| | This journal provides immediate access to some articles. This Week in PNAS Proc Natl Acad Sci U S A. 2007 July 31; 104(31): 12583–12584. doi: 10.1073/iti3107104.PMCID: PMC1937508 Commentary Our share of the planetary pie Jonathan A. Foley, Chad Monfreda, Navin Ramankutty, and David Zaks PMCID: PMC1937509 Single-molecule Chemistry and Biology Special Feature Introductory Perspective Single-Molecule Chemistry and Biology Special Feature: Introduction to the Special Feature on Single-Molecule Chemistry and Biology Robert J. Silbey PMCID: PMC1937511 Research Articles Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase Guobin Luo, Mina Wang, William H. Konigsberg, and X. Sunney Xie PMCID: PMC1937514 Strongly emissive individual DNA-encapsulated Ag nanoclusters as single-molecule fluorophores Tom Vosch, Yasuko Antoku, Jung-Cheng Hsiang, Chris I. Richards, Jose I. Gonzalez, and Robert M. Dickson PMCID: PMC1937515 Principal-components analysis of shape fluctuations of single DNA molecules Adam E. Cohen and W. E. Moerner PMCID: PMC1937516 Local viscosity of supercooled glycerol near Tg probed by rotational diffusion of ensembles and single dye molecules Rob Zondervan, Florian Kulzer, Gregorius C. G. Berkhout, and Michel Orrit PMCID: PMC1937517 Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic “fingerprinting” Shixin Liu, Gregory Bokinsky, Nils G. Walter, and Xiaowei Zhuang PMCID: PMC1937518 Single-molecule FRET reveals sugar-induced conformational dynamics in LacY Devdoot S. Majumdar, Irina Smirnova, Vladimir Kasho, Eyal Nir, Xiangxu Kong, Shimon Weiss, and H. Ronald Kaback PMCID: PMC1937519 Fueling protein–DNA interactions inside porous nanocontainers Ibrahim Cisse, Burak Okumus, Chirlmin Joo, and Taekjip Ha PMCID: PMC1937520 Probing nucleation, reverse annealing, and chaperone function along the reaction path of HIV-1 single-strand transfer Yining Zeng, Hsiao-Wei Liu, Christy F. Landes, Yoen Joo Kim, Xiaojing Ma, Yongjin Zhu, Karin Musier-Forsyth, and Paul F. Barbara PMCID: PMC1937521 Perspectives New directions in single-molecule imaging and analysis W. E. Moerner PMCID: PMC1937512 From the Cover: Single-molecule Chemistry And Biology Special Feature:
Single-molecule fluorescence spectroscopy in (bio)catalysis Maarten B. J. Roeffaers, Gert De Cremer, Hiroshi Uji-i, Benîot Muls, Bert F. Sels, Pierre A. Jacobs, Frans C. De Schryver, Dirk E. De Vos, and Johan Hofkens PMCID: PMC1937513 Physical Sciences Applied Mathematics Efficient Monte Carlo sampling by parallel marginalization Jonathan Weare PMCID: PMC1937522 Combinatorial promoter design for engineering noisy gene expression Kevin F. Murphy, Gábor Balázsi, and James J. Collins PMCID: PMC1931564 Chemistry Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase Guobin Luo, Mina Wang, William H. Konigsberg, and X. Sunney Xie PMCID: PMC1937514 Strongly emissive individual DNA-encapsulated Ag nanoclusters as single-molecule fluorophores Tom Vosch, Yasuko Antoku, Jung-Cheng Hsiang, Chris I. Richards, Jose I. Gonzalez, and Robert M. Dickson PMCID: PMC1937515 Physics Principal-components analysis of shape fluctuations of single DNA molecules Adam E. Cohen and W. E. Moerner PMCID: PMC1937516 Local viscosity of supercooled glycerol near Tg probed by rotational diffusion of ensembles and single dye molecules Rob Zondervan, Florian Kulzer, Gregorius C. G. Berkhout, and Michel Orrit PMCID: PMC1937517 Statistics Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity Q. K. Beg, A. Vazquez, J. Ernst, M. A. de Menezes, Z. Bar-Joseph, A.-L. Barabási, and Z. N. Oltvai PMCID: PMC1937523 Biological Sciences Biochemistry Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase Guobin Luo, Mina Wang, William H. Konigsberg, and X. Sunney Xie PMCID: PMC1937514 Single A326G mutation converts human CYP24A1 from 25-OH-D3-24-hydroxylase into -23-hydroxylase, generating 1α,25-(OH)2D3-26,23-lactone David E. Prosser, Martin Kaufmann, Brendan O'Leary, Valarie Byford, and Glenville Jones PMCID: PMC1937525 Increased prostate cell proliferation and loss of cell differentiation in mice lacking prostate epithelial androgen receptor Chun-Te Wu, Saleh Altuwaijri, William A. Ricke, Shu-Pin Huang, Shuyuan Yeh, Caixia Zhang, Yuanjie Niu, Meng-Ying Tsai, and Chawnshang Chang PMCID: PMC1937526 Crystal structure of the GINS complex and functional insights into its role in DNA replication Y. Paul Chang, Ganggang Wang, Vladimir Bermudez, Jerard Hurwitz, and Xiaojiang S. Chen PMCID: PMC1937527 Epigenetic regulation of the Drosophila chromosome 4 by the histone H3K9 methyltransferase dSETDB1 Tsai-Yu Tzeng, Chi-Hua Lee, Li-Wei Chan, and C.-K. James Shen PMCID: PMC1937528 Design of protein–membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V Kenneth Segers, Olivier Sperandio, Markus Sack, Rainer Fischer, Maria A. Miteva, Jan Rosing, Gerry A. F. Nicolaes, and Bruno O. Villoutreix PMCID: PMC1937529 Phage escape libraries for checkmate analysis Tobin J. Dickerson, Kathleen M. McKenzie, Amanda S. Hoyt, Malcolm R. Wood, Kim D. Janda, Sydney B. Brenner, and Richard A. Lerner PMCID: PMC1937530 From the Cover:
Protein roadblocks and helix discontinuities are barriers to the initiation of mismatch repair Anna Pluciennik and Paul Modrich PMCID: PMC1913546 A closer look at energy transduction in muscle Hirofumi Onishi and Manuel F. Morales PMCID: PMC1924791 Reevaluating the relationship between EPR spectra and enzyme structure for the iron–sulfur clusters in NADH:quinone oxidoreductase Gregory Yakovlev, Torsten Reda, and Judy Hirst PMCID: PMC1925037 Biophysics Principal-components analysis of shape fluctuations of single DNA molecules Adam E. Cohen and W. E. Moerner PMCID: PMC1937516 Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic “fingerprinting” Shixin Liu, Gregory Bokinsky, Nils G. Walter, and Xiaowei Zhuang PMCID: PMC1937518 Single-molecule FRET reveals sugar-induced conformational dynamics in LacY Devdoot S. Majumdar, Irina Smirnova, Vladimir Kasho, Eyal Nir, Xiangxu Kong, Shimon Weiss, and H. Ronald Kaback PMCID: PMC1937519 Fueling protein–DNA interactions inside porous nanocontainers Ibrahim Cisse, Burak Okumus, Chirlmin Joo, and Taekjip Ha PMCID: PMC1937520 Probing nucleation, reverse annealing, and chaperone function along the reaction path of HIV-1 single-strand transfer Yining Zeng, Hsiao-Wei Liu, Christy F. Landes, Yoen Joo Kim, Xiaojing Ma, Yongjin Zhu, Karin Musier-Forsyth, and Paul F. Barbara PMCID: PMC1937521 Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity Q. K. Beg, A. Vazquez, J. Ernst, M. A. de Menezes, Z. Bar-Joseph, A.-L. Barabási, and Z. N. Oltvai PMCID: PMC1937523 Combinatorial promoter design for engineering noisy gene expression Kevin F. Murphy, Gábor Balázsi, and James J. Collins PMCID: PMC1931564 Quantitative characterization of cell synchronization in yeast Sune Danø, Mads Find Madsen, and Preben Graae Sørensen PMCID: PMC1937535 An unusual cytokine:Ig-domain interaction revealed in the crystal structure of leukemia inhibitory factor (LIF) in complex with the LIF receptor Trevor Huyton, Jian-Guo Zhang, Cindy S. Luo, Mei-Zhen Lou, Douglas J. Hilton, Nicos A. Nicola, and Thomas P. J. Garrett PMCID: PMC1937536 Reversibility in nucleocytoplasmic transport Ronen Benjamine Kopito and Michael Elbaum PMCID: PMC1937537 Energy transport in peptide helices Virgiliu Botan, Ellen H. G. Backus, Rolf Pfister, Alessandro Moretto, Marco Crisma, Claudio Toniolo, Phuong H. Nguyen, Gerhard Stock, and Peter Hamm PMCID: PMC1937538 Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping Neal Crampton, Masatoshi Yokokawa, David T. F. Dryden, J. Michael Edwardson, Desirazu N. Rao, Kunio Takeyasu, Shige H. Yoshimura, and Robert M. Henderson PMCID: PMC1937539 Identification of a chloride ion binding site in Na+/Cl−-dependent transporters Lucy R. Forrest, Sotiria Tavoulari, Yuan-Wei Zhang, Gary Rudnick, and Barry Honig PMCID: PMC1937540 15N photochemically induced dynamic nuclear polarization magic-angle spinning NMR analysis of the electron donor of photosystem II Anna Diller, Esha Roy, Peter Gast, Hans J. van Gorkom, Huub J. M. de Groot, Clemens Glaubitz, Gunnar Jeschke, Jörg Matysik, and A. Alia PMCID: PMC1937541 Design of helical, oligomeric HIV-1 fusion inhibitor peptides with potent activity against enfuvirtide-resistant virus John J. Dwyer, Karen L. Wilson, Donna K. Davison, Stephanie A. Freel, Jennifer E. Seedorff, Stephen A. Wring, Nicolai A. Tvermoes, Thomas J. Matthews, Michael L. Greenberg, and Mary K. Delmedico PMCID: PMC1937542 Cell Biology RPA and ATR link transcriptional stress to p53 Frederick A. Derheimer, Heather M. O'Hagan, Heather M. Krueger, Sheela Hanasoge, Michelle T. Paulsen, and Mats Ljungman PMCID: PMC1937543 Protein 4.1B suppresses prostate cancer progression and metastasis Sunny Y. Wong, Herbert Haack, Joseph L. Kissil, Marc Barry, Roderick T. Bronson, Steven S. Shen, Charles A. Whittaker, Denise Crowley, and Richard O. Hynes PMCID: PMC1924789 Elevated NF-κB responses and FLIP levels in leukemic but not normal lymphocytes: reduction by salicylate allows TNF-induced apoptosis Colin Rae, Susana Langa, Steven J. Tucker, and David J. MacEwan PMCID: PMC1937545 Developmental Biology Metabolic plasticity during mammalian development is directionally dependent on early nutritional status Peter D. Gluckman, Karen A. Lillycrop, Mark H. Vickers, Anthony B. Pleasants, Emma S. Phillips, Alan S. Beedle, Graham C. Burdge, and Mark A. Hanson PMCID: PMC1937546 Evolution Coevolution of robustness, epistasis, and recombination favors asexual reproduction Thomas MacCarthy and Aviv Bergman PMCID: PMC1931480 Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function Radek Szklarczyk, Jaap Heringa, Sergei Kosakovsky Pond, and Anton Nekrutenko PMCID: PMC1937548 Genetics Identification of a locus control region for quadruplicated green-sensitive opsin genes in zebrafish Taro Tsujimura, Akito Chinen, and Shoji Kawamura PMCID: PMC1937549 High-resolution analysis of Drosophila heterochromatin organization using SuUR Su(var)3-9 double mutants Eugenia N. Andreyeva, Tatyana D. Kolesnikova, Olga V. Demakova, Maria Mendez-Lago, Galina V. Pokholkova, Elena S. Belyaeva, Fabrizio Rossi, Patrizio Dimitri, Alfredo Villasante, and Igor F. Zhimulev PMCID: PMC1937550 Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789 Wu Wei, John H. McCusker, Richard W. Hyman, Ted Jones, Ye Ning, Zhiwei Cao, Zhenglong Gu, Dan Bruno, Molly Miranda, Michelle Nguyen, Julie Wilhelmy, Caridad Komp, Raquel Tamse, Xiaojing Wang, Peilin Jia, Philippe Luedi, Peter J. Oefner, Lior David, Fred S. Dietrich, Yixue Li, Ronald W. Davis, and Lars M. Steinmetz PMCID: PMC1933262 A unified genetic theory for sporadic and inherited autism Xiaoyue Zhao, Anthony Leotta, Vlad Kustanovich, Clara Lajonchere, Daniel H. Geschwind, Kiely Law, Paul Law, Shanping Qiu, Catherine Lord, Jonathan Sebat, Kenny Ye, and Michael Wigler PMCID: PMC1933261 Immunology Vaccination with an NY-ESO-1 peptide of HLA class I/II specificities induces integrated humoral and T cell responses in ovarian cancer Kunle Odunsi, Feng Qian, Junko Matsuzaki, Paulette Mhawech-Fauceglia, Christopher Andrews, Eric W. Hoffman, Linda Pan, Gerd Ritter, Jeannine Villella, Bridget Thomas, Kerry Rodabaugh, Shashikant Lele, Protul Shrikant, Lloyd J. Old, and Sacha Gnjatic PMCID: PMC1937553 From the Cover:
TNF-α suppresses the expression of clock genes by interfering with E-box-mediated transcription Gionata Cavadini, Saskia Petrzilka, Philipp Kohler, Corinne Jud, Irene Tobler, Thomas Birchler, and Adriano Fontana PMCID: PMC1937554 Innate immunity and transcription of MGAT-III and Toll-like receptors in Alzheimer's disease patients are improved by bisdemethoxycurcumin Milan Fiala, Philip T. Liu, Araceli Espinosa-Jeffrey, Mark J. Rosenthal, George Bernard, John M. Ringman, James Sayre, Laura Zhang, Justin Zaghi, Sheila Dejbakhsh, Ben Chiang, James Hui, Michelle Mahanian, Anita Baghaee, Pamela Hong, and John Cashman PMCID: PMC1937555 Medical Sciences INAUGURAL ARTICLE by a Recently Elected Academy Member: The role of skeletal muscle insulin resistance in the pathogenesis of the metabolic syndrome Kitt Falk Petersen, Sylvie Dufour, David B. Savage, Stefan Bilz, Gina Solomon, Shin Yonemitsu, Gary W. Cline, Douglas Befroy, Laura Zemany, Barbara B. Kahn, Xenophon Papademetris, Douglas L. Rothman, and Gerald I. Shulman PMCID: PMC1924794 Feedback activation of factor XI by thrombin does not occur in plasma Donna L. Pedicord, Dietmar Seiffert, and Yuval Blat PMCID: PMC1937556 Fasting-dependent glucose and lipid metabolic response through hepatic sirtuin 1 Joseph T. Rodgers and Pere Puigserver PMCID: PMC1937557 Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma Paul H. Huang, Akitake Mukasa, Rudy Bonavia, Ryan A. Flynn, Zachary E. Brewer, Webster K. Cavenee, Frank B. Furnari, and Forest M. White PMCID: PMC1937558 Epinephrine enhances lysosomal enzyme delivery across the blood–brain barrier by up-regulation of the mannose 6-phosphate receptor Akihiko Urayama, Jeffrey H. Grubb, William A. Banks, and William S. Sly PMCID: PMC1937559 Attenuated Salmonella engineered to produce human cytokine LIGHT inhibit tumor growth Markus Loeffler, Gaelle Le'Negrate, Maryla Krajewska, and John C. Reed PMCID: PMC1937560 Cellular cofactors affecting hepatitis C virus infection and replication Glenn Randall, Maryline Panis, Jacob D. Cooper, Timothy L. Tellinghuisen, Karen E. Sukhodolets, Sebastien Pfeffer, Markus Landthaler, Pablo Landgraf, Sherry Kan, Brett D. Lindenbach, Minchen Chien, David B. Weir, James J. Russo, Jingyue Ju, Michael J. Brownstein, Robert Sheridan, Chris Sander, Mihaela Zavolan, Thomas Tuschl, and Charles M. Rice PMCID: PMC1937561 Transcriptional network governing the angiogenic switch in human pancreatic cancer Amir Abdollahi, Christian Schwager, Jörg Kleeff, Irene Esposito, Sophie Domhan, Peter Peschke, Kai Hauser, Philip Hahnfeldt, Lynn Hlatky, Jürgen Debus, Jeffrey M. Peters, Helmut Friess, Judah Folkman, and Peter E. Huber PMCID: PMC1931565 Microbiology ppGpp regulation of RpoS degradation via anti-adaptor protein IraP Alexandre Bougdour and Susan Gottesman PMCID: PMC1937563 Evidence that RNA silencing functions as an antiviral defense mechanism in fungi Gert C. Segers, Xuemin Zhang, Fuyou Deng, Qihong Sun, and Donald L. Nuss PMCID: PMC1937564 Clonal success of piliated penicillin nonsusceptible pneumococci K. Sjöström, C. Blomberg, J. Fernebro, J. Dagerhamn, E. Morfeldt, M. A. Barocchi, S. Browall, M. Moschioni, M. Andersson, F. Henriques, B. Albiger, Rino Rappuoli, S. Normark, and B. Henriques-Normark PMCID: PMC1929012 Neuroscience Visuomotor system uses target features unavailable to conscious awareness Gordon Binsted, Kyle Brownell, Zofia Vorontsova, Matthew Heath, and Deborah Saucier PMCID: PMC1937524 Sumoylation in axons triggers retrograde transport of the RNA-binding protein La Erna A. van Niekerk, Dianna E. Willis, Jay H. Chang, Kerstin Reumann, Tilman Heise, and Jeffery L. Twiss PMCID: PMC1937566 Smad-interacting protein-1 (Zfhx1b) acts upstream of Wnt signaling in the mouse hippocampus and controls its formation Amaya Miquelajauregui, Tom Van de Putte, Alexander Polyakov, Anjana Nityanandam, Sridhar Boppana, Eve Seuntjens, Anton Karabinos, Yujiro Higashi, Danny Huylebroeck, and Victor Tarabykin PMCID: PMC1929013 Silencing of genes in cultured Drosophila neurons by RNA interference Shail K. Sharma and Marshall Nirenberg PMCID: PMC1937568 General design principle for scalable neural circuits in a vertebrate retina Sunhwa Lee and Charles F. Stevens PMCID: PMC1931479 Pharmacology Voluntary exercise together with oral caffeine markedly stimulates UVB light-induced apoptosis and decreases tissue fat in SKH-1 mice Yao-Ping Lu, Bonnie Nolan, You-Rong Lou, Qing-Yun Peng, George C. Wagner, and Allan H. Conney PMCID: PMC1937570 Sustainability Science From the Cover:
Quantifying and mapping the human appropriation of net primary production in earth's terrestrial ecosystems Helmut Haberl, K. Heinz Erb, Fridolin Krausmann, Veronika Gaube, Alberte Bondeau, Christoph Plutzar, Simone Gingrich, Wolfgang Lucht, and Marina Fischer-Kowalski PMCID: PMC1911196 Invasive range expansion by the Humboldt squid, Dosidicus gigas, in the eastern North Pacific Louis D. Zeidberg and Bruce H. Robison PMCID: PMC1937572 Social Sciences Psychology Visuomotor system uses target features unavailable to conscious awareness Gordon Binsted, Kyle Brownell, Zofia Vorontsova, Matthew Heath, and Deborah Saucier PMCID: PMC1937524 |
