Supplemental Data

22 December

Millennial-Scale Dynamics of Southern Amazonian Rain Forests Francis E. Mayle, Rachel Burbridge, and Timothy J. Killeen Supplementary Information

Transmembrane Molecular Pump Activity of Niemann-Pick C1 Protein Joanna P. Davies, Fannie W. Chen, and Yiannis A. Ioannou Supplementary Information

Evidence for Genetic Linkage of Alzheimer's Disease to Chromosome 10q Lars Bertram, Deborah Blacker, Kristina Mullin, Devon Keeney, Jennifer Jones, Sanjay Basu, Stephen Yhu, Melvin G. McInnis, Rodney C. P. Go, Konstantinos Vekrellis, Dennis J. Selkoe, Aleister J. Saunders, and Rudolph E. Tanzi Supplementary Information

Linkage of Plasma Ab42 to a Quantitative Locus on Chromosome 10 in Late-Onset Alzheimer's Disease Pedigrees Nilufer Ertekin-Taner, Neill Graff-Radford, Linda H. Younkin, Christopher Eckman, Matthew Baker, Jennifer Adamson, James Ronald, John Blangero, Michael Hutton, and Steven G. Younkin Supplementary Information

Susceptibility Locus for Alzheimer's Disease on Chromosome 10 Amanda Myers, Peter Holmans, Helen Marshall, Jennifer Kwon, David Meyer, Dzanan Ramic, Shantia Shears, Jeremy Booth, Fabienne Wavrant DeVrieze, Richard Crook, Marian Hamshere, Richard Abraham, Nigel Tunstall, Francis Rice, Stephanie Carty, Sara Lillystone, Pat Kehoe, Varuni Rudrasingham, Lesley Jones, Simon Lovestone, Jordi Perez-Tur, Julie Williams, Michael J. Owen, John Hardy, and Alison M. Goate Supplementary Information

Genome-Wide Location and Function of DNA Binding Proteins Bing Ren, François Robert, John J. Wyrick, Oscar Aparicio, Ezra G. Jennings, Itamar Simon, Julia Zeitlinger, Jörg Schreiber, Nancy Hannett, Elenita Kanin, Thomas L. Volkert, Christopher J. Wilson, Stephen P. Bell, and Richard A. Young Supplementary Information

Distinct Roles for TBP and TBP-Like Factor in Early Embryonic Gene Transcription in Xenopus Gert Jan C. Veenstra, Daniel L. Weeks, and Alan P. Wolffe Supplementary Information

A Global Geometric Framework for Nonlinear Dimensionality Reduction Joshua B. Tenenbaum, Vin de Silva, and John C. Langford Supplementary Information

15 December

Arabidopsis Transcription Factors: Genome-Wide Comparative Analysis Among Eukaryotes J. L. Riechmann, J. Heard, G. Martin, L. Reuber, C. -Z., Jiang, J. Keddie, L. Adam, O. Pineda, O. J. Ratcliffe, R. R. Samaha, R. Creelman, M. Pilgrim, P. Broun, J. Z. Zhang, D. Ghandehari, B. K. Sherman, and G. -L. Yu Supplementary Information

Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock Stacey L. Harmer, John B. Hogenesch, Marty Straume, Hur-Song Chang, Bin Han, Tong Zhu, Xun Wang, Joel A. Kreps, and Steve A. Kay Supplementary Information

Molybdenum Nanowires by Electrodeposition Michael P. Zach, Kwok H. Ng, and Reginald M. Penner Supplementary Information

Creating Long-Lived Superhydrophobic Polymer Surfaces Through Mechanically Assembled Monolayers Jan Genzer and Kirill Efimenko Supplementary Information

Docosahexaenoic Acid, a Ligand for the Retinoid X Receptor in Mouse Brain Alexander Mata de Urquiza, Suya Liu, Maria Sjöberg, Rolf H. Zetterström, William Griffiths, Jan Sjövall, and Perlmann Supplementary Information

Global Analysis of the Genetic Network Controlling a Bacterial Cell Cycle Michael T. Laub, Harley H. McAdams, Tamara Feldblyum, Claire M. Fraser, and Lucy Shapiro Supplementary Information

The Bacterial Flagellar Cap as the Rotary Promoter of Flagellin Self-Assembly Koji Yonekura, Saori Maki, David Gene Morgan, David J. DeRosier, Ferenc Vonderviszt, Katsumi Imada, and Keiichi Namba Supplementary Information

Development of CD8- a Positive Dendritic Cells from a Common Myeloid Progenitor David Traver, Koichi Akashi, Markus Manz, Miriam Merad, Toshihiro Miyamoto, Edgar G. Engleman, and L. Weissman Supplementary Information

Functional Requirement for Class I MHC in CNS Development and Plasticity Gene S. Huh, Lisa M. Boulanger, Hongping Du, Patricio A. Riquelme, Tilmann M. Brotz, and Carla J. Shatz Supplementary Information

8 December

Planar Hexacoordinate Carbon: A Viable Possibility Kai Exner and Paul von Ragué Schleyer Supplementary Information

Synchronous Radiocarbon and Climate Shifts During the Last Deglaciation Konrad A. Hughen, John R. Southon, Scott J. Lehman, and Jonathan T. Overpeck Supplementary Information

A Primitive Enantiornithine Bird and the Origin of Feathers Fucheng Zhang and Zhonghe Zhou Supplementary Information

Identification of Synergistic Signals Initiating Inner Ear Development Raj K. Ladher, Kelly U. Anakwe, Austin L. Gurney, Gary C. Schoenwolf, and Philippa H. Francis-West Supplementary Information

Multigenerational Cortical Inheritance of the Rax2 Protein in Orienting Polarity and Division in Yeast Tracy Chen, Takatoshi Hiroko, Amitabha Chaudhuri, Fumika Inose, Matthew Lord, Shigeko Tanaka, John Chant, and Atsushi Fujita Supplementary Information

Rescue of Photoreceptor Degeneration in Rhodopsin-Null Drosophila Mutants by Activated Rac1 Hui-Yun Chang and Donald F. Ready Supplementary Information

1 December

Scientific Whaling: Source of Illegal Products for Market? C. Scott Baker, G. M. Lento, F. Cipriano, M. L. Dalebout, S. R. Palumbi;, Mutsuo Goto, and Seiji Ohsumi Supplementary Information

Formation of Sphalerite (ZnS) Deposits in Natural Biofilms of Sulfate-Reducing Bacteria Matthias Labrenz, Gregory K. Druschel, Tamara Thomsen-Ebert, Benjamin Gilbert, Susan A. Welch, Kenneth M. Kemner, Graham A. Logan, Roger E. Summons, Gelsomina De Stasio, Philip L. Bond, Barry Lai, Shelly D. Kelly, and Jillian F. Banfield Supplementary Information

Tropical Climate at the Last Glacial Maximum Inferred from Glacier Mass-Balance Modeling Steven W. Hostetler and Peter U. Clark Supplementary Information

Support for the Lunar Cataclysm Hypothesis from Lunar Meteorite Impact Melt Ages B. A. Cohen, T. D. Swindle, and D. A. Kring Supplementary Information

Reinterpreting Space, Time Lags, and Functional Responses in Ecological Models Matt J. Keeling, Howard B. Wilson, and Steve W. Pacala Supplementary Information

Requirement of the RNA Editing Deaminase ADAR1 Gene for Embryonic Erythropoiesis Q. Wang, J. Khillan, P. Gadue, and K. Nishikura Supplementary Information

Requirement of the RNA Editing Deaminase ADAR1 Gene for Embryonic Erythropoiesis Q. Wang, J. Khillan, P. Gadue, and K. Nishikura Supplementary Information

Down-Regulation of the Macrophage Lineage Through Interaction with OX2 (CD200) Robert M. Hoek, Sigrid R. Ruuls, Craig A. Murphy, Gavin J. Wright, Ruth Goddard, Sandra M. Zurawski, Bianca Blom, Margit E. Homola, Wolfgang J. Streit, Marion H. Brown, A. Neil Barclay, and Jonathon D. Sedgwick Supplementary Information

From Marrow to Brain: Expression of Neuronal Phenotypes in Adult Mice Timothy R. Brazelton, Fabio M. V. Rossi, Gilmor I. Keshet, and Helen M. Blau Supplementary Information

Turning Blood into Brain: Cells Bearing Neuronal Antigens Generated in Vivo from Bone Marrow Éva Mezey, Karen J. Chandross, Gyöngyi Harta, Richard A. Maki, and Scott R. McKercher Supplementary Information

24 November

Mechanisms of Ordering in Striped Patterns Christopher Harrison, Douglas H. Adamson, Zhengdong Cheng, John M. Sebastian, Srinivasan Sethuraman, David A. Huse, Richard A. Register, and P. M. Chaikin Supplementary Information

Alloying at Surfaces by the Migration of Reactive Two-Dimensional Islands A. K. Schmid, N. C. Bartelt, and R. Q. Hwang Supplementary Information

High Shear Strain of Olivine Aggregates: Rheological and Seismic Consequences M. Bystricky, K. Kunze, L. Burlini, and J. -P. Burg Supplementary Information

Quantitative Imaging of Lateral ErbB1 Receptor Signal Propagation in the Plasma Membrane Peter J. Verveer, Fred S. Wouters, Andrew R. Reynolds, and Philippe I. H. Bastiaens Supplementary Information

Biochemical Basis of Oxidative Protein Folding in the Endoplasmic Reticulum Benjamin P. Tu, Siew C. Ho-Schleyer, Kevin J. Travers, and Jonathan S. Weissman Supplementary Information

b-Arrestin 2: A Receptor-Regulated MAPK Scaffold for the Activation of JNK3 Patricia H. McDonald, Chi-Wing Chow, William E. Miller, Stéphane A. Laporte, Michael E. Field, Fang-Tsyr Lin, Roger J. Davis, and Robert J. Lefkowitz Supplementary Information

"Fluorescent Timer": Protein That Changes Color with Time Alexey Terskikh, Arkady Fradkov, Galina Ermakova, Andrey Zaraisky, Patrick Tan, Andrey V. Kajava, Xiaoning Zhao, Sergey Lukyanov, Mikhail Matz, Stuart Kim, Irving Weissman, and Paul Siebert Supplementary Information

17 November

Early Development of Ocular Dominance Columns Justin C. Crowley and Lawrence C. Katz Supplementary Information

Regional Changes in Carbon Dioxide Fluxes of Land and Oceans Since 1980 Philippe Bousquet, Philippe Peylin, Philippe Ciais, Corinne Le Quéré, Pierre Friedlingstein, and Pieter P. Tans Supplementary Information

Protection Against Cutaneous Leishmaniasis Resulting from Bites of Uninfected Sand Flies Shaden Kamhawi, Yasmine Belkaid, Govind Modi, Edgar Rowton, and David Sacks Supplementary Information

Regulation of Antigen-Specific CD8+ T Cell Homeostasis by Perforin and Interferon- g Vladimir P. Badovinac, Amy R. Tvinnereim, and John T. Harty Supplementary Information

PSD-95 Involvement in Maturation of Excitatory Synapses Alaa El-Din El-Husseini, Eric Schnell, Dane M. Chetkovich, Roger A. Nicoll, and David S. Bredt Supplementary Information

Intracellular Parasitism by Histoplasma capsulatum: Fungal Virulence and Calcium Dependence Tricia Schurtz Sebghati, Jacquelyn T. Engle, and William E. Goldman Supplementary Information

10 November

Allosteric Effects of Pit-1 DNA Sites on Long-Term Repression in Cell Type Specification Kathleen M. Scully, Eric M. Jacobson, Kristen Jepsen, Victoria Lunyak, Hector Viadiu, Catherine Carrière, David W. Rose, Farideh Hooshmand, Aneel K. Aggarwal, and Michael G. Rosenfeld Supplementary Information

African Hot Spot Volcanism: Small-Scale Convection in the Upper Mantle Beneath Cratons Scott D. King and and Jeroen Ritsema Supplementary Information

Direct Condensation of Carboxylic Acids with Alcohols Catalyzed by Hafnium(IV) Salts Kazuaki Ishihara, Suguru Ohara, and Hisashi Yamamoto Supplementary Information

Solar Wind Record on the Moon: Deciphering Presolar from Planetary Nitrogen Ko Hashizume, Marc Chaussidon, Bernard Marty, and François Robert Supplementary Information

Contributions of Land-Use History to Carbon Accumulation in U.S. Forests John P. Caspersen, Stephen W. Pacala, Jennifer C. Jenkins, George C. Hurtt, Paul R. Moorcroft, and Richard A. Birdsey Supplementary Information

Transgene and Transposon Silencing in Chlamydomonas reinhardtii by a DEAH-Box RNA Helicase Dancia Wu-Scharf, Byeong-ryool Jeong, Chaomei Zhang, and Heriberto Cerutti Supplementary Information

Aureusidin Synthase: A Polyphenol Oxidase Homolog Responsible for Flower Coloration T. Nakayama, K. Yonekura-Sakakibara, T. Sato, S. Kikuchi, Y. Fukui, M. Fukuchi-Mizutani, T. Ueda, M. Nakao, Y. Tanaka, T. Kusumi, and T. Nishino Supplementary Information

NMDA Receptor-Dependent Synaptic Reinforcement as a Crucial Process for Memory Consolidation Eiji Shimizu, Ya-Ping Tang, Claire Rampon, and Joe Z. Tsien Supplementary Information

Survival for Immunity: The Price of Immune System Activation for Bumblebee Workers Yannick Moret and Paul Schmid-Hempel Supplementary Information

3 November

First-Principles Theory for the H + H2O, D2O Reactions Dong H. Zhang, Michael A. Collins, and Soo-Y. Lee Supplementary Information

Emissions of Methyl Halides and Methane from Rice Paddies K. R. Redeker, N.-Y. Wang, J. C. Low, A. McMillan, S. C. Tyler, and R. J. Cicerone Supplementary Information

A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, and W. F. Doolittle Supplementary Information

Recovery and Management Options for Spring/Summer Chinook Salmon in the Columbia River Basin Peter Kareiva, Michelle Marvier, and Michelle McClure Supplementary Information

A Basal Transcription Factor That Activates or Represses Transcription Patricia J. Willy, Ryuji Kobayashi, and James T. Kadonaga Supplementary Information

Oxidative Damage Linked to Neurodegeneration by Selective a-Synuclein Nitration in Synucleinopathy Lesions Benoit I. Giasson, John E. Duda, Ian V. J. Murray, Qiping Chen, and José Souza Supplementary Information

Role of Bacillus subtilis SpoIIIE in DNA Transport Across the Mother Cell-Prespore Division Septum Jonathan Bath, Ling Juan Wu, Jeffery Errington, and James C. Wang Supplementary Information

27 October

U.S. Priorities-HIV Prevention Joseph A. Catania, Stephen F. Morin, Jesse Canchola, Lance Pollack, Jason Chang, and Thomas J. Coates Supplementary Information

Neurodegeneration Prevented by Lentiviral Vector Delivery of GDNF in Primate Models of Parkinson's Disease Jeffrey H. Kordower, Marina E. Emborg, Jocelyne Bloch, Shuang Y. Ma, Yaping Chu, Liza Leventhal, Jodi McBride, Er-Yun Chen, Stéphane Palfi, Ben Zion Roitberg, W. Douglas Brown, James E. Holden, Robert Pyzalski, Michael D. Taylor, Paul Carvey, ZaoDung Ling, Didier Trono, Philippe Hantraye, Nicole Déglon, and Patrick Aebischer Supplementary Information

A Low Temperature Transfer of ALH84001 from Mars to Earth Benjamin P. Weiss, Joseph L. Kirschvink, Franz J. Baudenbacher, Hojatollah Vali, Nick T. Peters, Francis A. Macdonald, and John P. Wikswo Supplementary Information

Impacts of Climatic Change and Fishing on Pacific Salmon Abundance Over the Past 300 Years Bruce P. Finney, Irene Gregory-Eaves, Jon Sweetman, Marianne S. V. Douglas, and John P. Smol Supplementary Information

Integration of Multiple Signals Through Cooperative Regulation of the N-WASP-Arp2/3 Complex Kenneth E. Prehoda, Jessica Scott, R. , Mullins, and Wendell A. Lim Supplementary Information

Direct Coupling Between Meiotic DNA Replication and Recombination Initiation Valérie Borde, Alastair S. H. Goldman, and Michael Lichten Supplementary Information

Genomic Analysis of Gene Expression in C. elegans A. A. Hill, C. P. Hunter, B. T. Tsung, G. Tucker-Kellogg, and E. L. Brown Supplementary Information

Song Replay During Sleep and Computational Rules for Sensorimotor Vocal Learning Amish S. Dave and Daniel Margoliash Supplementary Information

20 October

Imaging Precessional Motion of the Magnetization Vector Y. Acremann, C. H. Back, M. Buess, O. Portmann, A. Vaterlaus, D. Pescia, and H. Melchior Supplementary Information

A Stable Bicyclic Compound with Two Si=Si Double Bonds Takeaki Iwamoto, Makoto Tamura, Chizuko Kabuto, and Mitsuo Kira Supplementary Information

Detection of Daily Clouds on Titan Caitlin A. Griffith, Joseph L. Hall, and Thomas R. Geballe Supplementary Information

CD95/CD95 Ligand Interactions on Epithelial Cells in Host Defense to Pseudomonas aeruginosa Heike Grassmé, Susanne Kirschnek, Joachim Riethmueller, Andrea Riehle, Gabriele von Kürthy, Florian Lang, Michael Weller, and Erich Gulbins Supplementary Information

13 October

Blue-Fluorescent Antibodies Anton Simeonov, Masayuki Matsushita, Eric A. Juban, Elizabeth H. Z. Thompson, Timothy Z. Hoffman, Albert E. Beuscher, Matthew J. , Peter , Wolfgang , James K. , Raymond C. , David P. , Peter G. , Richard A. , and Kim D. Supplementary Information

The Last Glacial-Holocene Transition in Southern Chile K. D. Bennett, S. G. Haberle, and S. H. Lumley Supplementary Information

A Niche Maintaining Germ Line Stem Cells in the Drosophila Ovary Ting Xie and Allan C. Spradling Supplementary Information

Deleterious Mutations and the Evolution of Sex Peter D. Keightley and and Adam Eyre-Walker Supplementary Information

A Myosin I Isoform in the Nucleus Lidija Pestic-Dragovich, Ljuba Stojiljkovic, Anatoly A. Philimonenko, Grzegorz Nowak, Yunbo Ke, Robert E. Settlage, Jeffrey Shabanowitz, Donald F. Hunt, Pavel Hozak, and Primal de Lanerolle Supplementary Information

Plasma Membrane Compartmentalization in Yeast by Messenger RNA Transport and a Septin Diffusion Barrier Peter A. Takizawa, Joseph L. DeRisi, James E. Wilhelm, and Ronald D. Vale Supplementary Information

Molecular Analysis of FRIGIDA , a Major Determinant of Natural Variation in Arabidopsis Flowering Time Urban Johanson, Joanne West, Clare Lister, Scott Michaels, Richard Amasino, Caroline Dean1 Supplementary Information

Selfish DNA in Protein-Coding Genes of Rickettsia Hiroyuki Ogata, Stéphane Audic, Valérie Barbe, François Artiguenave, Pierre-Edouard Fournier, Didier Raoult, and Jean-Michel Claverie Supplementary Information

Replaying the Game: Hypnagogic Images in Normals and Amnesics Robert Stickgold, April Malia, Denise Maguire, David Roddenberry, and Margaret O'Connor Supplementary Information

6 October

Islamic Women in Science Farkhonda Hassan Supplementary Information

Optically Defined Multifunctional Patterning of Photosensitive Thin-Film Silica Mesophases Dhaval A. Doshi, Nicola K. Huesing, Mengcheng Lu, Hongyou Fan, Yunfeng Lu, Kelly Simmons-Potter, B. G. Potter Jr., Alan J. Hurd, and C. Jeffrey Brinker Supplementary Information

Dynamically Controlled Protein Tunneling Paths in Photosynthetic Reaction Centers Ilya A. Balabin and José Onuchic Supplementary Information

Potent Analgesic Effects of GDNF in Neuropathic Pain States Timothy J. Boucher, Kenji Okuse, David L. H. Bennett, John B. Munson, John N. Wood, and Stephen B. Supplementary Information

Molecular and Neuronal Substrate for the Selective Attenuation of Anxiety Karin Löw, Florence Crestani, Ruth Keist, Dietmar Benke, Ina Brünig, Jack A. Benson, Jean-Marc Fritschy, Thomas Rülicke, Horst Bluethmann, Hanns Möhler, and Uwe Rudolph Supplementary Information

Function of GATA Transcription Factors in Preadipocyte-Adipocyte Transition Qiang Tong, Gökhan Dalgin, Haiyan Xu, Chao-Nan Ting, Jeffrey M. Leiden, and Gökhan S. Hotamisligil Supplementary Information

Regulation of C. elegans Life-Span by Insulinlike Signaling in the Nervous System Catherine A. Wolkow, Koutarou D. Kimura, Ming-Sum Lee, Gary Ruvkun Supplementary Information

Structure of the Protease Domain of Memapsin 2 (b-Secretase) Complexed with Inhibitor Lin Hong, Gerald Koelsch, Xinli Lin, Shili Wu, Simon Terzyan, Arun K. Ghosh, Xuenjun C. Zhang, and Jordan Tang Supplementary Information