July 17, 2007 ͉ vol. 104 ͉ no. 29 ͉ 11863–12228 Proceedings of the National Academy ofPNAS Sciences of the United States of America www.pnas.org Cover image: Methane-oxidizing bacteria (Methylosinus trichosporium OB3b) cluster on copper- doped glass. Methanotrophic bacteria suppress methane, a major greenhouse gas. Expression of the bacterial enzyme methane monooxygenase is regulated by copper. Solid-phase copper geochemistry determines whether the metal is available for use. See the article by Knapp et al. on pages 12040–12045. Image courtesy of Ezra Kulczycki. From the Cover 12040 Copper geochemistry and methanotrophs 11901 Fabricating complex nanoparticles 11957 Fast dynamics of supercoiled DNA 12151 Inhibiting a TB virulence factor 12175 Stem cells reduce primate Parkinson’s symptoms Contents INAUGURAL ARTICLES 11874 Late Pleistocene and Holocene environmental history of the Iguala Valley, Central Balsas Watershed of Mexico THIS WEEK IN PNAS D. R. Piperno, J. E. Moreno, J. Iriarte, I. Holst, M. Lachniet, J. G. Jones, A. J. Ranere, and R. Castanzo ➜ 11863 In This Issue See Profile on page 11871 11882 A comparative analysis of frog early development Eugenia M. del Pino, Michael Venegas-Ferrı´n, Andre´s COMMENTARIES Romero-Carvajal, Paola Montenegro-Larrea, Natalia Sa´enz-Ponce, Iva´n M. Moya, Ingrid Alarco´n, Norihiro 11865 Developmental genomics of the most dangerous animal Sudou, Shinji Yamamoto, and Masanori Taira Matthew P. Scott ➜ See companion article on page 11304 in issue 27 PHYSICAL SCIENCES of volume 104 11867 Physiology versus pathology in Parkinson’s disease APPLIED PHYSICAL SCIENCES Ken Nakamura and Robert H. Edwards 11889 Dissecting biological ‘‘dark matter’’ with single-cell ➜ See companion article on page 11441 in issue 27 genetic analysis of rare and uncultivated TM7 of volume 104 microbes from the human mouth Yann Marcy, Cleber Ouverney, Elisabeth M. Bik, Tina 11869 Neural stem cells for Parkinson’s disease: To protect Lo¨sekann, Natalia Ivanova, Hector Garcia Martin, and repair Ernest Szeto, Darren Platt, Philip Hugenholtz, Paul R. Sanberg David A. Relman, and Stephen R. Quake ➜ See companion article on page 12175 CHEMISTRY PROFILE 11895 Electrochemical attosyringe Franc¸ois O. Laforge, James Carpino, Susan A. Rotenberg, and Michael V. Mirkin 11871 Profile of Dolores R. Piperno Tinsley H. Davis ENGINEERING ➜ See Inaugural Article on page 11874 11901 Making polymeric micro- and nanoparticles of complex shapes Julie A. Champion, Yogesh K. Katare, Freely available online through the PNAS open access option. and Samir Mitragotri PNAS ͉ July 17, 2007 ͉ vol. 104 ͉ no. 29 ͉ iii–vi Downloaded by guest on September 30, 2021 12169 Retinotopic mapping of adult human visual cortex 11951 Directed evolution can rapidly improve the activity with high-density diffuse optical tomography of chimeric assembly-line enzymes Benjamin W. Zeff, Brian R. White, Hamid Dehghani, Michael A. Fischbach, Jonathan R. Lai, Eric D. Bradley L. Schlaggar, and Joseph P. Culver Roche, Christopher T. Walsh, and David R. Liu SOCIAL SCIENCES BIOPHYSICS 11957 Fast dynamics of supercoiled DNA revealed by single-molecule experiments ANTHROPOLOGY Aure´lienCrut, Daniel A. Koster, Ralf Seidel, 11874 Late Pleistocene and Holocene environmental history of Chris H. Wiggins, and Nynke H. Dekker the Iguala Valley, Central Balsas Watershed of Mexico D. R. Piperno, J. E. Moreno, J. Iriarte, I. Holst, M. Lachniet, 11963 The design and characterization of two proteins with J. G. Jones, A. J. Ranere, and R. Castanzo 88% sequence identity but different structure ➜ See Profile on page 11871 and function Patrick A. Alexander, Yanan He, Yihong Chen, 11905 Precolumbian use of chili peppers in the Valley John Orban, and Philip N. Bryan of Oaxaca, Mexico 11969 Identifying important structural characteristics of arsenic Linda Perry and Kent V. Flannery resistance proteins by using designed three-stranded coiled coils BIOLOGICAL SCIENCES Debra S. Touw, Christer E. Nordman, Jeanne A. Stuckey, and Vincent L. Pecoraro ANTHROPOLOGY 11975 Substrate-dependent transmembrane signaling 11910 Congruence of molecules and morphology using in TonB-dependent transporters is not conserved a narrow allometric approach Miyeon Kim, Gail E. Fanucci, and David S. Cafiso Christopher C. Gilbert and James B. Rossie 11981 The mechanism of rate-limiting motions in enzyme function APPLIED BIOLOGICAL SCIENCES Eric D. Watt, Hiroko Shimada, Evgenii L. 11915 Antithrombogenic property of bone marrow Kovrigin, and J. Patrick Loria mesenchymal stem cells in nanofibrous vascular grafts 11987 Protein folding by zipping and assembly Craig K. Hashi, Yiqian Zhu, Guo-Yuan Yang, S. Banu Ozkan, G. Albert Wu, John D. William L. Young, Benjamin S. Hsiao, Karin Chodera, and Ken A. Dill Wang, Benjamin Chu, and Song Li 11993 Observation of sequential steps in the folding of intestinal fatty acid binding protein using BIOCHEMISTRY a slow folding mutant and 19F NMR 11921 Hot spots in prion protein for pathogenic conversion Hua Li and Carl Frieden Kazuo Kuwata, Noriyuki Nishida, Tomoharu Matsumoto, Yuji O. Kamatari, Junji Hosokawa-Muto, Kota Kodama, CELL BIOLOGY Hironori K. Nakamura, Kiminori Kimura, Makoto ⌬ Kawasaki, Yuka Takakura, Susumu Shirabe, Jiro 11999 Np63 regulates thymic development through enhanced Takata, Yasufumi Kataoka, and Shigeru Katamine expression of FgfR2 and Jag2 Eleonora Candi, Alessandro Rufini, Alessandro Terrinoni, 11927 Discovery of antiandrogen activity of nonsteroidal Alessandro Giamboi-Miraglia, Anna Maria Lena, Roberto scaffolds of marketed drugs Mantovani, Richard Knight, and Gerry Melino W. H. Bisson, A. V. Cheltsov, N. Bruey-Sedano, B. Lin, 12005 Essential role for MFG-E8 as ligand for ␣v␤5 integrin J. Chen, N. Goldberger, L. T. May, A. Christopoulos, in diurnal retinal phagocytosis J. T. Dalton, P. M. Sexton, X.-K. Zhang, and R. Abagyan Emeline F. Nandrot, Monika Anand, Dena Almeida, Kamran Atabai, Dean Sheppard, and Silvia C. Finnemann 11933 Src phosphorylation of cortactin enhances actin assembly Shandiz Tehrani, Nenad Tomasevic, Scott Weed, 12011 Functional specialization of ␤-arrestin interactions Roman Sakowicz, and John A. Cooper revealed by proteomic analysis Kunhong Xiao, Daniel B. McClatchy, Arun K. Shukla, 11939 Structural consequences of disease-causing mutations Yang Zhao, Minyong Chen, Sudha K. Shenoy, in the ATRX-DNMT3-DNMT3L (ADD) domain John R. Yates III, and Robert J. Lefkowitz of the chromatin-associated protein ATRX Anthony Argentaro, Ji-Chun Yang, Lynda Chapman, 12017 AMP-activated protein kinase (AMPK) action in skeletal Monika S. Kowalczyk, Richard J. Gibbons, Douglas R. muscle via direct phosphorylation of PGC-1␣ Higgs, David Neuhaus, and Daniela Rhodes Sibylle Ja¨ger, Christoph Handschin, Julie St.-Pierre, and Bruce M. Spiegelman 11945 Packing contacts can mediate highly specific interactions between artificial transmembrane proteins 12023 Otopetrin 1 activation by purinergic nucleotides and the PDGF␤ receptor regulates intracellular calcium Jennifer B. Ptacek, Anne P. B. Edwards, Inna Hughes, Mitsuyoshi Saito, Paul H. Schlesinger, Lisa L. Freeman-Cook, and Daniel DiMaio and David M. Ornitz iv ͉ www.pnas.org Downloaded by guest on September 30, 2021 DEVELOPMENTAL BIOLOGY 12081 Natural killer cells actively patrol peripheral lymph 11882 A comparative analysis of frog early development nodes forming stable conjugates to eliminate MHC-mismatched targets Eugenia M. del Pino, Michael Venegas-Ferrı´n, Andre´s Romero-Carvajal, Paola Montenegro-Larrea, Natalia Kym R. Garrod, Sindy H. Wei, Ian Parker, Sa´enz-Ponce, Iva´n M. Moya, Ingrid Alarco´n, Norihiro and Michael D. Cahalan ؉ Sudou, Shinji Yamamoto, and Masanori Taira 12087 Association of cervical cancer with the presence of CD4 regulatory T cells specific for human 12029 Vertebrate Ctr1 coordinates morphogenesis and papillomavirus antigens progenitor cell fate and regulates embryonic Sjoerd H. van der Burg, Sytse J. Piersma, Annemieke de Jong, stem cell differentiation Jeanette M. van der Hulst, Kitty M. C. Kwappenberg, Muriel Tomomi Haremaki, Stuart T. Fraser, Yien-Ming Kuo, van den Hende, Marij J. P. Welters, Jon J. Van Rood, Margaret H. Baron, and Daniel C. Weinstein Gert Jan Fleuren, Cornelis J. M. Melief, Gemma G. Kenter, and Rienk Offringa ENVIRONMENTAL SCIENCES 12093 Peripheral deletion of mature alloreactive B cells induced by costimulation blockade 11874 Late Pleistocene and Holocene environmental history of Yijin Li, Lianli Ma, Jikun Shen, and Anita S. Chong the Iguala Valley, Central Balsas Watershed of Mexico D. R. Piperno, J. E. Moreno, J. Iriarte, I. Holst, M. Lachniet, 12099 IL-6-dependent and -independent pathways in the J. G. Jones, A. J. Ranere, and R. Castanzo development of interleukin 17-producing T helper cells ➜ See Profile on page 11871 Akihiro Kimura, Tetsuji Naka, and Tadamitsu Kishimoto 12105 Akt1 and Akt2 are required for ␣␤ thymocyte survival 12035 Hurricanes benefit bleached corals and differentiation Derek P. Manzello, Marilyn Brandt, Tyler B. Smith, Diego Marisa M. Juntilla, Jessica A. Wofford, Morris J. Birnbaum, Lirman, James C. Hendee, and Richard S. Nemeth Jeffrey C. Rathmell, and Gary A. Koretzky 12040 Methane monooxygenase gene expression mediated MEDICAL SCIENCES by methanobactin in the presence of mineral copper sources 12111 Somatic loss of BRCA1 and p53 in mice induces Charles W. Knapp, David A. Fowle, Ezra Kulczycki, mammary tumors with features of human Jennifer A. Roberts, and David W. Graham BRCA1-mutated basal-like breast cancer Xiaoling Liu, Henne Holstege, Hanneke