May 15, 2007 ͉ vol. 104 ͉ no. 20 ͉ 8197–8562

Proceedings of the National Academy ofPNAS Sciences of the United States of America www.pnas.org Cover image: Mu¨ller glial cells act as living optical fibers, transporting light through the inverted retina of vertebrates. With their funnel-shaped endfeet, Mu¨ller cells collect light at the retinal surface and guide it to photoreceptor cells on the opposite side. Images are thus transmitted through optically distorting tissue. See the article by Franze et al. on pages 8287–8292. Image courtesy of Jens Grosche. From the Cover

8287 Living optical fibers 8257 Rhomboid gating 8352 Costa Rica’s vanishing amphibians 8403 DNA mutation showers

8520 Nav1.8 channel blocker inhibits pain

Contents PHYSICAL SCIENCES

APPLIED PHYSICAL SCIENCES 8207 Single-molecule mass spectrometry in solution THIS WEEK IN PNAS using a solitary nanopore Joseph W. F. Robertson, Claudio G. Rodrigues, Vincent M. Stanford, Kenneth A. Rubinson, 8197 In This Issue Oleg V. Krasilnikov, and John J. Kasianowicz 8212 The directed cooperative assembly of proteorhodopsin into 2D and 3D polarized arrays COMMENTARIES Hongjun Liang, Gregg Whited, Chi Nguyen, and Galen D. Stucky

8199 From rhomboid function to structure and back again CHEMISTRY Raquel L. Lieberman and Michael S. Wolfe ➜ See companion article on page 8257 8218 A nanoinjector based on carbon nanotubes Xing Chen, Andras Kis, A. Zettl, and Carolyn R. Bertozzi 8201 Climate change implicated in amphibian 8223 Array feature size influences nucleic acid surface capture and lizard declines in DNA microarrays David B. Wake David S. Dandy, Peng Wu, and David W. Grainger ➜ See companion article on page 8352 ENGINEERING 8203 Mutations in clusters and showers 8229 A kinematic description of the trajectories of Listeria John W. Drake monocytogenes propelled by actin comet tails ➜ See companion article on page 8403 V. B. Shenoy, D. T. Tambe, A. Prasad, and J. A. Theriot

8205 Subtype-selective sodium channel blockers promise SOCIAL SCIENCES a new era of pain research Birgit T. Priest and Gregory J. Kaczorowski ➜ See companion article on page 8520 PSYCHOLOGY 8235 The neural basis of the interaction between theory of mind and moral judgment Liane Young, Fiery Cushman, Marc Hauser, Freely available online through the PNAS open access option. and Rebecca Saxe

PNAS ͉ May 15, 2007 ͉ vol. 104 ͉ no. 20 ͉ iii–ix Downloaded by guest on September 26, 2021 8241 Effect of congenital blindness on the semantic 8281 Rigidity-driven growth and migration of epithelial representation of some everyday concepts cells on microstructured anisotropic substrates Andrew C. Connolly, Lila R. Gleitman, Alexandre Saez, Marion Ghibaudo, Axel Buguin, and Sharon L. Thompson-Schill Pascal Silberzan, and Benoıˆt Ladoux

8490 Neural interactions between flicker-induced 8287 Mu¨ller cells are living optical fibers in the self-organized visual hallucinations and vertebrate retina physical stimuli Kristian Franze, Jens Grosche, Serguei N. Skatchkov, Vincent A. Billock and Brian H. Tsou Stefan Schinkinger, Christian Foja, Detlev Schild, Ortrud Uckermann, Kort Travis, Andreas Reichenbach, and Jochen Guck BIOLOGICAL SCIENCES 8293 Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA APPLIED BIOLOGICAL SCIENCES Yoshitaka Bessho, Rie Shibata, Shun-ichi Sekine, 8247 APEx 2-hybrid, a quantitative –protein interaction Kazutaka Murayama, Kyoko Higashijima, Chie assay for antibody discovery and engineering Hori-Takemoto, Mikako Shirouzu, Seiki Kuramitsu, Ki Jun Jeong, Min Jeong Seo, Brent L. Iverson, and Shigeyuki Yokoyama and George Georgiou 8299 Stabilization of RAD-51–DNA filaments via an interaction 8253 Prandiology of and the CAFE assay domain in BRCA2 William W. Ja, Gil B. Carvalho, Elizabeth M. Mak, Mark I. R. Petalcorin, Vitold E. Galkin, Xiong Yu, Noelle N. de la Rosa, Annie Y. Fang, Jonathan C. Edward H. Egelman, and Simon J. Boulton Liong, Ted Brummel, and Seymour Benzer 8305 Crystal structure of the Sec4p⅐Sec2p complex in the nucleotide exchanging intermediate state BIOCHEMISTRY Yusuke Sato, Shuya Fukai, Ryuichiro Ishitani, 8257 Enzymatic analysis of a rhomboid intramembrane and Osamu Nureki protease implicates transmembrane helix 5 as 8311 Intrinsic disorder as a mechanism to optimize the lateral gate allosteric coupling in Rosanna P. Baker, Keith Young, Liang Feng, Yigong Vincent J. Hilser and E. Brad Thompson Shi, and Sinisa Urban ➜ See Commentary on page 8199 8316 Inhibiting HIV-1 integrase by shifting its oligomerization equilibrium 8263 Contribution of hydrophobic and electrostatic Zvi Hayouka, Joseph Rosenbluh, Aviad Levin, interactions to the membrane integration of the Shoshana Loya, Mario Lebendiker, Dmitry ؉ Shaker K channel voltage sensor domain Veprintsev, Moshe Kotler, Amnon Hizi, Liyan Zhang, Yoko Sato, Tara Hessa, Gunnar Abraham Loyter, and Assaf Friedler von Heijne, Jong-Kook Lee, Itsuo Kodama, Masao Sakaguchi, and Nobuyuki Uozumi CELL BIOLOGY 8269 Directed evolution of gene-shuffled IFN-␣ molecules 8218 A cell nanoinjector based on carbon nanotubes with activity profiles tailored for treatment of chronic Xing Chen, Andras Kis, A. Zettl, and Carolyn R. Bertozzi viral diseases Amy D. Brideau-Andersen, Xiaojian Huang, Siu-Chi Chang 8322 Opening of connexin 43 hemichannels is increased Sun, Teddy T. Chen, Diane Stark, Ian J. Sas, Linda Zadik, by lowering intracellular redox potential Glenn N. Dawes, Douglas R. Guptill, Robert McCord, Mauricio A. Retamal, Kurt A. Schalper, Kenji F. Shoji, ´ Sridhar Govindarajan, Ajoy Roy, Shumin Yang, Judy Michael V. L. Bennett, and Juan C. Saez Gao, Yong Hong Chen, Niels Jørgen Ø. Skartved, 8328 Profiling signaling polarity in chemotactic cells Annette K. Pedersen, David Lin, Christopher P. Yingchun Wang, Shi-Jian Ding, Wei Wang, Jon M. Jacobs, Locher, Indrani Rebbapragada, Anne Dam Wei-Jun Qian, Ronald J. Moore, Feng Yang, David G. Jensen, Steven H. Bass, Torben L. Nissen, Camp II, Richard D. Smith, and Richard L. Klemke Sridhar Viswanathan, Graham R. Foster, Julian A. Symons, and Phillip A. Patten 8334 Surveillance mechanism linking Bub1 loss to the p53 pathway 8275 of an essential trypanosome Ole V. Gjoerup, Jiaping Wu, Devin Chandler-Militello, polyamine biosynthetic by a catalytically Grace L. Williams, Jean Zhao, Brian Schaffhausen, dead homolog Parmjit S. Jat, and Thomas M. Roberts Erin K. Willert, Richard Fitzpatrick, and Margaret A. Phillips DEVELOPMENTAL BIOLOGY BIOPHYSICS 8340 Decondensing the protamine domain for transcription 8207 Single-molecule mass spectrometry in solution Rui Pires Martins and Stephen A. Krawetz using a solitary nanopore Joseph W. F. Robertson, Claudio G. Rodrigues, 8346 The conserved transcriptome in human and rodent Vincent M. Stanford, Kenneth A. Rubinson, male gametogenesis Oleg V. Krasilnikov, and John J. Kasianowicz Fre´de´ric Chalmel, Antoine D. Rolland, Christa Niederhauser- Wiederkehr, Sanny S. W. Chung, Philippe Demougin, 8229 A kinematic description of the trajectories of Listeria Alexandre Gattiker, James Moore, Jean-Jacques monocytogenes propelled by actin comet tails Patard, Debra J. Wolgemuth, Bernard Je´gou, V. B. Shenoy, D. T. Tambe, A. Prasad, and J. A. Theriot and Michael Primig

PNAS ͉ May 15, 2007 ͉ vol. 104 ͉ no. 20 ͉ v Downloaded by guest on September 26, 2021 ECOLOGY 8421 A silent chemokine receptor regulates steady-state 8352 Amphibian and reptile declines over 35 years leukocyte homing in vivo at La Selva, Costa Rica Kornelia Heinzel, Claudia Benz, and Conrad C. Bleul Steven M. Whitfield, Kristen E. Bell, Thomas Philippi, 8427 Immunization with hepatitis C virus-like particles results Mahmood Sasa, Federico Bolan˜os, Gerardo Chaves, in control of hepatitis C virus infection in chimpanzees Jay M. Savage, and Maureen A. Donnelly Gamal A. Elmowalid, Ming Qiao, Sook-Hyang Jeong, ➜ See Commentary on page 8201 Brian B. Borg, Thomas F. Baumert, Ronda K. Sapp, 8357 Evolutionary responses of discontinuous gas exchange Zongyi Hu, Krishna Murthy, and T. Jake Liang in insects 8433 Agalactosylated IgG antibodies depend on cellular Craig R. White, Tim M. Blackburn, John S. Terblanche, Fc receptors for in vivo activity Elrike Marais, Marc Gibernau, and Steven L. Chown Falk Nimmerjahn, Robert M. Anthony, 8362 Trophic cascade facilitates coral recruitment in and Jeffrey V. Ravetch a marine reserve Peter J. Mumby, Alastair R. Harborne, Jodene Williams, MEDICAL SCIENCES Carrie V. Kappel, Daniel R. Brumbaugh, Fiorenza Micheli, 8438 Activated Cdc42-associated kinase Ack1 promotes Katherine E. Holmes, Craig P. Dahlgren, Claire B. Paris, prostate progression via androgen receptor and Paul G. Blackwell tyrosine phosphorylation 8368 Habitat specialization, body size, and family identity Nupam P. Mahajan, Yuanbo Liu, Samarpan Majumder, explain lepidopteran density–area relationships in Maria R. Warren, Carol E. Parker, James L. Mohler, a cross-continental comparison H. Shelton Earp, and Young E. Whang Peter A. Hamba¨ck, Keith S. Summerville, Ingolf 8444 Effective therapy of murine models of human Steffan-Dewenter, Jochen Krauss, Go¨ran Englund, leukemia and lymphoma with radiolabeled and Thomas O. Crist anti-CD30 antibody, HeFi-1 8374 Multitrophic interaction facilitates parasite–host Meili Zhang, Zhengsheng Yao, Hiral Patel, Kayhan relationship between an invasive beetle and Garmestani, Zhuo Zhang, Vladimir S. Talanov, Paul S. the honey bee Plascjak, Carolyn K. Goldman, John E. Janik, Martin W. Baldwyn Torto, Drion G. Boucias, Richard T. Arbogast, Brechbiel, and Thomas A. Waldmann James H. Tumlinson, and Peter E. A. Teal 8449 Hepatitis C virus epitope-specific neutralizing antibodies in Igs prepared from human plasma EVOLUTION Pei Zhang, Charles G. Wu, Kathleen Mihalik, Maria Luisa 8379 Evolution of nematode-trapping cells of predatory Virata-Theimer, Mei-ying W. Yu, Harvey J. Alter, fungi of the Orbiliaceae based on evidence from and Stephen M. Feinstone rRNA-encoding and multiprotein sequences 8455 Inhibition of GLI-mediated transcription and tumor cell Ying Yang, Ence Yang, Zhiqiang An, and Xingzhong Liu growth by small-molecule antagonists 8385 The neoselectionist theory of genome evolution Matthias Lauth, Åsa Bergstro¨m, Takashi Shimokawa, Giorgio Bernardi and Rune Toftgård 8391 Intracellular targeting of telomeric retrotransposon Gag 8461 Gene-trapped mouse embryonic stem cell-derived proteins of distantly related Drosophila species cardiac myocytes and human genetics implicate Elena Casacuberta, Fernando Azorín Marín, AKAP10 in heart rhythm regulation and Mary-Lou Pardue Whittemore G. Tingley, Ludmila Pawlikowska, Jonathan G. Zaroff, Taeryn Kim, Trieu Nguyen, 8397 Independent sorting-out of thousands of duplicated Stephen G. Young, Karen Vranizan, Pui-Yan Kwok, gene pairs in two yeast species descended from Mary A. Whooley, and Bruce R. Conklin a whole-genome duplication Devin R. Scannell, A. Carolin Frank, Gavin C. Conant, 8467 HIV-1 escape from the entry-inhibiting effects of Kevin P. Byrne, Megan Woolfit, and Kenneth H. Wolfe a -binding compound via cleavage of gp41 by the viral protease GENETICS Abdul A. Waheed, Sherimay D. Ablan, James D. Roser, Raymond C. Sowder, Carl P. Schaffner, Elena Chertova, 8403 Evidence for mutation showers and Eric O. Freed Jicheng Wang, Kelly D. Gonzalez, William A. Scaringe, Kimberly Tsai, Ning Liu, Dongqing Gu, Wenyan Li, MICROBIOLOGY Kathleen A. Hill, and Steve S. Sommer ➜ See Commentary on page 8203 8472 Simple sequence repeats in prokaryotic genomes Jan Mra´zek, Xiangxue Guo, and Apurva Shah 8409 Activation-induced cytidine deaminase action is strongly stimulated by mutations of the THO complex 8478 Synthesis of glycerol phosphate lipoteichoic acid Bele´nGo´mez-Gonza´lez and Andre´s Aguilera in Staphylococcus aureus Angelika Gru¨ndling and Olaf Schneewind

IMMUNOLOGY 8484 Integrated network analysis identifies nitric oxide 8415 Low-intensity transplant regimens facilitate recruitment response networks and dihydroxyacid dehydratase of donor-specific regulatory T cells that promote as a crucial target in hematopoietic engraftment Daniel R. Hyduke, Laura R. Jarboe, Linh M. Tran, Ling Weng, Julian Dyson, and Francesco Dazzi Katherine J. Y. Chou, and James C. Liao

PNAS ͉ May 15, 2007 ͉ vol. 104 ͉ no. 20 ͉ vii Downloaded by guest on September 26, 2021 NEUROSCIENCE 8526 Unique antiviral mechanism discovered in anti-hepatitis 8490 Neural interactions between flicker-induced B virus research with a natural product analogue self-organized visual hallucinations and Chunxiao Ying, Ying Li, Chung-Hang Leung, physical stimuli Michael D. Robek, and Yung-Chi Cheng Vincent A. Billock and Brian H. Tsou PLANT BIOLOGY 8496 Triggering sleep slow waves by transcranial 8532 A secretory pathway-localized cation diffusion facilitator magnetic stimulation confers plant manganese tolerance Marcello Massimini, Fabio Ferrarelli, Steve K. Esser, Edgar Peiter, Barbara Montanini, Anthony Gobert, Brady A. Riedner, Reto Huber, Michael Murphy, Pai Pedas, Søren Husted, Frans J. M. Maathuis, Michael J. Peterson, and Giulio Tononi Damien Blaudez, Michel Chalot, and Dale Sanders 8502 Caspase-9 regulates apoptosis/proliferation balance 8538 A substrate-independent, 14:3:3 protein-mediated plastid during metamorphic brain remodeling in Xenopus import pathway of NADPH:protochlorophyllide Laurent Coen, Karine Le Blay, Isaline Rowe, A and Barbara A. Demeneix Andreas Schemenewitz, Stephan Pollmann, Christiane Reinbothe, and Steffen Reinbothe 8508 ApoER2/VLDL receptor and Dab1 in the rostral migratory stream function in postnatal neuronal migration 8544 Helical microtubule arrays in a collection of twisting independently of tubulin mutants of Arabidopsis thaliana Nuno Andrade, Vukoslav Komnenovic, Sophia M. Blake, Takashi Ishida, Yayoi Kaneko, Megumi Iwano, Yves Jossin, Brian Howell, Andre Goffinet, and Takashi Hashimoto Wolfgang J. Schneider, and Johannes Nimpf 8550 A gene from the cellulose synthase-like C family encodes a ␤-1,4 glucan synthase 8514 Carbonic anhydrase XIV deficiency produces a functional Jean-Christophe Cocuron, Olivier Lerouxel, Georgia defect in the retinal light response Drakakaki, Ana P. Alonso, Aaron H. Liepman, Kenneth Judith Mosinger Ogilvie, Kevin K. Ohlemiller, Gul N. Shah, Keegstra, Natasha Raikhel, and Curtis G. Wilkerson Barbara Ulmasov, Timothy A. Becker, Abdul Waheed, Anne K. Hennig, Peter D. Lukasiewicz, and William S. Sly PSYCHOLOGY PHARMACOLOGY 8556 Temporal-callosal pathway diffusivity predicts phonological skills in children 8520 A-803467, a potent and selective Nav1.8 sodium channel Robert F. Dougherty, Michal Ben-Shachar, Gayle K. Deutsch, blocker, attenuates neuropathic and inflammatory pain Arvel Hernandez, Glenn R. Fox, and Brian A. Wandell in the rat Michael F. Jarvis, Prisca Honore, Char-Chang Shieh, Mark Chapman, Shailen Joshi, Xu-Feng Zhang, Michael Kort, xi–xii Author Index William Carroll, Brian Marron, Robert Atkinson, James xiii Subscription Form Thomas, Dong Liu, Michael Krambis, Yi Liu, Steve McGaraughty, Katharine Chu, Rosemarie Roeloffs, Chengmin Zhong, Joseph P. Mikusa, Gricelda Hernandez, Donna Gauvin, Carrie Wade, Supplement 1 Chang Zhu, Madhavi Pai, Marc Scanio, Lei Shi, Irene Drizin, Robert Gregg, Mark Matulenko, Ahmed Hakeem, Michael Gross, Matthew ARTHUR M. SACKLER COLLOQUIUM OF THE NATIONAL Johnson, Kennan Marsh, P. Kay Wagoner, ACADEMY OF SCIENCES James P. Sullivan, Connie R. Faltynek, and Douglas S. Krafte 8563–8676 In the Light of Evolution I: Adaptation and ➜ See Commentary on page 8205 Complex Design

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