specifically we present achievability bound for the channel dispersion - a quantity known to determine the delay required to achieve capacity. It is shown that a commonly used isotropic Gaussian input, which is only one of many possible capacity achieving distributions, is suboptimal. Optimal inputs minimizing channel dispersion turn out to include a family of modulation techniques known as orthogonal designs (in particular, Alamouti's scheme). For 8 transmit antennas numerical evaluation shows that up to 40% of additional penalty in delay is incurred by using isotropic codewords (compared to dispersion-optimal architecture exploiting transmit diversity).

关键词： Dispersion Fading Information theory Delays Transmitting antennas Vectors Signal to noise ratio

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Dense matter with eXTP

arXiv

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arXiv 2018年

作者： Watts, Anna L. Yu, Wenfei Poutanen, Juri Zhang, Shu Bhattacharyya, Sudip Bogdanov, Slavko Ji, Long Patruno, Alessandro Riley, Thomas E. Bakala, Pavel Baykal, Altan Bernardini, Federico Bombaci, Ignazio Brown, Edward Cavecchi, Yuri Chakrabarty, Deepto Chenevez, Jérôme Degenaar, Nathalie Santo, Melania Del Salvo, Tiziana Di Doroshenko, Victor Falanga, Maurizio Ferdman, Robert D. Feroci, Marco Gambino, Angelo F. Ge, MingYu Greif, Svenja K. Guillot, Sebastien Gungor, Can Hartmann, Dieter H. Hebeler, Kai Heger, Alexander Homan, Jeroen Iaria, Rosario in’t Zand, Jean Kargaltsev, Oleg Kurkela, Aleksi Lai, Xiaoyu Li, Ang Li, XiangDong Li, Zhaosheng Linares, Manuel Lu, FangJun Mahmoodifar, Simin Méndez, Mariano Miller, M. Coleman Morsink, Sharon Nättilä, Joonas Possenti, Andrea Prescod-Weinstein, Chanda Qu, JinLu Riggio, Alessandro Salmi, Tuomo Sanna, Andrea Santangelo, Andrea Schatz, Hendrik Schwenk, Achim Song, LiMing Šrámková, Eva Stappers, Benjamin Stiele, Holger Strohmayer, Tod Tews, Ingo Tolos, Laura Török, Gabriel Tsang, David Urbanec, Martin Vacchi, Andrea Xu, RenXin Xu, Ypeng Zane, Silvia Zhang, Guobao Zhang, ShuangNan Zhang, Wenda Zheng, ShiJie Zhou, Xia Anton Pannekoek Institute for Astronomy University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Shanghai Astronomical Observatory Shanghai200030 China Tuorla Observatory Department of Physics and Astronomy University of Turku Väisäläntie 20 PiikkiöFIN-21500 Finland Nordita KTH Royal Institute of Technology Stockholm University Roslagstullsbacken 23 StockholmSE-10691 Sweden Institute of High Energy Physics CAS Beijing100049 China Tata Institute of Fundamental Research Mumbai400005 India Columbia Astrophysics Laboratory Columbia University 550 West 120th Street New YorkNY10027 United States Institut für Astronomie und Astrophysik Tübingen Universität Tübingen Sand 1 TübingenD-72076 Germany Leiden Observatory Leiden University PO Box 9513 Leiden2300 RA Netherlands Research Center for Computational Physics and Data Processing Silesian University in Opava Bezrucovo nam. 13 OpavaCZ-74601 Czech Republic Physics Department Middle East Technical University Ankara06531 Turkey INAF Osservatorio Astronomico di Roma Via Frascati 33 Monteporzio CatoneI-00078 Italy New York University Abu Dhabi PO Box 129188 Abu Dhabi United Arab Emirates Dipartimento di Fisica Enrico Fermi University of Pisa PisaI-56127 Italy INFN Italian National Institute for Nuclear Physics Pisa Section Pisa56127 Italy Department of Physics and Astronomy Michigan State University East LansingMI48824 United States Department of Astrophysical Sciences Princeton University Peyton Hall PrincetonNJ08544 United States Mathematical Sciences and STAG Research Centre University of Southampton SouthamptonSO17 1BJ United Kingdom MIT Kavli Institute for Astrophysics and Space Research CambridgeMA02139 United States DTU Space Technical University of Denmark Elektrovej 327-328 Kgs Lyngby2800 Denmark INAF/IASF Palermo via Ugo La Malfa 153 PalermoI-90146 Italy Universita degli Studi di Palermo Dipartimento di Fisica e Chimica via Archira 36 Palermo90123 Italy

In this White Paper we present the potential of the Enhanced X-ray Timing and Polarimetry (eXTP) mission for determining the nature of dense matter;neutron star cores host an extreme density regime which cannot be replicated in a terrestrial laboratory. The tightest statistical constraints on the dense matter equation of state will come from pulse profile modelling of accretion-powered pulsars, burst oscillation sources, and rotation-powered pulsars. Additional constraints will derive from spin measurements, burst spectra, and properties of the accretion flows in the vicinity of the neutron star. Under development by an international Consortium led by the Institute of High Energy Physics of the Chinese Academy of science, the eXTP mission is expected to be launched in the mid 2020s. Copyright © 2018, The Authors. All rights reserved.

关键词： Pulsars

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Footstep planning on uneven terrain with mixed-integer convex optimization

Footstep planning on uneven terrain with mixed-integer conve...

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IEEE-RAS International Conference on Humanoid Robots

作者： Robin Deits Russ Tedrake MIT Computer Science and Artificial Intelligence Laboratory Cambridge MA USA Faculty of Electrical Engineering and Computer Science MIT Cambridge MA USA

We present a new method for planning footstep placements for a robot walking on uneven terrain with obstacles, using a mixed-integer quadratically-constrained quadratic program (MIQCQP). Our approach is unique in that it handles obstacle avoidance, kinematic reachability, and rotation of footstep placements, which typically have required non-convex constraints, in a single mixed-integer optimization that can be efficiently solved to its global optimum. Reachability is enforced through a convex inner approximation of the reachable space for the robot's feet. Rotation of the footsteps is handled by a piecewise linear approximation of sine and cosine, designed to ensure that the approximation never overestimates the robot's reachability. Obstacle avoidance is ensured by decomposing the environment into convex regions of obstacle-free configuration space and assigning each footstep to one such safe region. We demonstrate this technique in simple 2D and 3D environments and with real environments sensed by a humanoid robot. We also discuss computational performance of the algorithm, which is currently capable of planning short sequences of a few steps in under one second or longer sequences of 10-30 footsteps in tens of seconds to minutes on common laptop computer hardware. Our implementation is available within the Drake MATLAB toolbox [1].

关键词： Piecewise linear approximation Robots Foot Linear approximation Planning Collision avoidance

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GMM weights adaptation based on subspace approaches for speaker verification

GMM weights adaptation based on subspace approaches for spea...

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Speaker and Language Recognition Workshop, Odyssey 2014

作者： Dehak, Najim Plchot, Oldrich Bahari, Mohamad Hasan Burget, Lukas Van Hamme, Hugo Dehak, Reda MIT Computer Science and Artificial Intelligence Laboratory Cambridge United States Brno University of Technology Speech@FIT Brno Czech Republic KU Leuven Department of Electrical Engineering Leuven Belgium Paris France

In this paper, we explored the use of Gaussian Mixture Model (GMM) weights adaptation for speaker verification. We compared two different subspace weight adaptation approaches: Subspace Multinomial Model (SMM) and Non-Negative factor Analysis (NFA). Both techniques achieved similar results and seemed to outperform the retraining maximum likelihood (ML) weight adaptation. However, the training process for the NFA approach is substantially faster than theSMMtechnique. The i-vector fusion between each weight adaptation approach and the classical i-vector yielded slight improvements on the telephone part of the NIST 2010 Speaker Recognition Evaluation. © Odyssey 2014: Speaker and Language Recognition Workshop. All rights Reserved.

关键词： Gaussian distribution

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Towards Scalable Algorithms with Formal Guarantees for Lyapunov Analysis of Control Systems via Algebraic Optimization

Towards Scalable Algorithms with Formal Guarantees for Lyapu...

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IEEE Annual Conference on Decision and Control

作者： Amir Ali Ahmadi Pablo A. Parrilo Department of Operations Research and Financial Engineering at Princeton University Department of Electrical Engineering and Computer Science at MIT

ISBN: (纸本)9781467360890

Exciting recent developments at the interface of optimization and control have shown that several fundamental problems in dynamics and control, such as stability, collision avoidance, robust performance, and controller synthesis can be addressed by a synergy of classical tools from Lyapunov theory and modern computational techniques from algebraic optimization. In this paper, we give a brief overview of our recent research efforts (with various coauthors) to (i) enhance the scalability of the algorithms in this field, and (ii) understand their worst case performance guarantees as well as fundamental limitations. Our results are tersely surveyed and challenges/opportunities that lie ahead are stated.

关键词： control systems Scalability Algebra Synergism algorithms Collision avoidance Robust control Standing Orders

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Erratum to an anatomically realistic temperature phantom for radiofrequency heating measurements (Magn Reson Med 2015;73:442-450)

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Magnetic resonance in medicine 2016年第5期76卷 1642页

作者： Nadine N Graedel Jonathan R Polimeni Bastien Guerin Borjan Gagoski Giorgio Bonmassar Lawrence L Wald A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown Massachusetts USA. Harvard Medical School Boston Massachusetts USA. A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown Massachusetts USA. guerin@nmr.mgh.harvard.edu. Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge Massachusetts USA. Harvard-MIT Division of Health Sciences and Technology Cambridge Massachusetts USA.

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Local algorithms for sparse spanning graphs 17

Local algorithms for sparse spanning graphs

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17th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX 2014 and the 18th International Workshop on Randomization and Computation, RANDOM 2014

作者： Levi, Reut Ron, Dana Rubinfeld, Ronitt School of Computer Science Tel Aviv University Tel Aviv69978 Israel School of Electrical Engineering Tel Aviv University Tel Aviv69978 Israel CSAIL MIT CambridgeMA02139 United States

ISBN: (纸本)9783939897743

We initiate the study of the problem of designing sublinear-time (local) algorithms that, given an edge (u, v) in a connected graph G = (V,E), decide whether (u, v) belongs to a sparse spanning graph G0 = (V,E0) of G. Namely, G0 should be connected and |E0| should be upper bounded by (1 + ∈)|V | for a given parameter ∈ > 0. To this end the algorithms may query the incidence relation of the graph G, and we seek algorithms whose query complexity and running time (per given edge (u, v)) is as small as possible. Such an algorithm may be randomized but (for a fixed choice of its random coins) its decision on different edges in the graph should be consistent with the same spanning graph G0 and independent of the order of queries. We first show that for general (bounded-degree) graphs, the query complexity of any such algorithm must be Ω (√ |V |). This lower bound holds for graphs that have high expansion. We then turn to design and analyze algorithms both for graphs with high expansion (obtaining a result that roughly matches the lower bound) and for graphs that are (strongly) non-expanding (obtaining results in which the complexity does not depend on |V |). The complexity of the problem for graphs that do not fall into these two categories is left as an open question. ©.

关键词： Graph theory

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