6 results
Key role of the REC lobe during CRISPR–Cas9 activation by ‘sensing’, ‘regulating’, and ‘locking’ the catalytic HNH domain
- Giulia Palermo, Janice S. Chen, Clarisse G. Ricci, Ivan Rivalta, Martin Jinek, Victor S. Batista, Jennifer A. Doudna, J. Andrew McCammon
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- Journal:
- Quarterly Reviews of Biophysics / Volume 51 / 2018
- Published online by Cambridge University Press:
- 03 August 2018, e9
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Understanding the conformational dynamics of CRISPR (clustered regularly interspaced short palindromic repeat)–Cas9 is of the utmost importance for improving its genome editing capability. Here, molecular dynamics simulations performed using Anton-2 – a specialized supercomputer capturing micro-to-millisecond biophysical events in real time and at atomic-level resolution – reveal the activation process of the endonuclease Cas9 toward DNA cleavage. Over the unbiased simulation, we observe that the spontaneous approach of the catalytic domain HNH to the DNA cleavage site is accompanied by a remarkable structural remodeling of the recognition (REC) lobe, which exerts a key role for DNA cleavage. Specifically, the significant conformational changes and the collective conformational dynamics of the REC lobe indicate a mechanism by which the REC1–3 regions ‘sense’ nucleic acids, ‘regulate’ the HNH conformational transition, and ultimately ‘lock’ the HNH domain at the cleavage site, contributing to its catalytic competence. By integrating additional independent simulations and existing experimental data, we provide a solid validation of the activated HNH conformation, which had been so far poorly characterized, and we deliver a comprehensive understanding of the role of REC1–3 in the activation process. Considering the importance of the REC lobe in the specificity of Cas9, this study poses the basis for fully understanding how the REC components control the cleavage of off-target sequences, laying the foundation for future engineering efforts toward improved genome editing.
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- By Rose Teteki Abbey, K. C. Abraham, David Tuesday Adamo, LeRoy H. Aden, Efrain Agosto, Victor Aguilan, Gillian T. W. Ahlgren, Charanjit Kaur AjitSingh, Dorothy B E A Akoto, Giuseppe Alberigo, Daniel E. Albrecht, Ruth Albrecht, Daniel O. Aleshire, Urs Altermatt, Anand Amaladass, Michael Amaladoss, James N. Amanze, Lesley G. Anderson, Thomas C. Anderson, Victor Anderson, Hope S. Antone, María Pilar Aquino, Paula Arai, Victorio Araya Guillén, S. Wesley Ariarajah, Ellen T. Armour, Brett Gregory Armstrong, Atsuhiro Asano, Naim Stifan Ateek, Mahmoud Ayoub, John Alembillah Azumah, Mercedes L. García Bachmann, Irena Backus, J. Wayne Baker, Mieke Bal, Lewis V. Baldwin, William Barbieri, António Barbosa da Silva, David Basinger, Bolaji Olukemi Bateye, Oswald Bayer, Daniel H. Bays, Rosalie Beck, Nancy Elizabeth Bedford, Guy-Thomas Bedouelle, Chorbishop Seely Beggiani, Wolfgang Behringer, Christopher M. Bellitto, Byard Bennett, Harold V. Bennett, Teresa Berger, Miguel A. Bernad, Henley Bernard, Alan E. Bernstein, Jon L. Berquist, Johannes Beutler, Ana María Bidegain, Matthew P. Binkewicz, Jennifer Bird, Joseph Blenkinsopp, Dmytro Bondarenko, Paulo Bonfatti, Riet en Pim Bons-Storm, Jessica A. Boon, Marcus J. Borg, Mark Bosco, Peter C. Bouteneff, François Bovon, William D. Bowman, Paul S. Boyer, David Brakke, Richard E. Brantley, Marcus Braybrooke, Ian Breward, Ênio José da Costa Brito, Jewel Spears Brooker, Johannes Brosseder, Nicholas Canfield Read Brown, Robert F. Brown, Pamela K. Brubaker, Walter Brueggemann, Bishop Colin O. Buchanan, Stanley M. Burgess, Amy Nelson Burnett, J. Patout Burns, David B. Burrell, David Buttrick, James P. Byrd, Lavinia Byrne, Gerado Caetano, Marcos Caldas, Alkiviadis Calivas, William J. Callahan, Salvatore Calomino, Euan K. Cameron, William S. Campbell, Marcelo Ayres Camurça, Daniel F. Caner, Paul E. Capetz, Carlos F. Cardoza-Orlandi, Patrick W. Carey, Barbara Carvill, Hal Cauthron, Subhadra Mitra Channa, Mark D. Chapman, James H. Charlesworth, Kenneth R. Chase, Chen Zemin, Luciano Chianeque, Philip Chia Phin Yin, Francisca H. Chimhanda, Daniel Chiquete, John T. Chirban, Soobin Choi, Robert Choquette, Mita Choudhury, Gerald Christianson, John Chryssavgis, Sejong Chun, Esther Chung-Kim, Charles M. A. Clark, Elizabeth A. Clark, Sathianathan Clarke, Fred Cloud, John B. Cobb, W. Owen Cole, John A Coleman, John J. Collins, Sylvia Collins-Mayo, Paul K. Conkin, Beth A. Conklin, Sean Connolly, Demetrios J. Constantelos, Michael A. Conway, Paula M. Cooey, Austin Cooper, Michael L. Cooper-White, Pamela Cooper-White, L. William Countryman, Sérgio Coutinho, Pamela Couture, Shannon Craigo-Snell, James L. Crenshaw, David Crowner, Humberto Horacio Cucchetti, Lawrence S. Cunningham, Elizabeth Mason Currier, Emmanuel Cutrone, Mary L. Daniel, David D. Daniels, Robert Darden, Rolf Darge, Isaiah Dau, Jeffry C. Davis, Jane Dawson, Valentin Dedji, John W. de Gruchy, Paul DeHart, Wendy J. Deichmann Edwards, Miguel A. De La Torre, George E. Demacopoulos, Thomas de Mayo, Leah DeVun, Beatriz de Vasconcellos Dias, Dennis C. Dickerson, John M. Dillon, Luis Miguel Donatello, Igor Dorfmann-Lazarev, Susanna Drake, Jonathan A. Draper, N. Dreher Martin, Otto Dreydoppel, Angelyn Dries, A. J. Droge, Francis X. D'Sa, Marilyn Dunn, Nicole Wilkinson Duran, Rifaat Ebied, Mark J. Edwards, William H. Edwards, Leonard H. Ehrlich, Nancy L. Eiesland, Martin Elbel, J. Harold Ellens, Stephen Ellingson, Marvin M. Ellison, Robert Ellsberg, Jean Bethke Elshtain, Eldon Jay Epp, Peter C. Erb, Tassilo Erhardt, Maria Erling, Noel Leo Erskine, Gillian R. Evans, Virginia Fabella, Michael A. Fahey, Edward Farley, Margaret A. Farley, Wendy Farley, Robert Fastiggi, Seena Fazel, Duncan S. Ferguson, Helwar Figueroa, Paul Corby Finney, Kyriaki Karidoyanes FitzGerald, Thomas E. FitzGerald, John R. Fitzmier, Marie Therese Flanagan, Sabina Flanagan, Claude Flipo, Ronald B. Flowers, Carole Fontaine, David Ford, Mary Ford, Stephanie A. Ford, Jim Forest, William Franke, Robert M. Franklin, Ruth Franzén, Edward H. Friedman, Samuel Frouisou, Lorelei F. Fuchs, Jojo M. Fung, Inger Furseth, Richard R. Gaillardetz, Brandon Gallaher, China Galland, Mark Galli, Ismael García, Tharscisse Gatwa, Jean-Marie Gaudeul, Luis María Gavilanes del Castillo, Pavel L. Gavrilyuk, Volney P. Gay, Metropolitan Athanasios Geevargis, Kondothra M. George, Mary Gerhart, Simon Gikandi, Maurice Gilbert, Michael J. Gillgannon, Verónica Giménez Beliveau, Terryl Givens, Beth Glazier-McDonald, Philip Gleason, Menghun Goh, Brian Golding, Bishop Hilario M. Gomez, Michelle A. Gonzalez, Donald K. Gorrell, Roy Gottfried, Tamara Grdzelidze, Joel B. Green, Niels Henrik Gregersen, Cristina Grenholm, Herbert Griffiths, Eric W. Gritsch, Erich S. Gruen, Christoffer H. Grundmann, Paul H. Gundani, Jon P. Gunnemann, Petre Guran, Vidar L. Haanes, Jeremiah M. Hackett, Getatchew Haile, Douglas John Hall, Nicholas Hammond, Daphne Hampson, Jehu J. Hanciles, Barry Hankins, Jennifer Haraguchi, Stanley S. Harakas, Anthony John Harding, Conrad L. Harkins, J. William Harmless, Marjory Harper, Amir Harrak, Joel F. Harrington, Mark W. Harris, Susan Ashbrook Harvey, Van A. Harvey, R. Chris Hassel, Jione Havea, Daniel Hawk, Diana L. Hayes, Leslie Hayes, Priscilla Hayner, S. Mark Heim, Simo Heininen, Richard P. Heitzenrater, Eila Helander, David Hempton, Scott H. Hendrix, Jan-Olav Henriksen, Gina Hens-Piazza, Carter Heyward, Nicholas J. Higham, David Hilliard, Norman A. Hjelm, Peter C. Hodgson, Arthur Holder, M. Jan Holton, Dwight N. Hopkins, Ronnie Po-chia Hsia, Po-Ho Huang, James Hudnut-Beumler, Jennifer S. Hughes, Leonard M. Hummel, Mary E. Hunt, Laennec Hurbon, Mark Hutchinson, Susan E. Hylen, Mary Beth Ingham, H. Larry Ingle, Dale T. Irvin, Jon Isaak, Paul John Isaak, Ada María Isasi-Díaz, Hans Raun Iversen, Margaret C. Jacob, Arthur James, Maria Jansdotter-Samuelsson, David Jasper, Werner G. Jeanrond, Renée Jeffery, David Lyle Jeffrey, Theodore W. Jennings, David H. Jensen, Robin Margaret Jensen, David Jobling, Dale A. Johnson, Elizabeth A. Johnson, Maxwell E. Johnson, Sarah Johnson, Mark D. Johnston, F. Stanley Jones, James William Jones, John R. Jones, Alissa Jones Nelson, Inge Jonsson, Jan Joosten, Elizabeth Judd, Mulambya Peggy Kabonde, Robert Kaggwa, Sylvester Kahakwa, Isaac Kalimi, Ogbu U. Kalu, Eunice Kamaara, Wayne C. Kannaday, Musimbi Kanyoro, Veli-Matti Kärkkäinen, Frank Kaufmann, Léon Nguapitshi Kayongo, Richard Kearney, Alice A. Keefe, Ralph Keen, Catherine Keller, Anthony J. Kelly, Karen Kennelly, Kathi Lynn Kern, Fergus Kerr, Edward Kessler, George Kilcourse, Heup Young Kim, Kim Sung-Hae, Kim Yong-Bock, Kim Yung Suk, Richard King, Thomas M. King, Robert M. Kingdon, Ross Kinsler, Hans G. Kippenberg, Cheryl A. Kirk-Duggan, Clifton Kirkpatrick, Leonid Kishkovsky, Nadieszda Kizenko, Jeffrey Klaiber, Hans-Josef Klauck, Sidney Knight, Samuel Kobia, Robert Kolb, Karla Ann Koll, Heikki Kotila, Donald Kraybill, Philip D. W. Krey, Yves Krumenacker, Jeffrey Kah-Jin Kuan, Simanga R. Kumalo, Peter Kuzmic, Simon Shui-Man Kwan, Kwok Pui-lan, André LaCocque, Stephen E. Lahey, John Tsz Pang Lai, Emiel Lamberts, Armando Lampe, Craig Lampe, Beverly J. Lanzetta, Eve LaPlante, Lizette Larson-Miller, Ariel Bybee Laughton, Leonard Lawlor, Bentley Layton, Robin A. Leaver, Karen Lebacqz, Archie Chi Chung Lee, Marilyn J. Legge, Hervé LeGrand, D. L. LeMahieu, Raymond Lemieux, Bill J. Leonard, Ellen M. Leonard, Outi Leppä, Jean Lesaulnier, Nantawan Boonprasat Lewis, Henrietta Leyser, Alexei Lidov, Bernard Lightman, Paul Chang-Ha Lim, Carter Lindberg, Mark R. Lindsay, James R. Linville, James C. Livingston, Ann Loades, David Loades, Jean-Claude Loba-Mkole, Lo Lung Kwong, Wati Longchar, Eleazar López, David W. 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Van Bavel, Steven Vanderputten, Peter Van der Veer, Huub Van de Sandt, Louis Van Tongeren, Luke A. Veronis, Noel Villalba, Ramón Vinke, Tim Vivian, David Voas, Elena Volkova, Katharina von Kellenbach, Elina Vuola, Timothy Wadkins, Elaine M. Wainwright, Randi Jones Walker, Dewey D. Wallace, Jerry Walls, Michael J. Walsh, Philip Walters, Janet Walton, Jonathan L. Walton, Wang Xiaochao, Patricia A. Ward, David Harrington Watt, Herold D. Weiss, Laurence L. Welborn, Sharon D. Welch, Timothy Wengert, Traci C. West, Merold Westphal, David Wetherell, Barbara Wheeler, Carolinne White, Jean-Paul Wiest, Frans Wijsen, Terry L. Wilder, Felix Wilfred, Rebecca Wilkin, Daniel H. Williams, D. Newell Williams, Michael A. Williams, Vincent L. Wimbush, Gabriele Winkler, Anders Winroth, Lauri Emílio Wirth, James A. Wiseman, Ebba Witt-Brattström, Teofil Wojciechowski, John Wolffe, Kenman L. Wong, Wong Wai Ching, Linda Woodhead, Wendy M. Wright, Rose Wu, Keith E. Yandell, Gale A. Yee, Viktor Yelensky, Yeo Khiok-Khng, Gustav K. K. Yeung, Angela Yiu, Amos Yong, Yong Ting Jin, You Bin, Youhanna Nessim Youssef, Eliana Yunes, Robert Michael Zaller, Valarie H. Ziegler, Barbara Brown Zikmund, Joyce Ann Zimmerman, Aurora Zlotnik, Zhuo Xinping
- Edited by Daniel Patte, Vanderbilt University, Tennessee
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- Book:
- The Cambridge Dictionary of Christianity
- Published online:
- 05 August 2012
- Print publication:
- 20 September 2010, pp xi-xliv
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Contributors
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- By Isabella Aboderin, W. Andrew Achenbaum, Katherine R. Allen, Toni C. Antonucci, Sara Arber, Claudine Attias‐Donfut, Paul B. Baltes, Sandhi Maria Barreto, Vern L. Bengtson, Simon Biggs, Joanna Bornat, Julie B. Boron, Mike Boulton, Clive E. Bowman, Marjolein Broese van Groenou, Edna Brown, Robert N. Butler, Bill Bytheway, Neena L. Chappell, Neil Charness, Kaare Christensen, Peter G. Coleman, Ingrid Arnet Connidis, Neal E. Cutler, Sara J. Czaja, Svein Olav Daatland, Lia Susana Daichman, Adam Davey, Bleddyn Davies, Freya Dittmann‐Kohli, Glen H. Elder, Carroll L. Estes, Mike Featherstone, Amy Fiske, Alexandra Freund, Daphna Gans, Linda K. George, Roseann Giarrusso, Chris Gilleard, Jay Ginn, Edlira Gjonça, Elena L. Grigorenko, Jaber F. Gubrium, Sarah Harper, Jutta Heckhausen, Akiko Hashimoto, Jon Hendricks, Mike Hepworth, Charlotte Ikels, James S. Jackson, Yuri Jang, Bernard Jeune, Malcolm L. Johnson, Randi S. Jones, Alexandre Kalache, Robert L. Kane, Rosalie A. Kane, Ingrid Keller, Rose Anne Kenny, Thomas B. L. Kirkwood, Kees Knipscheer, Martin Kohli, Gisela Labouvie‐Vief, Kristina Larsson, Shu‐Chen Li, Charles F. Longino, Ariela Lowenstein, Erick McCarthy, Gerald E. McClearn, Brendan McCormack, Elizabeth MacKinlay, Alfons Marcoen, Michael Marmot, Tom Margrain, Victor W. Marshall, Elizabeth A. Maylor, Ruud ter Meulen, Harry R. Moody, Robert A. Neimeyer, Demi Patsios, Margaret J. Penning, Stephen A. Petrill, Chris Phillipson, Leonard W. Poon, Norella M. Putney, Jill Quadagno, Pat Rabbitt, Jennifer Reid Keene, Sandra G. Reynolds, Steven R. Sabat, Clive Seale, Merril Silverstein, Hannes B. Staehelin, Ursula M. Staudinger, Robert J. Sternberg, Debra Street, Philip Taylor, Fleur Thomése, Mats Thorslund, Jinzhou Tian, Theo van Tilburg, Fernando M. Torres‐Gil, Josy Ubachs‐Moust, Christina Victor, K. Warner Shaie, Anthony M. Warnes, James L. Werth, Sherry L. Willis, François‐Charles Wolff, Bob Woods
- Edited by Malcolm L. Johnson, University of Bristol
- Edited in association with Vern L. Bengtson, University of Southern California, Peter G. Coleman, University of Southampton, Thomas B. L. Kirkwood, University of Newcastle upon Tyne
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- The Cambridge Handbook of Age and Ageing
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- 05 June 2016
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- 01 December 2005, pp xii-xvi
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Collagen-Inspired Nano-fibrous Poly(L-lactic acid) Scaffolds for Bone Tissue Engineering Created from Reverse Solid Freeform Fabrication
- Victor J. Chen, Laura A. Smith, Peter X. Ma
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- MRS Online Proceedings Library Archive / Volume 823 / 2004
- Published online by Cambridge University Press:
- 17 March 2011, W11.13
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- 2004
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Reverse solid freeform (SFF) fabrication was used to create highly-controlled macroporous structures in nano-fibrous poly (L-lactic acid) (PLLA) scaffolds. By using a computer-aided design (CAD) program to create a negative template for the scaffold, the three-dimensional (3-D) mold was created on a 3-D printer using a wax. After the template was printed, a solution of PLLA in tetrahydrofuran (THF) was cast into the mold, and was subsequently phase separated at -70°C which gives the nano-fibrous morphology. This resulted in a 3-D nano-fibrous scaffold with a uniform fiber mesh throughout the entire matrix, and greatly increased the surface area within the scaffold. Fiber diameters in these scaffolds were 50-500 nm, similar to type I collagen, and the densities of the fiber meshes can be altered by changing the polymer concentration. To examine the scaffold's potential for tissue regeneration, MC3T3-E1 osteoblasts were seeded and cultured on the scaffolds. Results show that the osteoblasts attached and proliferated on the scaffolds. After 6 weeks in culture, bone-like tissue was evident within the nano-fibrous scaffolds. By having the ability to control the macroporous architecture, interconnectivity, orientation, and external shape of the scaffold, as well as the nanometer-scaled fibrous features in the pore walls, this SFF fabrication/phase separation technique has great potential to design and create ideal scaffolds for bone tissue engineering.
Nano-fibrous scaffolding architecture enhances protein adsorption and cell attachment
- Kyung Mi Woo, Victor J. Chen, Peter X. Ma
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- Journal:
- MRS Online Proceedings Library Archive / Volume 735 / 2002
- Published online by Cambridge University Press:
- 11 February 2011, C5.2
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- 2002
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Tissue engineering aims at resolving problems such as donor shortage and immune rejection faced in transplantation. Scaffolds (artificial extracellular matrices) play critical roles in tissue engineering. Recently, we developed nano-fibrous poly(L-lactic acid) (PLLA) scaffolds under the hypothesis that synthetic nano-fibrous scaffolding, mimicking the structure of natural collagen fibers, could create a more favorable microenvironment for cells. This is the first report that the nano-fibrous architecture built in three-dimensional scaffolds improved the features of protein adsorption, which mediates cell interactions with scaffolds. Scaffolds with nano-fibrous pore walls adsorbed 4 times more serum proteins than scaffolds with solid pore walls. More interestingly, the nano-fibrous architecture selectively enhanced protein adsorption including fibronectin and vitronectin, even though both scaffolds were made from the same PLLA material. Furthermore, nano-fibrous scaffolds also allowed more than 1.7 times of osteoblastic cell attachment than scaffolds with “solid” pore walls. These results demonstrate that the biomimetic nano-fibrous architecture serves as superior scaffolding for tissue engineering.
Biomimetic Poly(L-Lactic Acid) Scaffolds with Interconnected Macropores, Collagen-Like Nano-Scale Fibers, and Bone-Like Apatite
- Victor J. Chen, Peter X. Ma
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- Journal:
- MRS Online Proceedings Library Archive / Volume 735 / 2002
- Published online by Cambridge University Press:
- 11 February 2011, C6.5
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- 2002
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Highly porous nano-fibrous poly(L-lactic acid) (PLLA) scaffolds were prepared and incubated in a simulated body fluid which resulted in the in situ formation of partially carbonated bone-like apatite. The macroporous interconnected architecture was created with a three-dimensional mold of thermally-bonded paraffin microspheres. PLLA solution was cast over the paraffin mold and was thermally induced to phase separate to form nano-scale fibers that mimic the fibrous structures of type I collagen. To potentially improve the osteoconductivity of these scaffolds, they were incubated in a buffered simulated body fluid at 37°C for certain periods of time to allow for apatite formation. It was seen that over time, the apatite particles increased in size. In addition, the growth of apatite particles on the nano-fibrous scaffolds was compared with the growth of particles on similar porous PLLA scaffolds with a solid-walled (not nano-fibrous) morphology. It was seen that the initial number of particles per unit area and the overall increase in mass of the scaffolds were significantly higher in the nano-fibrous scaffolds than in the solid-walled scaffolds. These novel scaffolds have well-defined architectures at three different size scales: (i) interconnected spherical pores ∼250–400 m in diameter; (ii) fibrous collagen-like matrix with fibers 50–500 nm in diameter; and (iii) carbonated bone-like apatite particles at the nanometer to micrometer scales; the scaffolds may serve as superior support for bone tissue regeneration.