| | This journal provides immediate access to some articles. This Week in PNAS Proc Natl Acad Sci U S A. 2007 February 20; 104(8): 2555–2556. doi: 10.1073/iti0807104.PMCID: PMC1815219 Commentaries Dissecting hydrophobicity Giulia Galli PMCID: PMC1815220 Ancient chemoreceptors retain their flexibility John S. Parkinson PMCID: PMC1815221 An elusive marine photosynthetic bacterium is finally unveiled Marcelino T. Suzuki and Oded Béjà PMCID: PMC1815222 Physical Sciences Chemistry INAUGURAL ARTICLE by a Recently Elected Academy Member: Metal to metal multiple bonds in ordered assemblies Malcolm H. Chisholm PMCID: PMC1815223 A stochastic, cantilever approach to the evaluation of solution phase thermodynamic quantities Phillip W. Snyder, Gwangrog Lee, Piotr E. Marszalek, Robert L. Clark, and Eric J. Toone PMCID: PMC1815225 From the Cover:
Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water Je-Luen Li, Roberto Car, Chao Tang, and Ned S. Wingreen PMCID: PMC1815233 Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations Peter J. Bond and Mark S. P. Sansom PMCID: PMC1797625 Substrate binding and protein conformational dynamics measured by 2D-IR vibrational echo spectroscopy Ilya J. Finkelstein, Haruto Ishikawa, Seongheun Kim, Aaron M. Massari, and M. D. Fayer PMCID: PMC1815234 Engineering Drying a tuberculosis vaccine without freezing Yun-Ling Wong, Samantha Sampson, Willem Andreas Germishuizen, Sunali Goonesekera, Giovanni Caponetti, Jerry Sadoff, Barry R. Bloom, and David Edwards PMCID: PMC1815227 Physics Electrostatics at the oil–water interface, stability, and order in emulsions and colloids Mirjam E. Leunissen, Alfons van Blaaderen, Andrew D. Hollingsworth, Matthew T. Sullivan, and Paul M. Chaikin PMCID: PMC1800788 Biological Sciences Applied Biological Sciences Drying a tuberculosis vaccine without freezing Yun-Ling Wong, Samantha Sampson, Willem Andreas Germishuizen, Sunali Goonesekera, Giovanni Caponetti, Jerry Sadoff, Barry R. Bloom, and David Edwards PMCID: PMC1815227 Adenovirus-mediated gene delivery into mouse spermatogonial stem cells Masanori Takehashi, Mito Kanatsu-Shinohara, Kimiko Inoue, Narumi Ogonuki, Hiromi Miki, Shinya Toyokuni, Atsuo Ogura, and Takashi Shinohara PMCID: PMC1815228 An in vitro and in vivo disconnect uncovered through high-throughput identification of botulinum neurotoxin A antagonists Lisa M. Eubanks, Mark S. Hixon, Wei Jin, Sukwon Hong, Colin M. Clancy, William H. Tepp, Michael R. Baldwin, Carl J. Malizio, Michael C. Goodnough, Joseph T. Barbieri, Eric A. Johnson, Dale L. Boger, Tobin J. Dickerson, and Kim D. Janda PMCID: PMC1815229 Biochemistry Tissue-specific activity of the blind mole rat and the two nucleotide-mutated mouse αB-crystallin promoter in transgenic mice Yan Li, R. Barry Hough, and Joram Piatigorsky PMCID: PMC1796782 Alkynyl sugar analogs for the labeling and visualization of glycoconjugates in cells Tsui-Ling Hsu, Sarah R. Hanson, Kuniyuki Kishikawa, Sheng-Kai Wang, Masaaki Sawa, and Chi-Huey Wong PMCID: PMC1815231 Toward understanding phosphoseryl-tRNACys formation: The crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase Satwik Kamtekar, Michael J. Hohn, Hee-Sung Park, Michael Schnitzbauer, Anselm Sauerwald, Dieter Söll, and Thomas A. Steitz PMCID: PMC1815232 Biophysics A stochastic, cantilever approach to the evaluation of solution phase thermodynamic quantities Phillip W. Snyder, Gwangrog Lee, Piotr E. Marszalek, Robert L. Clark, and Eric J. Toone PMCID: PMC1815225 From the Cover:
Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water Je-Luen Li, Roberto Car, Chao Tang, and Ned S. Wingreen PMCID: PMC1815233 Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations Peter J. Bond and Mark S. P. Sansom PMCID: PMC1797625 Substrate binding and protein conformational dynamics measured by 2D-IR vibrational echo spectroscopy Ilya J. Finkelstein, Haruto Ishikawa, Seongheun Kim, Aaron M. Massari, and M. D. Fayer PMCID: PMC1815234 A synthetic time-delay circuit in mammalian cells and mice Wilfried Weber, Jörg Stelling, Markus Rimann, Bettina Keller, Marie Daoud-El Baba, Cornelia C. Weber, Dominique Aubel, and Martin Fussenegger PMCID: PMC1796999 A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures Samrat Mukhopadhyay, Rajaraman Krishnan, Edward A. Lemke, Susan Lindquist, and Ashok A. Deniz PMCID: PMC1815236 Ultrafast dynamics of protein collapse from single-molecule photon statistics Daniel Nettels, Irina V. Gopich, Armin Hoffmann, and Benjamin Schuler PMCID: PMC1815237 Conformational entropy of alanine versus glycine in protein denatured states Kathryn A. Scott, Darwin O. V. Alonso, Satoshi Sato, Alan R. Fersht, and Valerie Daggett PMCID: PMC1815238 Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes Björn M. Reinhard, Sassan Sheikholeslami, Alexander Mastroianni, A. Paul Alivisatos, and Jan Liphardt PMCID: PMC1815239 A single-molecule barcoding system using nanoslits for DNA analysis Kyubong Jo, Dalia M. Dhingra, Theo Odijk, Juan J. de Pablo, Michael D. Graham, Rod Runnheim, Dan Forrest, and David C. Schwartz PMCID: PMC1815240 Rational redesign of the folding pathway of a modular protein Alan R. Lowe and Laura S. Itzhaki PMCID: PMC1815241 Exploring the proton pump mechanism of cytochrome c oxidase in real time Ilya Belevich, Dmitry A. Bloch, Nikolai Belevich, Mårten Wikström, and Michael I. Verkhovsky PMCID: PMC1796784 Cell Biology Dido disruption leads to centrosome amplification and mitotic checkpoint defects compromising chromosome stability Varvara Trachana, Karel H. M. van Wely, Astrid Alonso Guerrero, Agnes Fütterer, and Carlos Martínez-A PMCID: PMC1815243 Munc18-1 binds directly to the neuronal SNARE complex Irina Dulubova, Mikhail Khvotchev, Siqi Liu, Iryna Huryeva, Thomas C. Südhof, and Josep Rizo PMCID: PMC1815244 Glucocorticoid-stimulated preadipocyte differentiation is mediated through acetylation of C/EBPβ by GCN5 Nadine Wiper-Bergeron, Houssein Abdou Salem, Julianna J. Tomlinson, Dongmei Wu, and Robert J. G. Haché PMCID: PMC1815245 Interaction between chromatin proteins MECP2 and ATRX is disrupted by mutations that cause inherited mental retardation Xinsheng Nan, Jianghui Hou, Alan Maclean, Jamal Nasir, Maria Jose Lafuente, Xinhua Shu, Skirmantas Kriaucionis, and Adrian Bird PMCID: PMC1796997 Developmental Biology The EGF repeat and discoidin domain protein, SED1/MFG-E8, is required for mammary gland branching morphogenesis Michael A. Ensslin and Barry D. Shur PMCID: PMC1815247 Basement membrane remodeling is essential for Drosophila disc eversion and tumor invasion Ajay Srivastava, Jose Carlos Pastor-Pareja, Tatsushi Igaki, Raymond Pagliarini, and Tian Xu PMCID: PMC1815248 Polychaete trunk neuroectoderm converges and extends by mediolateral cell intercalation Patrick R. H. Steinmetz, Fabiola Zelada-Gonzáles, Carola Burgtorf, Joachim Wittbrodt, and Detlev Arendt PMCID: PMC1815249 DDB1 is essential for genomic stability in developing epidermis Yong Cang, Jianxuan Zhang, Sally A. Nicholas, Arianna L. Kim, Pengbo Zhou, and Stephen P. Goff PMCID: PMC1797626 Mice cloned from skin cells Jinsong Li, Valentina Greco, Géraldine Guasch, Elaine Fuchs, and Peter Mombaerts PMCID: PMC1815251 Dual mode of paraxial mesoderm formation during chick gastrulation Tadahiro Iimura, Xuesong Yang, Cornelis J. Weijer, and Olivier Pourquié PMCID: PMC1815252 CD34+ hematopoietic stem-progenitor cell microRNA expression and function: A circuit diagram of differentiation control Robert W. Georgantas, III, Richard Hildreth, Sebastien Morisot, Jonathan Alder, Chang-gong Liu, Shelly Heimfeld, George A. Calin, Carlo M. Croce, and Curt I. Civin PMCID: PMC1796783 Ecology Enemy release after introduction of disease-resistant genotypes into plant–pathogen systems Robert C. Godfree, Peter H. Thrall, and Andrew G. Young PMCID: PMC1815254 Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem Alban Ramette and James M. Tiedje PMCID: PMC1815255 Evolution Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome Andrew M. Shedlock, Christopher W. Botka, Shaying Zhao, Jyoti Shetty, Tingting Zhang, Jun S. Liu, Patrick J. Deschavanne, and Scott V. Edwards PMCID: PMC1815256 Adaptive climatic molecular evolution in wild barley at the Isa defense locus James K. Cronin, Peter C. Bundock, Robert J. Henry, and Eviatar Nevo PMCID: PMC1815257 Tissue-driven hypothesis of genomic evolution and sequence-expression correlations Xun Gu and Zhixi Su PMCID: PMC1815258 Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics Jody Hey and Rasmus Nielsen PMCID: PMC1815259 Genetics Prion species barrier between the closely related yeast proteins is detected despite coaggregation Buxin Chen, Gary P. Newnam, and Yury O. Chernoff PMCID: PMC1815260 The Saccharomyces cerevisiae 14-3-3 proteins Bmh1 and Bmh2 directly influence the DNA damage-dependent functions of Rad53 Takehiko Usui and John H. J. Petrini PMCID: PMC1797148 Gene expression and functional evidence of epithelial-to-mesenchymal transition in papillary thyroid carcinoma invasion Vasily Vasko, Allan V. Espinosa, William Scouten, Huiling He, Herbert Auer, Sandya Liyanarachchi, Alexander Larin, Victoria Savchenko, Gary L. Francis, Albert de la Chapelle, Motoyasu Saji, and Matthew D. Ringel PMCID: PMC1815262 A genetic network for the clock of Neurospora crassa Yihai Yu, Wubei Dong, Cara Altimus, Xiaojia Tang, James Griffith, Melissa Morello, Lisa Dudek, Jonathan Arnold, and Heinz-Bernd Schüttler PMCID: PMC1797628 From the Cover:
Genetic analysis of the calcineurin pathway identifies members of the EGR gene family, specifically EGR3, as potential susceptibility candidates in schizophrenia Kazuo Yamada, David J. Gerber, Yoshimi Iwayama, Tetsuo Ohnishi, Hisako Ohba, Tomoko Toyota, Jun Aruga, Yoshio Minabe, Susumu Tonegawa, and Takeo Yoshikawa PMCID: PMC1815264 Immunology Dendritic cells with TGF-β1 differentiate naïve CD4+CD25− T cells into islet-protective Foxp3+ regulatory T cells Xunrong Luo, Kristin V. Tarbell, Hua Yang, Kathryn Pothoven, Samantha L. Bailey, Ruchuang Ding, Ralph M. Steinman, and Manikkam Suthanthiran PMCID: PMC1815265 Transcription factor T-bet regulates skin sclerosis through its function in innate immunity and via IL-13 Antonios O. Aliprantis, Jingsong Wang, John W. Fathman, Raphael Lemaire, David M. Dorfman, Robert Lafyatis, and Laurie H. Glimcher PMCID: PMC1815266 Tetramer visualization of gut-homing gluten-specific T cells in the peripheral blood of celiac disease patients Melinda Ráki, Lars-Egil Fallang, Margit Brottveit, Elin Bergseng, Hanne Quarsten, Knut E. A. Lundin, and Ludvig M. Sollid PMCID: PMC1800789 VEGF kinoid vaccine, a therapeutic approach against tumor angiogenesis and metastases Farhad Haghighi Rad, Hélène Le Buanec, Sébastien Paturance, Patrick Larcier, Philippe Genne, Bernhard Ryffel, Armand Bensussan, Bernard Bizzini, Robert C. Gallo, Daniel Zagury, and Georges Uzan PMCID: PMC1797624 The catalytic subunit of DNA–protein kinase (DNA-PKcs) is not required for Ig class-switch recombination Kerstin Kiefer, Jennifer Oshinsky, Jiyoon Kim, Pamela B. Nakajima, Gayle C. Bosma, and Melvin J. Bosma PMCID: PMC1815269 Distinct modes of action applied by transcription factors STAT1 and IRF1 to initiate transcription of the IFN-γ-inducible gbp2 gene Katrin Ramsauer, Matthias Farlik, Gordin Zupkovitz, Christian Seiser, Andrea Kröger, Hansjörg Hauser, and Thomas Decker PMCID: PMC1815270 Medical Sciences INAUGURAL ARTICLE by a Recently Elected Academy Member: Hepatitis B virus X protein enhances androgen receptor-responsive gene expression depending on androgen level Chi-Ming Chiu, Shiou-Hwei Yeh, Pei-Jer Chen, Ti-Jung Kuo, Ching-Ju Chang, Po-Jen Chen, Wan-Jen Yang, and Ding-Shinn Chen PMCID: PMC1783528 Critical role of dipeptidyl peptidase I in neutrophil recruitment during the development of experimental abdominal aortic aneurysms Monica B. Pagano, Michel A. Bartoli, Terri L. Ennis, Dongli Mao, Pamela M. Simmons, Robert W. Thompson, and Christine T. N. Pham PMCID: PMC1797622 The Fas pathway is involved in pancreatic β cell secretory function Desiree M. Schumann, Kathrin Maedler, Isobel Franklin, Daniel Konrad, Joachim Størling, Marianne Böni-Schnetzler, Asllan Gjinovci, Michael O. Kurrer, Benoit R. Gauthier, Domenico Bosco, Axel Andres, Thierry Berney, Melanie Greter, Burkhard Becher, Alexander V. Chervonsky, Philippe A. Halban, Thomas Mandrup-Poulsen, Claes B. Wollheim, and Marc Y. Donath PMCID: PMC1815272 Receptors of the protein C activation and activated protein C signaling pathways are colocalized in lipid rafts of endothelial cells Jong-Sup Bae, Likui Yang, and Alireza R. Rezaie PMCID: PMC1815273 Proteomics of specific treatment-related alterations in Fabry disease: A strategy to identify biological abnormalities David F. Moore, Oleg V. Krokhin, Ronald C. Beavis, Markus Ries, Chevalia Robinson, Ehud Goldin, Roscoe O. Brady, John A. Wilkins, and Raphael Schiffmann PMCID: PMC1797627 Evidence for a functional RNA element in the hepatitis C virus core gene Laura K. McMullan, Arash Grakoui, Matthew J. Evans, Kathleen Mihalik, Montserrat Puig, Andrea D. Branch, Stephen M. Feinstone, and Charles M. Rice PMCID: PMC1815275 Microbiology From the Cover:
Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors Roger P. Alexander and Igor B. Zhulin PMCID: PMC1797150 From the Cover:
Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis Bernhard M. Fuchs, Stefan Spring, Hanno Teeling, Christian Quast, Jörg Wulf, Martha Schattenhofer, Shi Yan, Steve Ferriera, Justin Johnson, Frank Oliver Glöckner, and Rudolf Amann PMCID: PMC1815277 Cholesterol-dependent actin remodeling via RhoA and Rac1 activation by the Streptococcus pneumoniae toxin pneumolysin Asparouh I. Iliev, Jasmin Roya Djannatian, Roland Nau, Timothy J. Mitchell, and Fred S. Wouters PMCID: PMC1815278 Herpes simplex virus type 1 mediates fusion through a hemifusion intermediate by sequential activity of glycoproteins D, H, L, and B Ravi P. Subramanian and Robert J. Geraghty PMCID: PMC1815279 Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module Peter Hebbeln, Dmitry A. Rodionov, Anja Alfandega, and Thomas Eitinger PMCID: PMC1815280 Resistance of human T cell leukemia virus type 1 to APOBEC3G restriction is mediated by elements in nucleocapsid David Derse, Shawn A. Hill, Gerald Princler, Patricia Lloyd, and Gisela Heidecker PMCID: PMC1815281 Single-enzyme conversion of FMNH2 to 5,6-dimethylbenzimidazole, the lower ligand of B12 Michael J. Gray and Jorge C. Escalante-Semerena PMCID: PMC1815282 Molecular analysis of human forearm superficial skin bacterial biota Zhan Gao, Chi-hong Tseng, Zhiheng Pei, and Martin J. Blaser PMCID: PMC1815283 Cleavage of p65/RelA of the NF-κB pathway by Chlamydia Sonya P. Lad, Jiali Li, Jean da Silva Correia, Qilin Pan, Shilpa Gadwal, Richard J. Ulevitch, and Erguang Li PMCID: PMC1815284 Genome-wide transcription map of an archaeal cell cycle Magnus Lundgren and Rolf Bernander PMCID: PMC1815285 Neuroscience Selective defect of in vivo glycolysis in early Huntington's disease striatum William J. Powers, Tom O. Videen, Joanne Markham, Lori McGee-Minnich, JoAnn V. Antenor-Dorsey, Tamara Hershey, and Joel S. Perlmutter PMCID: PMC1797149 Nitric oxide S-nitrosylates serine racemase, mediating feedback inhibition of d-serine formation Asif K. Mustafa, Manish Kumar, Balakrishnan Selvakumar, Gary P. H. Ho, Jeffrey T. Ehmsen, Roxanne K. Barrow, L. Mario Amzel, and Solomon H. Snyder PMCID: PMC1815287 Properties of glutamate receptors of Alzheimer's disease brain transplanted to frog oocytes Annalisa Bernareggi, Zulma Dueñas, Jorge Mauricio Reyes-Ruiz, Fabio Ruzzier, and Ricardo Miledi PMCID: PMC1815288 Spatial memory and the human hippocampus Yael Shrager, Peter J. Bayley, Bruno Bontempi, Ramona O. Hopkins, and Larry R. Squire PMCID: PMC1815289 Cannabinoid action in the olfactory epithelium Dirk Czesnik, Detlev Schild, Josko Kuduz, and Ivan Manzini PMCID: PMC1815290 Fibroblast growth factor blocks Sonic hedgehog signaling in neuronal precursors and tumor cells Marie P. Fogarty, Brian A. Emmenegger, Linda L. Grasfeder, Trudy G. Oliver, and Robert J. Wechsler-Reya PMCID: PMC1815291 Protein kinase A activates protein phosphatase 2A by phosphorylation of the B56δ subunit Jung-Hyuck Ahn, Thomas McAvoy, Sergey V. Rakhilin, Akinori Nishi, Paul Greengard, and Angus C. Nairn PMCID: PMC1815292 The function neutralizing anti-TrkA antibody MNAC13 reduces inflammatory and neuropathic pain Gabriele Ugolini, Sara Marinelli, Sonia Covaceuszach, Antonino Cattaneo, and Flaminia Pavone PMCID: PMC1815293 Molecular determinants for the interaction between AMPA receptors and the clathrin adaptor complex AP-2 Kathrin Kastning, Viktoria Kukhtina, Josef T. Kittler, Guojun Chen, Arndt Pechstein, Sven Enders, Sang Hyoung Lee, Morgan Sheng, Zhen Yan, and Volker Haucke PMCID: PMC1815294 Differentiation of ES cells into cerebellar neurons Enrique Salero and Mary E. Hatten PMCID: PMC1796781 Pharmacology From the Cover:
An obligatory requirement for the heterotrimeric G protein Gi3 in the antiautophagic action of insulin in the liver Antje Gohla, Karinna Klement, Roland P. Piekorz, Katja Pexa, Stephan vom Dahl, Karsten Spicher, Vladyslav Dreval, Dieter Häussinger, Lutz Birnbaumer, and Bernd Nrnberg PMCID: PMC1815296 Physiology Night eating and obesity in the EP3R-deficient mouse Manuel Sanchez-Alavez, Izabella Klein, Sara E. Brownell, Iustin V. Tabarean, Christopher N. Davis, Bruno Conti, and Tamas Bartfai PMCID: PMC1800735 Corrections Correction for Gindulyte et al., The transition state for formation of the peptide bond in the ribosome PMCID: PMC1815298 Corrects: Asta Gindulyte, et al. The transition state for formation of the peptide bond in the ribosome. Proc Natl Acad Sci U S A. 2006 September 5; 103(36): 13327–13332. Correction for Tang et al., LPS-induced TNF-α factor (LITAF)-deficient mice express reduced LPS-induced cytokine: Evidence for LITAF-dependent LPS signaling pathways PMCID: PMC1815299 Corrects: Xiaoren Tang, et al. LPS-induced TNF-α factor (LITAF)-deficient mice express reduced LPS-induced cytokine: Evidence for LITAF-dependent LPS signaling pathways. Proc Natl Acad Sci U S A. 2006 September 12; 103(37): 13777–13782. |
