| | This journal provides immediate access to some articles. This Week in PNAS Proc Natl Acad Sci U S A. 2006 November 21; 103(47): 17581–17582. doi: 10.1073/iti4706103.PMCID: PMC1693786 Commentaries Timeless genes and jetlag Russell N. Van Gelder PMCID: PMC1693787 Better intracytoplasmic sperm injection without sperm membranes and acrosome Eduardo R. S. Roldan PMCID: PMC1693788 Dynein shifts into second gear Michael P. Koonce PMCID: PMC1693789 Perspective Low micronutrient intake may accelerate the degenerative diseases of aging through allocation of scarce micronutrients by triage Bruce N. Ames PMCID: PMC1693790 Eukaryotic Transposable Elements and Genome Evolution Special Feature Introduction Transposable elements and the evolution of eukaryotic genomes Susan R. Wessler PMCID: PMC1693792 Research Articles RNA from the 5′ end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site Shawn M. Christensen, Junqiang Ye, and Thomas H. Eickbush PMCID: PMC1693793 From the Cover: Eukaryotic Transposable Elements and Genome Evolution Special Feature:
Emergence of primate genes by retrotransposon-mediated sequence transduction Jinchuan Xing, Hui Wang, Victoria P. Belancio, Richard Cordaux, Prescott L. Deininger, and Mark A. Batzer PMCID: PMC1693794 Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis Sara L. Sawyer and Harmit S. Malik PMCID: PMC1693795 Dramatic amplification of a rice transposable element during recent domestication Ken Naito, Eunyoung Cho, Guojun Yang, Matthew A Campbell, Kentaro Yano, Yutaka Okumoto, Takatoshi Tanisaka, and Susan R. Wessler PMCID: PMC1693796 Recurrent duplication-driven transposition of DNA during hominoid evolution Matthew E. Johnson, Ze Cheng, V. Anne Morrison, Steven Scherer, Mario Ventura, Richard A. Gibbs, Eric D. Green, Evan E. Eichler, and NISC Comparative Sequencing Program PMCID: PMC1693797 Transposon insertion site profiling chip (TIP-chip) Sarah J. Wheelan, Lisa Z. Scheifele, Francisco Martínez-Murillo, Rafael A. Irizarry, and Jef D. Boeke PMCID: PMC1693798 Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution Clémentine Vitte and Jeffrey L. Bennetzen PMCID: PMC1693799 Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus Qinghua Wang and Hugo K. Dooner PMCID: PMC1693800 Physical Sciences Applied Physical Sciences Cooperative deformation of mineral and collagen in bone at the nanoscale Himadri S. Gupta, Jong Seto, Wolfgang Wagermaier, Paul Zaslansky, Peter Boesecke, and Peter Fratzl PMCID: PMC1635545 Chemistry Self-organization of nano-lines and dots triggered by a local mechanical stimulus Fabio Biscarini, Massimiliano Cavallini, Rajendra Kshirsagar, Giovanni Bottari, David A. Leigh, Salvador León, and Francesco Zerbetto PMCID: PMC1693801 Synthetic selectivity through avoidance of valence frustration Marie Hutin, Gérald Bernardinelli, and Jonathan R. Nitschke PMCID: PMC1693802 Polymeric coatings that inactivate both influenza virus and pathogenic bacteria Jayanta Haldar, Deqiang An, Luis Álvarez de Cienfuegos, Jianzhu Chen, and Alexander M. Klibanov PMCID: PMC1693804 Computer Sciences Bayesian estimation of the shape skeleton Jacob Feldman and Manish Singh PMCID: PMC1635976 Biological Sciences Applied Biological Sciences From the Cover:
Simultaneous removal of sperm plasma membrane and acrosome before intracytoplasmic sperm injection improves oocyte activation/embryonic development Kazuto Morozumi, Tomohide Shikano, Shunichi Miyazaki, and Ryuzo Yanagimachi PMCID: PMC1693803 Polymeric coatings that inactivate both influenza virus and pathogenic bacteria Jayanta Haldar, Deqiang An, Luis Álvarez de Cienfuegos, Jianzhu Chen, and Alexander M. Klibanov PMCID: PMC1693804 Genetically modified pigs produced with a nonviral episomal vector Stefano Manzini, Alessia Vargiolu, Isa M Stehle, Maria Laura Bacci, Maria Grazia Cerrito, Roberto Giovannoni, Augusta Zannoni, Maria Rosaria Bianco, Monica Forni, Pierluigi Donini, Michele Papa, Hans J Lipps, and Marialuisa Lavitrano PMCID: PMC1635978 Immunoabsorbent nanoparticles based on a tobamovirus displaying protein A Stefan Werner, Sylvestre Marillonnet, Gerd Hause, Victor Klimyuk, and Yuri Gleba PMCID: PMC1635023 Lentiviral vectors with a defective integrase allow efficient and sustained transgene expression in vitro and in vivo Stéphanie Philippe, Chamsy Sarkis, Martine Barkats, Hamid Mammeri, Charline Ladroue, Caroline Petit, Jacques Mallet, and Che Serguera PMCID: PMC1693807 Biochemistry RNA from the 5′ end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site Shawn M. Christensen, Junqiang Ye, and Thomas H. Eickbush PMCID: PMC1693793 Chromatin structure can strongly facilitate enhancer action over a distance Mikhail A. Rubtsov, Yury S. Polikanov, Vladimir A. Bondarenko, Yuh-Hwa Wang, and Vasily M. Studitsky PMCID: PMC1693808 A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity Christopher P. Selby and Aziz Sancar PMCID: PMC1621107 Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity Yihua Huang, Richard Baxter, Barbara S. Smith, Carrie L. Partch, Christopher L. Colbert, and Johann Deisenhofer PMCID: PMC1635974 Designer short peptide surfactants stabilize G protein-coupled receptor bovine rhodopsin Xiaojun Zhao, Yusuke Nagai, Philip J. Reeves, Patrick Kiley, H. Gobind Khorana, and Shuguang Zhang PMCID: PMC1693811 Crystal structures of human cardiac β-myosin II S2-Δ provide insight into the functional role of the S2 subfragment Wulf Blankenfeldt, Nicolas H. Thomä, John S. Wray, Mathias Gautel, and Ilme Schlichting PMCID: PMC1693812 Oligozoospermia with normal fertility in male mice lacking the androgen receptor in testis peritubular myoid cells Caixia Zhang, Shuyuan Yeh, Yen-Ta Chen, Cheng-Chia Wu, Kuang-Hsiang Chuang, Hung-Yun Lin, Ruey-Sheng Wang, Yu-Jia Chang, Chamindrani Mendis-Handagama, Liquan Hu, Henry Lardy, and Chawnshang Chang PMCID: PMC1693813 Specificity in substrate and cofactor recognition by the N-terminal domain of the chaperone ClpX Guillaume Thibault, Jovana Yudin, Philip Wong, Vladimir Tsitrin, Remco Sprangers, Rongmin Zhao, and Walid A. Houry PMCID: PMC1693814 Specific SNARE complex binding mode of the Sec1/Munc-18 protein, Sec1p John Togneri, Yi-Shan Cheng, Mary Munson, Frederick M. Hughson, and Chavela M. Carr PMCID: PMC1693815 Biophysics From the Cover:
Two modes of microtubule sliding driven by cytoplasmic dynein Tomohiro Shima, Takahide Kon, Kenji Imamula, Reiko Ohkura, and Kazuo Sutoh PMCID: PMC1634414 Cooperative deformation of mineral and collagen in bone at the nanoscale Himadri S. Gupta, Jong Seto, Wolfgang Wagermaier, Paul Zaslansky, Peter Boesecke, and Peter Fratzl PMCID: PMC1635545 Understanding ensemble protein folding at atomic detail Isaac A. Hubner, Eric J. Deeds, and Eugene I. Shakhnovich PMCID: PMC1635542 Atomic structures of peptide self-assembly mimics Koki Makabe, Dan McElheny, Valentia Tereshko, Aaron Hilyard, Grzegorz Gawlak, Shude Yan, Akiko Koide, and Shohei Koide PMCID: PMC1693819 Viscoelastic properties of individual glial cells and neurons in the CNS Yun-Bi Lu, Kristian Franze, Gerald Seifert, Christian Steinhäuser, Frank Kirchhoff, Hartwig Wolburg, Jochen Guck, Paul Janmey, Er-Qing Wei, Josef Käs, and Andreas Reichenbach PMCID: PMC1693820 Secondary structure provides a template for the folding of nearby polypeptides Tomoshi Kameda and Shoji Takada PMCID: PMC1693821 Structural changes in troponin in response to Ca2+ and myosin binding to thin filaments during activation of skeletal muscle Yin-Biao Sun, Birgit Brandmeier, and Malcolm Irving PMCID: PMC1693822 Cell Biology Golgi twins in late mitosis revealed by genetically encoded tags for live cell imaging and correlated electron microscopy Guido M. Gaietta, Ben N. G. Giepmans, Thomas J. Deerinck, W. Bryan Smith, Lucy Ngan, Juan Llopis, Stephen R. Adams, Roger Y. Tsien, and Mark H. Ellisman PMCID: PMC1635977 Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism Alexandr P. Kornev, Nina M. Haste, Susan S. Taylor, and Lynn F. Ten Eyck PMCID: PMC1693824 Some G protein heterotrimers physically dissociate in living cells Gregory J. Digby, Robert M. Lober, Pooja R. Sethi, and Nevin A. Lambert PMCID: PMC1693825 Pleiotrophin disrupts calcium-dependent homophilic cell–cell adhesion and initiates an epithelial–mesenchymal transition P. Perez-Pinera, S. Alcantara, T. Dimitrov, J. A. Vega, and T. F. Deuel PMCID: PMC1693826 ELYS is a dual nucleoporin/kinetochore protein required for nuclear pore assembly and proper cell division Beth A. Rasala, Arturo V. Orjalo, Zhouxin Shen, Steven Briggs, and Douglass J. Forbes PMCID: PMC1635652 Developmental Biology Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR Luigi Warren, David Bryder, Irving L. Weissman, and Stephen R. Quake PMCID: PMC1693828 An efficient promoter trap for detection of patterned gene expression and subsequent functional analysis in Drosophila Camilla Larsen, Xavier Franch-Marro, Volker Hartenstein, Cyrille Alexandre, and Jean-Paul Vincent PMCID: PMC1635159 Ecology A common pumiliotoxin from poison frogs exhibits enantioselective toxicity against mosquitoes Paul J. Weldon, Matthew Kramer, Scott Gordon, Thomas F. Spande, and John W. Daly PMCID: PMC1693830 Evolution INAUGURAL ARTICLE by a Recently Elected Academy Member: Life-history evolution under a production constraint James H. Brown and Richard M. Sibly PMCID: PMC1693791 From the Cover: Eukaryotic Transposable Elements and Genome Evolution Special Feature:
Emergence of primate genes by retrotransposon-mediated sequence transduction Jinchuan Xing, Hui Wang, Victoria P. Belancio, Richard Cordaux, Prescott L. Deininger, and Mark A. Batzer PMCID: PMC1693794 Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis Sara L. Sawyer and Harmit S. Malik PMCID: PMC1693795 Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry Christopher L. Dupont, Song Yang, Brian Palenik, and Philip E. Bourne PMCID: PMC1635651 Genetics Dramatic amplification of a rice transposable element during recent domestication Ken Naito, Eunyoung Cho, Guojun Yang, Matthew A Campbell, Kentaro Yano, Yutaka Okumoto, Takatoshi Tanisaka, and Susan R. Wessler PMCID: PMC1693796 Recurrent duplication-driven transposition of DNA during hominoid evolution Matthew E. Johnson, Ze Cheng, V. Anne Morrison, Steven Scherer, Mario Ventura, Richard A. Gibbs, Eric D. Green, Evan E. Eichler, and NISC Comparative Sequencing Program PMCID: PMC1693797 Transposon insertion site profiling chip (TIP-chip) Sarah J. Wheelan, Lisa Z. Scheifele, Francisco Martínez-Murillo, Rafael A. Irizarry, and Jef D. Boeke PMCID: PMC1693798 Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution Clémentine Vitte and Jeffrey L. Bennetzen PMCID: PMC1693799 Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions Guenter Albrecht-Buehler PMCID: PMC1635160 Global mapping of c-Myc binding sites and target gene networks in human B cells Karen I. Zeller, XiaoDong Zhao, Charlie W. H. Lee, Kuo Ping Chiu, Fei Yao, Jason T. Yustein, Hong Sain Ooi, Yuriy L. Orlov, Atif Shahab, How Choong Yong, YuTao Fu, Zhiping Weng, Vladimir A. Kuznetsov, Wing-Kin Sung, Yijun Ruan, Chi V. Dang, and Chia-Lin Wei PMCID: PMC1635161 Pmr1, a Golgi Ca2+/Mn2+-ATPase, is a regulator of the target of rapamycin (TOR) signaling pathway in yeast Gina Devasahayam, Danilo Ritz, Stephen B. Helliwell, Daniel J. Burke, and Thomas W. Sturgill PMCID: PMC1693834 A large-scale full-length cDNA analysis to explore the budding yeast transcriptome Fumihito Miura, Noriko Kawaguchi, Jun Sese, Atsushi Toyoda, Masahira Hattori, Shinichi Morishita, and Takashi Ito PMCID: PMC1693835 Immunology Developmental switch of mouse hematopoietic stem cells from fetal to adult type occurs in bone marrow after birth Kazu Kikuchi and Motonari Kondo PMCID: PMC1693836 On the definition of a criterion of immunogenicity Thomas Pradeu and Edgardo D. Carosella PMCID: PMC1693837 Medical Sciences An immunocompetent mouse model for the tolerance of human chronic hepatitis B virus infection Li-Rung Huang, Hui-Lin Wu, Pei-Jer Chen, and Ding-Shinn Chen PMCID: PMC1635544 Oncogenic steroid receptor coactivator-3 is a key regulator of the white adipogenic program Jean-Francois Louet, Agnès Coste, Larbi Amazit, Mounia Tannour-Louet, Ray-Chang Wu, Sophia Y. Tsai, Ming-Jer Tsai, Johan Auwerx, and Bert W. O'Malley PMCID: PMC1693839 Radiation dose-rate effects, endogenous DNA damage, and signaling resonance Michael M. Vilenchik and Alfred G. Knudson PMCID: PMC1693840 Molecular mechanism for analgesia involving specific antagonism of α9α10 nicotinic acetylcholine receptors Michelle Vincler, Shannon Wittenauer, Renee Parker, Michael Ellison, Baldomero M. Olivera, and J. Michael McIntosh PMCID: PMC1635975 Evolution and expression of chimeric POTE–actin genes in the human genome Yoomi Lee, Tomoko Ise, Duc Ha, Ashley Saint Fleur, Yoonsoo Hahn, Xiu-Fen Liu, Satoshi Nagata, Byungkook Lee, Tapan K. Bera, and Ira Pastan PMCID: PMC1693842 Revertant mutants G550E and 4RK rescue cystic fibrosis mutants in the first nucleotide-binding domain of CFTR by different mechanisms Mónica Roxo-Rosa, Zhe Xu, André Schmidt, Mário Neto, Zhiwei Cai, Cláudio M. Soares, David N. Sheppard, and Margarida D. Amaral PMCID: PMC1693843 Microbiology Rationally designed small compounds inhibit pilus biogenesis in uropathogenic bacteria Jerome S. Pinkner, Han Remaut, Floris Buelens, Eric Miller, Veronica Åberg, Nils Pemberton, Mattias Hedenström, Andreas Larsson, Patrick Seed, Gabriel Waksman, Scott J. Hultgren, and Fredrik Almqvist PMCID: PMC1693844 Refolding of a paramyxovirus F protein from prefusion to postfusion conformations observed by liposome binding and electron microscopy Sarah A. Connolly, George P. Leser, Hsien-Shen Yin, Theodore S. Jardetzky, and Robert A. Lamb PMCID: PMC1635158 l,l-diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine Andrea J. McCoy, Nancy E. Adams, André O. Hudson, Charles Gilvarg, Thomas Leustek, and Anthony T. Maurelli PMCID: PMC1693846 Salmonella typhimurium disseminates within its host by manipulating the motility of infected cells Micah J. Worley, George S. Nieman, Kaoru Geddes, and Fred Heffron PMCID: PMC1635543 An unconventional pathway for reduction of CO2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics Daniel J. Lessner, Lingyun Li, Qingbo Li, Tomas Rejtar, Victor P. Andreev, Matthew Reichlen, Kevin Hill, James J. Moran, Barry L. Karger, and James G. Ferry PMCID: PMC1693848 The twin-arginine translocation pathway is a major route of protein export in Streptomyces coelicolor David A. Widdick, Kieran Dilks, Govind Chandra, Andrew Bottrill, Mike Naldrett, Mechthild Pohlschröder, and Tracy Palmer PMCID: PMC1693849 Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome T. H. Mauchline, J. E. Fowler, A. K. East, A. L. Sartor, R. Zaheer, A. H. F. Hosie, P. S. Poole, and T. M. Finan PMCID: PMC1635973 Neuroscience Construction of a mutated pro-nerve growth factor resistant to degradation and suitable for biophysical and cellular utilization Promila C. Pagadala, Laura A. Dvorak, and Kenneth E. Neet PMCID: PMC1693851 Neuroglobin-overexpressing transgenic mice are resistant to cerebral and myocardial ischemia Adil A. Khan, Yaoming Wang, Yunjuan Sun, Xiao Ou Mao, Lin Xie, Erin Miles, Justin Graboski, Sylvia Chen, Lisa M. Ellerby, Kunlin Jin, and David A. Greenberg PMCID: PMC1693852 Lipocalin-type prostaglandin D synthase produces prostaglandin D2 involved in regulation of physiological sleep Wei-Min Qu, Zhi-Li Huang, Xin-Hong Xu, Kosuke Aritake, Naomi Eguchi, Fumio Nambu, Shu Narumiya, Yoshihiro Urade, and Osamu Hayaishi PMCID: PMC1693853 Inhibition of dynamin completely blocks compensatory synaptic vesicle endocytosis A. Jamila Newton, Tom Kirchhausen, and Venkatesh N. Murthy PMCID: PMC1693854 The spine neck filters membrane potentials Roberto Araya, Jiang Jiang, Kenneth B. Eisenthal, and Rafael Yuste PMCID: PMC1693855 LRRTM3 promotes processing of amyloid-precursor protein by BACE1 and is a positional candidate gene for late-onset Alzheimer's disease John Majercak, William J. Ray, Amy Espeseth, Adam Simon, Xiao-Ping Shi, Carrie Wolffe, Krista Getty, Shane Marine, Erica Stec, Marc Ferrer, Berta Strulovici, Steven Bartz, Adam Gates, Min Xu, Qian Huang, Lei Ma, Paul Shughrue, Julja Burchard, Dennis Colussi, Beth Pietrak, Jason Kahana, Dirk Beher, Thomas Rosahl, Mark Shearman, Daria Hazuda, Alan B. Sachs, Kenneth S. Koblan, Guy R. Seabrook, and David J. Stone PMCID: PMC1635650 Conservation and evolution of gene coexpression networks in human and chimpanzee brains Michael C. Oldham, Steve Horvath, and Daniel H. Geschwind PMCID: PMC1693857 Pharmacology Human Opiorphin, a natural antinociceptive modulator of opioid-dependent pathways Anne Wisner, Evelyne Dufour, Michaël Messaoudi, Amine Nejdi, Audrey Marcel, Marie-Noelle Ungeheuer, and Catherine Rougeot PMCID: PMC1693858 Physiology Angiotensin II causes hypertension and cardiac hypertrophy through its receptors in the kidney Steven D. Crowley, Susan B. Gurley, Maria J. Herrera, Phillip Ruiz, Robert Griffiths, Anil P. Kumar, Hyung-Suk Kim, Oliver Smithies, Thu H. Le, and Thomas M. Coffman PMCID: PMC1693859 Na channel inactivation from open and closed states Clay M. Armstrong PMCID: PMC1693860 Plant Biology Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus Qinghua Wang and Hugo K. Dooner PMCID: PMC1693800 A single chromoprotein with triple chromophores acts as both a phytochrome and a phototropin Takeshi Kanegae, Emi Hayashida, Chihiro Kuramoto, and Masamitsu Wada PMCID: PMC1693861 A pathogen-inducible endogenous siRNA in plant immunity Surekha Katiyar-Agarwal, Rebekah Morgan, Douglas Dahlbeck, Omar Borsani, Andy Villegas, Jr., Jian-Kang Zhu, Brian J. Staskawicz, and Hailing Jin PMCID: PMC1693862 Suppression of Arabidopsis vesicle-SNARE expression inhibited fusion of H2O2-containing vesicles with tonoplast and increased salt tolerance Yehoram Leshem, Naomi Melamed-Book, Olivier Cagnac, Gil Ronen, Yossi Nishri, Mazal Solomon, Gil Cohen, and Alex Levine PMCID: PMC1693863 Psychology Bayesian estimation of the shape skeleton Jacob Feldman and Manish Singh PMCID: PMC1635976 Recent fear is resistant to extinction Stephen Maren and Chun-hui Chang PMCID: PMC1693865 Correction Correction for Cannon et al., Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes PMCID: PMC1693866 Corrects: Steven B. Cannon, et al. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A. 2006 October 3; 103(40): 14959–14964. |
