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November 21, 2006 ͉ vol. 103 ͉ no. 47 ͉ 17581–18026 Proceedings of the National Academy ofPNAS Sciences of the United States of America www.pnas.org Cover image: The 24 human chromosomes showing all of the SVA mobile element-mediated sequence transduction events mapped to individual chromosomes (shown as light lines and dots). SVA is a composite retrotransposon named for its main components: SINE, VNTR, and Alu. Gene duplication and transduction events for the acyl-malonyl condensing enzyme (AMAC) gene are shown as red lines; AMAC is an enzyme involved in fatty acid synthesis. See the article by Xing et al. on pages 17608–17613. Image courtesy of Bang Wong (ClearScience, Cambridge, MA), Jinchuan Xing, and Mark A. Batzer; the single copies of each chromosome are adapted from a human male karyotype image (Copyright 2003, Howard Hughes Medical Institute). From the Cover 17608 Retrotransposon-mediated gene transduction 17661 Sperm structure and fertilization 17736 Modes of microtubule sliding 18002 RNA interference in plant immunity Contents INAUGURAL ARTICLE 17595 Life-history evolution under a production constraint THIS WEEK IN PNAS James H. Brown and Richard M. Sibly EUKARYOTIC TRANSPOSABLE ELEMENTS AND 17581 In This Issue GENOME EVOLUTION SPECIAL FEATURE COMMENTARIES INTRODUCTION 17600 Transposable elements and the evolution 17583 Timeless genes and jetlag of eukaryotic genomes Russell N. Van Gelder Susan R. Wessler ➜ See companion article on page 17313 in issue 46 of volume 103 RESEARCH ARTICLES RNA from the 5؅ end of the R2 retrotransposon 17602 17585 Better intracytoplasmic sperm injection controls R2 protein binding to and cleavage without sperm membranes of its DNA target site Eduardo R. S. Roldan Shawn M. Christensen, Junqiang Ye, ➜ See companion article on page 17661 and Thomas H. Eickbush 17587 Dynein shifts into second gear 17608 Emergence of primate genes by retrotransposon- mediated sequence transduction Michael P. Koonce ➜ See companion article on page 17736 Jinchuan Xing, Hui Wang, Victoria P. Belancio, Richard Cordaux, Prescott L. Deininger, and Mark A. Batzer PERSPECTIVE 17614 Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis 17589 Low micronutrient intake may accelerate the Sara L. Sawyer and Harmit S. Malik degenerative diseases of aging through allocation of scarce micronutrients by triage 17620 Dramatic amplification of a rice transposable Bruce N. Ames element during recent domestication Ken Naito, Eunyoung Cho, Guojun Yang, Matthew A. Campbell, Kentaro Yano, Yutaka Okumoto, Takatoshi Tanisaka, Freely available online through the PNAS open access option. and Susan R. Wessler PNAS ͉ November 21, 2006 ͉ vol. 103 ͉ no. 47 ͉ iii–x Downloaded by guest on October 4, 2021 17626 Recurrent duplication-driven transposition of DNA 17672 Genetically modified pigs produced with a nonviral during hominoid evolution episomal vector Matthew E. Johnson, NISC Comparative Sequencing Stefano Manzini, Alessia Vargiolu, Isa M. Stehle, Program, Ze Cheng, V. Anne Morrison, Steven Maria Laura Bacci, Maria Grazia Cerrito, Roberto Scherer, Mario Ventura, Richard A. Gibbs, Giovannoni, Augusta Zannoni, Maria Rosaria Eric D. Green, and Evan E. Eichler Bianco, Monica Forni, Pierluigi Donini, Michele Papa, Hans J. Lipps, and Marialuisa Lavitrano 17632 Transposon insertion site profiling chip (TIP-chip) Sarah J. Wheelan, Lisa Z. Scheifele, Francisco 17678 Immunoabsorbent nanoparticles based Marti´nez-Murillo, Rafael A. Irizarry, on a tobamovirus displaying protein A and Jef D. Boeke Stefan Werner, Sylvestre Marillonnet, Gerd Hause, Victor Klimyuk, and Yuri Gleba 17638 Analysis of retrotransposon structural diversity 17684 Lentiviral vectors with a defective integrase allow uncovers properties and propensities in efficient and sustained transgene expression angiosperm genome evolution in vitro and in vivo Cle´mentine Vitte and Jeffrey L. Bennetzen Ste´phanie Philippe, Chamsy Sarkis, Martine Barkats, Hamid Mammeri, Charline Ladroue, Caroline Petit, 17644 Remarkable variation in maize genome structure Jacques Mallet, and Che Serguera inferred from haplotype diversity at the bz locus Qinghua Wang and Hugo K. Dooner BIOCHEMISTRY ؅ PHYSICAL SCIENCES 17602 RNA from the 5 end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site APPLIED PHYSICAL SCIENCES Shawn M. Christensen, Junqiang Ye, and Thomas H. Eickbush 17741 Cooperative deformation of mineral and collagen in bone at the nanoscale 17690 Chromatin structure can strongly facilitate Himadri S. Gupta, Jong Seto, Wolfgang Wagermaier, enhancer action over a distance Paul Zaslansky, Peter Boesecke, and Peter Fratzl Mikhail A. Rubtsov, Yury S. Polikanov, Vladimir A. Bondarenko, Yuh-Hwa Wang, and Vasily M. Studitsky CHEMISTRY 17696 A cryptochrome͞photolyase class of enzymes with 17650 Self-organization of nano-lines and dots triggered single-stranded DNA-specific photolyase activity by a local mechanical stimulus Christopher P. Selby and Aziz Sancar Fabio Biscarini, Massimiliano Cavallini, Rajendra Kshirsagar, Giovanni Bottari, David A. Leigh, 17701 Crystal structure of cryptochrome 3 from Arabidopsis Salvador Leo´n, and Francesco Zerbetto thaliana and its implications for photolyase activity Yihua Huang, Richard Baxter, Barbara S. Smith, 17655 Synthetic selectivity through avoidance Carrie L. Partch, Christopher L. Colbert, of valence frustration and Johann Deisenhofer Marie Hutin, Ge´rald Bernardinelli, 17707 Designer short peptide surfactants stabilize G and Jonathan R. Nitschke protein-coupled receptor bovine rhodopsin 17667 Polymeric coatings that inactivate both influenza Xiaojun Zhao, Yusuke Nagai, Philip J. Reeves, Patrick virus and pathogenic bacteria Kiley, H. Gobind Khorana, and Shuguang Zhang ´ Jayanta Haldar, Deqiang An, Luis Alvarez de Cienfuegos, 17713 Crystal structures of human cardiac ␤-myosin II Jianzhu Chen, and Alexander M. Klibanov S2-⌬ provide insight into the functional role of the S2 subfragment COMPUTER SCIENCES Wulf Blankenfeldt, Nicolas H. Thoma¨, John S. Wray, 18014 Bayesian estimation of the shape skeleton Mathias Gautel, and Ilme Schlichting Jacob Feldman and Manish Singh 17718 Oligozoospermia with normal fertility in male mice lacking the androgen receptor in testis peritubular BIOLOGICAL SCIENCES myoid cells Caixia Zhang, Shuyuan Yeh, Yen-Ta Chen, Cheng-Chia Wu, Kuang-Hsiang Chuang, Hung-Yun Lin, Ruey-Sheng APPLIED BIOLOGICAL SCIENCES Wang, Yu-Jia Chang, Chamindrani Mendis-Handagama, 17661 Simultaneous removal of sperm plasma membrane Liquan Hu, Henry Lardy, and Chawnshang Chang and acrosome before intracytoplasmic sperm injection 17724 Specificity in substrate and cofactor recognition ͞ improves oocyte activation embryonic development by the N-terminal domain of the chaperone ClpX Kazuto Morozumi, Tomohide Shikano, Shunichi Guillaume Thibault, Jovana Yudin, Philip Wong, Miyazaki, and Ryuzo Yanagimachi Vladimir Tsitrin, Remco Sprangers, Rongmin Zhao, ➜ See Commentary on page 17585 and Walid A. Houry 17667 Polymeric coatings that inactivate both influenza 17730 Specific SNARE complex binding mode of the virus and pathogenic bacteria Sec1͞Munc-18 protein, Sec1p Jayanta Haldar, Deqiang An, Luis Alvarez´ de Cienfuegos, John Togneri, Yi-Shan Cheng, Mary Munson, Jianzhu Chen, and Alexander M. Klibanov Frederick M. Hughson, and Chavela M. Carr PNAS ͉ November 21, 2006 ͉ vol. 103 ͉ no. 47 ͉ v Downloaded by guest on October 4, 2021 BIOPHYSICS 17813 An efficient promoter trap for detection of patterned 17736 Two modes of microtubule sliding driven gene expression and subsequent functional analysis by cytoplasmic dynein in Drosophila Tomohiro Shima, Takahide Kon, Kenji Imamula, Camilla Larsen, Xavier Franch-Marro, Volker Hartenstein, Reiko Ohkura, and Kazuo Sutoh Cyrille Alexandre, and Jean-Paul Vincent ➜ See Commentary on page 17587 ECOLOGY 17741 Cooperative deformation of mineral and collagen in bone at the nanoscale 17818 A common pumiliotoxin from poison frogs exhibits Himadri S. Gupta, Jong Seto, Wolfgang Wagermaier, enantioselective toxicity against mosquitoes Paul Zaslansky, Peter Boesecke, and Peter Fratzl Paul J. Weldon, Matthew Kramer, Scott Gordon, Thomas F. Spande, and John W. Daly 17747 Understanding ensemble protein folding at atomic detail Isaac A. Hubner, Eric J. Deeds, and Eugene I. Shakhnovich EVOLUTION 17753 Atomic structures of peptide self-assembly mimics 17595 Life-history evolution under a production constraint Koki Makabe, Dan McElheny, Valentia Tereshko, James H. Brown and Richard M. Sibly Aaron Hilyard, Grzegorz Gawlak, Shude Yan, Akiko Koide, and Shohei Koide 17608 Emergence of primate genes by retrotransposon- 17759 Viscoelastic properties of individual glial cells mediated sequence transduction and neurons in the CNS Jinchuan Xing, Hui Wang, Victoria P. Belancio, Yun-Bi Lu, Kristian Franze, Gerald Seifert, Christian Richard Cordaux, Prescott L. Deininger, Steinha¨user, Frank Kirchhoff, Hartwig Wolburg, and Mark A. Batzer Jochen Guck, Paul Janmey, Er-Qing Wei, Josef 17614 Positive selection of yeast nonhomologous end-joining Ka¨s, and Andreas Reichenbach genes and a retrotransposon conflict hypothesis 17765 Secondary structure provides a template Sara L. Sawyer and Harmit S. Malik for the folding of nearby polypeptides Tomoshi Kameda, and Shoji Takada 17822 Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry Structural changes in troponin in response to Ca2؉ 17771 Christopher L. Dupont, Song Yang, Brian Palenik, and myosin binding
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