| | This journal provides immediate access to some articles. This Week in PNAS Proc Natl Acad Sci U S A. 2006 December 5; 103(49): 18381–18382. doi: 10.1073/iti4906103.PMCID: PMC1693670 Commentaries Vesicle transport, cilium formation, and membrane specialization: The origins of a sensory organelle Jeremy F. Reiter and Keith Mostov PMCID: PMC1693671 Disequilibrium and association in barley: Thinking outside the glass Patrick Hayes and Péter Szu″cs PMCID: PMC1693672 Revealing the ghost in the machine: Using spectral analysis to understand the influence of noise on population dynamics Tim G. Benton PMCID: PMC1693673 Perspective From the Academy: Colloquium Perspective: Toward cropping systems that enhance productivity and sustainability R. James Cook PMCID: PMC1693674 Review From the Academy: Colloquium Review: Unique characteristics of Xanthomonas oryzae pv. oryzae AvrXa21 and implications for plant innate immunity Sang-Won Lee, Sang-Wook Han, Laura E. Bartley, and Pamela C. Ronald PMCID: PMC1693675 Physical Sciences Applied Mathematics Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem Douglas L. Theobald and Deborah S. Wuttke PMCID: PMC1664551 From the Cover:
Power spectra reveal the influence of stochasticity on nonlinear population dynamics Daniel C. Reuman, Robert A. Desharnais, Robert F. Costantino, Omar S. Ahmad, and Joel E. Cohen PMCID: PMC1693752 Applied Physical Sciences High-resolution in situ x-ray study of the hydrophobic gap at the water–octadecyl-trichlorosilane interface Markus Mezger, Harald Reichert, Sebastian Schöder, John Okasinski, Heiko Schröder, Helmut Dosch, Dennis Palms, John Ralston, and Veijo Honkimäki PMCID: PMC1654137 Using cryo-EM to measure the dipole potential of a lipid membrane Liguo Wang, Pulkit S. Bose, and Fred J. Sigworth PMCID: PMC1693696 Chemistry Multiple valence superatoms J. U. Reveles, S. N. Khanna, P. J. Roach, and A. W. Castleman, Jr. PMCID: PMC1693677 Photoinduced electron flow in a self-assembling supramolecular extension cable Belén Ferrer, Guillaume Rogez, Alberto Credi, Roberto Ballardini, Maria Teresa Gandolfi, Vincenzo Balzani, Yi Liu, Hsian-Rong Tseng, and J. Fraser Stoddart PMCID: PMC1693678 Effect of urea on the structural dynamics of water Y. L. A. Rezus and H. J. Bakker PMCID: PMC1693679 Engineering Quantifying the relation between adhesion ligand–receptor bond formation and cell phenotype Hyun Joon Kong, Tanyarut Boontheekul, and David J. Mooney PMCID: PMC1693697 Geophysics The dynamics behind Titan's methane clouds Jonathan L. Mitchell, Raymond T. Pierrehumbert, Dargan M. W. Frierson, and Rodrigo Caballero PMCID: PMC1693680 Physics From the Cover:
Four-dimensional ultrafast electron microscopy of phase transitions Michael S. Grinolds, Vladimir A. Lobastov, Jonas Weissenrieder, and Ahmed H. Zewail PMCID: PMC1693681 A driving and coupling “Pac-Man” mechanism for chromosome poleward translocation in anaphase A Jian Liu and José N. Onuchic PMCID: PMC1693682 Statistics Reconstructing repressor protein levels from expression of gene targets in Escherichia coli R. Khanin, V. Vinciotti, and E. Wit PMCID: PMC1693707 Biological Sciences Agricultural Sciences Colloquium Paper: Combinatorially selected defense peptides protect plant roots from pathogen infection Zhiwei David Fang, James G. Laskey, Shaoxing Huang, Kristin D. Bilyeu, Roy O. Morris, Francis J. Schmidt, and James T. English PMCID: PMC1693683 Colloquium Paper: The root endophytic fungus Piriformospora indica requires host cell death for proliferation during mutualistic symbiosis with barley Sachin Deshmukh, Ralph Hückelhoven, Patrick Schäfer, Jafargholi Imani, Monica Sharma, Michael Weiss, Frank Waller, and Karl-Heinz Kogel PMCID: PMC1697795 Applied Biological Sciences Intracellular protein interaction mapping with FRET hybrids Xia You, Annalee W. Nguyen, Abeer Jabaiah, Mark A. Sheff, Kurt S. Thorn, and Patrick S. Daugherty PMCID: PMC1693684 Biochemistry Crystal structure of HIV-1 protease in situ product complex and observation of a low-barrier hydrogen bond between catalytic aspartates Amit Das, Vishal Prashar, Smita Mahale, L. Serre, J.-L. Ferrer, and M. V. Hosur PMCID: PMC1693685 Characterization of a core binding site for ADAMTS-13 in the A2 domain of von Willebrand factor Jing-Jiang Wu, Kazuo Fujikawa, Brad A. McMullen, and Dominic W. Chung PMCID: PMC1660488 Zinc binding to the HCCH motif of HIV-1 virion infectivity factor induces a conformational change that mediates protein–protein interactions Indrani Paul, Jian Cui, and Ernest L. Maynard PMCID: PMC1693687 Crystal structure of π initiator protein–iteron complex of plasmid R6K: Implications for initiation of plasmid DNA replication Michael K. Swan, Deepak Bastia, and Christopher Davies PMCID: PMC1693688 Unliganded and hormone-bound glucocorticoid receptors interact with distinct hydrophobic sites in the Hsp90 C-terminal domain L. Fang, D. Ricketson, L. Getubig, and B. Darimont PMCID: PMC1693689 Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate Brad Bennett, Paul Langan, Leighton Coates, Marat Mustyakimov, Benno Schoenborn, Elizabeth E. Howell, and Chris Dealwis PMCID: PMC1664550 Anthrax pathogen evades the mammalian immune system through stealth siderophore production Rebecca J. Abergel, Melissa K. Wilson, Jean E. L. Arceneaux, Trisha M. Hoette, Roland K. Strong, B. Rowe Byers, and Kenneth N. Raymond PMCID: PMC1693691 The mediator complex functions as a coactivator for GATA-1 in erythropoiesis via subunit Med1/TRAP220 Melanie Stumpf, Claudia Waskow, Marit Krötschel, Dominic van Essen, Patrick Rodriguez, Xiaoting Zhang, Boris Guyot, Robert G. Roeder, and Tilman Borggrefe PMCID: PMC1693692 Biophysics A driving and coupling “Pac-Man” mechanism for chromosome poleward translocation in anaphase A Jian Liu and José N. Onuchic PMCID: PMC1693682 Stepwise binding and bending of DNA by Escherichia coli integration host factor Sawako Sugimura and Donald M. Crothers PMCID: PMC1654134 Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF Serguei V. Kuznetsov, Sawako Sugimura, Paula Vivas, Donald M. Crothers, and Anjum Ansari PMCID: PMC1656971 Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem Douglas L. Theobald and Deborah S. Wuttke PMCID: PMC1664551 Using cryo-EM to measure the dipole potential of a lipid membrane Liguo Wang, Pulkit S. Bose, and Fred J. Sigworth PMCID: PMC1693696 Quantifying the relation between adhesion ligand–receptor bond formation and cell phenotype Hyun Joon Kong, Tanyarut Boontheekul, and David J. Mooney PMCID: PMC1693697 A structural model reveals energy transduction in dynein Adrian W. R. Serohijos, Yiwen Chen, Feng Ding, Timothy C. Elston, and Nikolay V. Dokholyan PMCID: PMC1693698 Exploring atomistic details of pH-dependent peptide folding Jana Khandogin, Jianhan Chen, and Charles L. Brooks, III PMCID: PMC1693699 Topographical complexity of multidimensional energy landscapes Gareth J. Rylance, Roy L. Johnston, Yasuhiro Matsunaga, Chun-Biu Li, Akinori Baba, and Tamiki Komatsuzaki PMCID: PMC1693700 Cell Biology From the Cover:
FAPP2, cilium formation, and compartmentalization of the apical membrane in polarized Madin–Darby canine kidney (MDCK) cells Otilia V. Vieira, Katharina Gaus, Paul Verkade, Joachim Fullekrug, Winchil L. C. Vaz, and Kai Simons PMCID: PMC1693701 Phosphorylation and cleavage of presenilin-associated rhomboid-like protein (PARL) promotes changes in mitochondrial morphology Danny V. Jeyaraju, Liqun Xu, Marie-Claude Letellier, Sirisha Bandaru, Rodolfo Zunino, Eric A. Berg, Heidi M. McBride, and Luca Pellegrini PMCID: PMC1693702 Global modulation of chromatin dynamics mediated by dephosphorylation of linker histone H1 is necessary for erythroid differentiation Dhananjay Yellajoshyula and David T. Brown PMCID: PMC1656952 Acetylation of MEK2 and IκB kinase (IKK) activation loop residues by YopJ inhibits signaling Rohit Mittal, Sew-Yeu Peak-Chew, and Harvey T. McMahon PMCID: PMC1654131 Smad4 cooperates with lymphoid enhancer-binding factor 1/T cell-specific factor to increase c-myc expression in the absence of TGF-β signaling S. Kyun Lim and F. Michael Hoffmann PMCID: PMC1693705 Mitochondrial deoxynucleotide pool sizes in mouse liver and evidence for a transport mechanism for thymidine monophosphate Paola Ferraro, Luca Nicolosi, Paolo Bernardi, Peter Reichard, and Vera Bianchi PMCID: PMC1693706 Reconstructing repressor protein levels from expression of gene targets in Escherichia coli R. Khanin, V. Vinciotti, and E. Wit PMCID: PMC1693707 Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4 Pierre-Olivier Mari, Bogdan I. Florea, Stephan P. Persengiev, Nicole S. Verkaik, Hennie T. Brüggenwirth, Mauro Modesti, Giuseppina Giglia-Mari, Karel Bezstarosti, Jeroen A. A. Demmers, Theo M. Luider, Adriaan B. Houtsmuller, and Dik C. van Gent PMCID: PMC1693708 Attenuation of signaling pathways stimulated by pathologically activated FGF-receptor 2 mutants prevents craniosynostosis V. P. Eswarakumar, F. Özcan, E. D. Lew, J. H. Bae, F. Tomé, C. J. Booth, D. J. Adams, I. Lax, and J. Schlessinger PMCID: PMC1693709 Two isoforms of tissue transglutaminase mediate opposing cellular fates Marc A. Antonyak, Jaclyn M. Jansen, Allison M. Miller, Thi K. Ly, Makoto Endo, and Richard A. Cerione PMCID: PMC1654133 Developmental Biology A two-step mechanism underlies the planar polarization of regenerating sensory hair cells Hernán López-Schier and A. J. Hudspeth PMCID: PMC1656970 Prediction of active nodes in the transcriptional network of neural tube patterning Chrissa Kioussi, Hung-Ping Shih, John Loflin, and Michael K. Gross PMCID: PMC1693712 Continuous tooth generation in mouse is induced by activated epithelial Wnt/β-catenin signaling Elina Järvinen, Isaac Salazar-Ciudad, Walter Birchmeier, Makoto M. Taketo, Jukka Jernvall, and Irma Thesleff PMCID: PMC1693713 Ecology Testosterone increases bioavailability of carotenoids: Insights into the honesty of sexual signaling J. Blas, L. Pérez-Rodríguez, G. R. Bortolotti, J. Viñuela, and T. A. Marchant PMCID: PMC1660487 Evolution Ameiotic recombination in asexual lineages of Daphnia Angela R. Omilian, Melania E. A. Cristescu, Jeffry L. Dudycha, and Michael Lynch PMCID: PMC1693715 Evidence for structural constraint on ovulin, a rapidly evolving Drosophila melanogaster seminal protein Alex Wong, Shannon N. Albright, and Mariana F. Wolfner PMCID: PMC1693716 Genetics Colloquium Paper: Deletion mapping of genetic regions associated with apomixis in Hieracium Andrew S. Catanach, Sylvia K. Erasmuson, Ellen Podivinsky, Brian R. Jordan, and Ross Bicknell PMCID: PMC1693717 From the Cover:
Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties Nils Rostoks, Luke Ramsay, Katrin MacKenzie, Linda Cardle, Prasanna R. Bhat, Mikeal L. Roose, Jan T. Svensson, Nils Stein, Rajeev K. Varshney, David F. Marshall, Andreas Graner, Timothy J. Close, and Robbie Waugh PMCID: PMC1693718 Active retrotransposition by a synthetic L1 element in mice Wenfeng An, Jeffrey S. Han, Sarah J. Wheelan, Edward S. Davis, Candice E. Coombes, Ping Ye, Christina Triplett, and Jef D. Boeke PMCID: PMC1693719 Klf4 and corticosteroids activate an overlapping set of transcriptional targets to accelerate in utero epidermal barrier acquisition Satyakam Patel, Zong Fang Xi, Eun Young Seo, David McGaughey, and Julia A. Segre PMCID: PMC1693720 Predicted seminal astacin-like protease is required for processing of reproductive proteins in Drosophila melanogaster Kristipati Ravi Ram, Laura K. Sirot, and Mariana F. Wolfner PMCID: PMC1693721 Activation of an oncogenic microRNA cistron by provirus integration Clifford L. Wang, Bruce B. Wang, Gábor Bartha, Lauri Li, Namitha Channa, Mark Klinger, Nigel Killeen, and Matthias Wabl PMCID: PMC1693722 Immunology Ligation of the cell surface receptor, CD46, alters T cell polarity and response to antigen presentation Jane Oliaro, Anupama Pasam, Nigel J. Waterhouse, Kylie A. Browne, Mandy J. Ludford-Menting, Joseph A. Trapani, and Sarah M. Russell PMCID: PMC1693723 Sharing of T cell receptors in antigen-specific responses is driven by convergent recombination Vanessa Venturi, Katherine Kedzierska, David A. Price, Peter C. Doherty, Daniel C. Douek, Stephen J. Turner, and Miles P. Davenport PMCID: PMC1693724 Autoantibody-mediated demyelination depends on complement activation but not activatory Fc-receptors Eduard Urich, Ilona Gutcher, Marco Prinz, and Burkhard Becher PMCID: PMC1693725 A critical role for TNF receptor-associated factor 1 and Bim down-regulation in CD8 memory T cell survival Laurent Sabbagh, Cathy C. Srokowski, Gayle Pulle, Laura M. Snell, Bradley J. Sedgmen, Yuanqing Liu, Erdyni N. Tsitsikov, and Tania H. Watts PMCID: PMC1693726 Divergent activities of an engineered antibody in murine and human systems have implications for therapeutic antibodies Carlos Vaccaro, Roger Bawdon, Sylvia Wanjie, Raimund J. Ober, and E. Sally Ward PMCID: PMC1693727 The promyelocytic leukemia protein functions as a negative regulator of IFN-γ signaling Youn-Hee Choi, Rosa Bernardi, Pier Paolo Pandolfi, and Etty N. Benveniste PMCID: PMC1693728 Medical Sciences Angiopoietin-like 4 prevents metastasis through inhibition of vascular permeability and tumor cell motility and invasiveness Ariane Galaup, Aurelie Cazes, Sebastien Le Jan, Josette Philippe, Elisabeth Connault, Emmanuelle Le Coz, Halima Mekid, Lluis M. Mir, Paule Opolon, Pierre Corvol, Catherine Monnot, and Stephane Germain PMCID: PMC1693729 Hypoxia facilitates Alzheimer's disease pathogenesis by up-regulating BACE1 gene expression Xiulian Sun, Guiqiong He, Hong Qing, Weihui Zhou, Frederick Dobie, Fang Cai, Matthias Staufenbiel, L. Eric Huang, and Weihong Song PMCID: PMC1693730 Prevention and reversal of cardiac hypertrophy by soluble epoxide hydrolase inhibitors Danyan Xu, Ning Li, Yuxia He, Valeriy Timofeyev, Ling Lu, Hsing-Ju Tsai, In-Hae Kim, Dipika Tuteja, Robertino Karlo P. Mateo, Anil Singapuri, Benjamin B. Davis, Reginald Low, Bruce D. Hammock, and Nipavan Chiamvimonvat PMCID: PMC1693731 A BTB/POZ protein, NAC-1, is related to tumor recurrence and is essential for tumor growth and survival Kentaro Nakayama, Naomi Nakayama, Ben Davidson, Jim J.-C. Sheu, Natini Jinawath, Antonio Santillan, Ritu Salani, Robert E. Bristow, Patrice J. Morin, Robert J. Kurman, Tian-Li Wang, and Ie-Ming Shih PMCID: PMC1693732 Microbiology A Legionella pneumophila-translocated substrate that is required for growth within macrophages and protection from host cell death Rita K. Laguna, Elizabeth A. Creasey, Zhiru Li, Nicole Valtz, and Ralph R. Isberg PMCID: PMC1656969 Entamoeba histolytica cell movement: A central role for self-generated chemokines and chemorepellents Mehreen Zaki, Natalie Andrew, and Robert H. Insall PMCID: PMC1693734 Neuroscience Oncoprotein Akt/PKB induces trophic effects in murine models of Parkinson's disease Vincent Ries, Claire Henchcliffe, Tatyana Kareva, Margarita Rzhetskaya, Ross Bland, Matthew J. During, Nikolai Kholodilov, and Robert E. Burke PMCID: PMC1654135 Relative blindsight in normal observers and the neural correlate of visual consciousness Hakwan C. Lau and Richard E. Passingham PMCID: PMC1693736 NMDA receptor surface mobility depends on NR2A-2B subunits Laurent Groc, Martin Heine, Sarah L. Cousins, F. Anne Stephenson, Brahim Lounis, Laurent Cognet, and Daniel Choquet PMCID: PMC1693737 Rapid and reversible changes in intrahippocampal connectivity during the course of hibernation in European hamsters Ana María Magariños, Bruce S. McEwen, Michel Saboureau, and Paul Pevet PMCID: PMC1693738 Sensory integration does not lead to sensory calibration Jeroen B. J. Smeets, John J. van den Dobbelsteen, Denise D. J. de Grave, Robert J. van Beers, and Eli Brenner PMCID: PMC1693739 Blocking the apolipoprotein E/amyloid-β interaction as a potential therapeutic approach for Alzheimer's disease Martin J. Sadowski, Joanna Pankiewicz, Henrieta Scholtzova, Pankaj D. Mehta, Frances Prelli, David Quartermain, and Thomas Wisniewski PMCID: PMC1654132 From the Cover:
Dendritic compartmentalization of chloride cotransporters underlies directional responses of starburst amacrine cells in retina Konstantin E. Gavrikov, James E. Nilson, Andrey V. Dmitriev, Charles L. Zucker, and Stuart C. Mangel PMCID: PMC1693741 Dendritic spines linearize the summation of excitatory potentials Roberto Araya, Kenneth B. Eisenthal, and Rafael Yuste PMCID: PMC1693742 Physiology Metabolic syndrome and obesity in an insect Rudolf J. Schilder and James H. Marden PMCID: PMC1693743 PKB and megalin determine the survival or death of renal proximal tubule cells Celso Caruso-Neves, Ana Acacia S. Pinheiro, Hui Cai, Jackson Souza-Menezes, and William B. Guggino PMCID: PMC1693744 Plant Biology Colloquium Paper: The plasma membrane Na+/H+ antiporter SOS1 interacts with RCD1 and functions in oxidative stress tolerance in Arabidopsis Surekha Katiyar-Agarwal, Jianhua Zhu, Kangmin Kim, Manu Agarwal, Xinmiao Fu, Alex Huang, and Jian-Kang Zhu PMCID: PMC1693745 Colloquium Paper: Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression Yoh Sakuma, Kyonoshin Maruyama, Feng Qin, Yuriko Osakabe, Kazuo Shinozaki, and Kazuko Yamaguchi-Shinozaki PMCID: PMC1693746 Colloquium Paper: Artificial evolution extends the spectrum of viruses that are targeted by a disease-resistance gene from potato Garry Farnham and David C. Baulcombe PMCID: PMC1693747 Colloquium Paper: Genetic basis for natural variation in seed vitamin E levels in Arabidopsis thaliana Laura U. Gilliland, Maria Magallanes-Lundback, Cori Hemming, Andrea Supplee, Maarten Koornneef, Leónie Bentsink, and Dean DellaPenna PMCID: PMC1693748 Colloquium Paper: Silencing leaf sorbitol synthesis alters long-distance partitioning and apple fruit quality Gianni Teo, Yasuo Suzuki, Sandie L. Uratsu, Bruce Lampinen, Nichole Ormonde, William K. Hu, Ted M. DeJong, and Abhaya M. Dandekar PMCID: PMC1693749 A different function for a member of an ancient and highly conserved cytochrome P450 family: From essential sterols to plant defense Xiaoquan Qi, Saleha Bakht, Bo Qin, Mike Leggett, Andrew Hemmings, Fred Mellon, John Eagles, Daniele Werck-Reichhart, Hubert Schaller, Agnes Lesot, Rachel Melton, and Anne Osbourn PMCID: PMC1656972 Premature arrest of the male flower meristem precedes sexual dimorphism in the dioecious plant Silene latifolia Jitka Zluvova, Michaël Nicolas, Adeline Berger, Ioan Negrutiu, and Françoise Monéger PMCID: PMC1693751 Population Biology From the Cover:
Power spectra reveal the influence of stochasticity on nonlinear population dynamics Daniel C. Reuman, Robert A. Desharnais, Robert F. Costantino, Omar S. Ahmad, and Joel E. Cohen PMCID: PMC1693752 Psychology Speech perception problems of the hearing impaired reflect inability to use temporal fine structure Christian Lorenzi, Gaëtan Gilbert, Héloïse Carn, Stéphane Garnier, and Brian C. J. Moore PMCID: PMC1693753 Sustainability Science Opposing forces of aerosol cooling and El Niño drive coral bleaching on Caribbean reefs Jennifer A. Gill, Andrew R. Watkinson, John P. McWilliams, and Isabelle M. Côté PMCID: PMC1693754 Social Sciences Psychology Sensory integration does not lead to sensory calibration Jeroen B. J. Smeets, John J. van den Dobbelsteen, Denise D. J. de Grave, Robert J. van Beers, and Eli Brenner PMCID: PMC1693739 Corrections Correction for Shekhter et al., Branch-cut singularities in thermodynamics of Fermi liquid systems PMCID: PMC1693755 Corrects: Arkady Shekhter, et al. From the Cover:
Branch-cut singularities in thermodynamics of Fermi liquid systems. Proc Natl Acad Sci U S A. 2006 October 24; 103(43): 15765–15769. Correction for Danon et al., Cryptochrome-1-dependent execution of programmed cell death induced by singlet oxygen in Arabidopsis thaliana PMCID: PMC1693756 Corrects: Antoine Danon, et al. Cryptochrome-1-dependent execution of programmed cell death induced by singlet oxygen in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2006 November 7; 103(45): 17036–17041. Correction for Ferguson et al., General structural motifs of amyloid protofilaments PMCID: PMC1693757 Corrects: Neil Ferguson, et al. General structural motifs of amyloid protofilaments. Proc Natl Acad Sci U S A. 2006 October 31; 103(44): 16248–16253. |
