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Table of Contents

July 5, 2005; 102 (27)  [Index By Author]  [Cover Photo]  [Masthead (PDF)]

FROM THE COVER

Insight into animal radiation

Mechanics of receptor-mediated endocytosis

Rapid reversible single-molecule photoswitching

Analyzing resting-state neural networks

Reflected light and color vision

IN THIS ISSUE

COMMENTARIES

PROFILES

PHYSICAL SCIENCES
    Applied Mathematics
    Chemistry
    Engineering
    Physics
    Statistics

SOCIAL SCIENCES
    Anthropology
    Psychology
    Social Sciences

BIOLOGICAL SCIENCES
    Biochemistry
    Biophysics
    Cell Biology
    Ecology
    Evolution
    Genetics

    Immunology
    Medical Sciences
    Microbiology
    Neuroscience
    Plant Biology
    Population Biology

CORRECTIONS

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IN THIS ISSUE

This Week in PNAS
PNAS 2005 102: 9431-9432. [Full Text] [Figures Only] [PDF]  

COMMENTARIES

Markus Sauer
Reversible molecular photoswitches: A key technology for nanoscience and fluorescence imaging
PNAS 2005 102: 9433-9434; published online before print June 27 2005, 10.1073/pnas.0504264102 [Extract] [Full Text] [Figures Only] [PDF]  
See companion article on page 9511

PROFILES

Regina Nuzzo
Profile of Bruce D. Smith
PNAS 2005 102: 9435-9437; published online before print June 27 2005, 10.1073/pnas.0503921102 [Extract] [Full Text] [Figures Only] [PDF]  

PHYSICAL SCIENCES

Applied Mathematics

David L. Donoho and Jared Tanner
Sparse nonnegative solution of underdetermined linear equations by linear programming
PNAS 2005 102: 9446-9451; published online before print June 23 2005, 10.1073/pnas.0502269102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Text]  

David L. Donoho and Jared Tanner
Neighborliness of randomly projected simplices in high dimensions
PNAS 2005 102: 9452-9457; published online before print June 22 2005, 10.1073/pnas.0502258102 [Abstract] [Full Text] [Figures Only] [PDF]  

Chemistry

Dhaval A. Doshi, Erik B. Watkins, Jacob N. Israelachvili, and Jaroslaw Majewski
Reduced water density at hydrophobic surfaces: Effect of dissolved gases
PNAS 2005 102: 9458-9462; published online before print June 23 2005, 10.1073/pnas.0504034102 [Abstract] [Full Text] [Figures Only] [PDF]  

Joshua J. Coon, Beatrix Ueberheide, John E. P. Syka, Deanna D. Dryhurst, Juan Ausio, Jeffrey Shabanowitz, and Donald F. Hunt
Protein identification using sequential ion/ion reactions and tandem mass spectrometry
PNAS 2005 102: 9463-9468; published online before print June 27 2005, 10.1073/pnas.0503189102 [Abstract] [Full Text] [Figures Only] [PDF]  

Engineering

Huajian Gao, Wendong Shi, and Lambert B. Freund
From The Cover: Mechanics of receptor-mediated endocytosis
PNAS 2005 102: 9469-9474; published online before print June 22 2005, 10.1073/pnas.0503879102 [Abstract] [Full Text] [Figures Only] [PDF]  
See Commentary on page 9997

Physics

Sowmianarayanan Rajamani, Thomas M. Truskett, and Shekhar Garde
Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover
PNAS 2005 102: 9475-9480; published online before print June 22 2005, 10.1073/pnas.0504089102 [Abstract] [Full Text] [Figures Only] [PDF]  

Statistics

Xiaoman Li and Wing H. Wong
Sampling motifs on phylogenetic trees
PNAS 2005 102: 9481-9486; published online before print June 27 2005, 10.1073/pnas.0501620102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information] OPEN ACCESS ARTICLE  

SOCIAL SCIENCES

Anthropology

Bruce D. Smith
Inaugural Article by a Recently Elected Academy Member:
Inaugural Article: Reassessing Coxcatlan Cave and the early history of domesticated plants in Mesoamerica
PNAS 2005 102: 9438-9445; published online before print May 20 2005, 10.1073/pnas.0502847102 [Abstract] [Full Text] [Figures Only] [PDF]  

Psychology

A. Kimball Romney, Roy G. D'Andrade, and Tarow Indow
From The Cover: The distribution of response spectra in the lateral geniculate nucleus compared with reflectance spectra of Munsell color chips
PNAS 2005 102: 9720-9725; published online before print June 23 2005, 10.1073/pnas.0503887102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  
See Commentary on page 10761

Dario Maestripieri
Early experience affects the intergenerational transmission of infant abuse in rhesus monkeys
PNAS 2005 102: 9726-9729; published online before print June 27 2005, 10.1073/pnas.0504122102 [Abstract] [Full Text] [Figures Only] [PDF]  

Social Sciences

Robert Erikson, John H. Goldthorpe, Michelle Jackson, Meir Yaish, and D. R. Cox
On class differentials in educational attainment
PNAS 2005 102: 9730-9733; published online before print June 23 2005, 10.1073/pnas.0502433102 [Abstract] [Full Text] [Figures Only] [PDF]  

BIOLOGICAL SCIENCES

Biochemistry

Xiangcang Ye, Sang Jun Han, Sophia Y. Tsai, Francesco J. DeMayo, Jianming Xu, Ming-Jer Tsai, and Bert W. O'Malley
Roles of steroid receptor coactivator (SRC)-1 and transcriptional intermediary factor (TIF) 2 in androgen receptor activity in mice
PNAS 2005 102: 9487-9492; published online before print June 27 2005, 10.1073/pnas.0503577102 [Abstract] [Full Text] [Figures Only] [PDF]  

Jong-Ik Hwang, Sangdun Choi, Iain D. C. Fraser, Mi Sook Chang, and Melvin I. Simon
Silencing the expression of multiple G{beta}-subunits eliminates signaling mediated by all four families of G proteins
PNAS 2005 102: 9493-9498; published online before print June 27 2005, 10.1073/pnas.0503503102 [Abstract] [Full Text] [Figures Only] [PDF]  

Martino Forino, Sherida Johnson, Thiang Y. Wong, Dmitri V. Rozanov, Alexei Y. Savinov, Wei Li, Roberto Fattorusso, Barbara Becattini, Andrew J. Orry, Dawoon Jung, Ruben A. Abagyan, Jeffrey W. Smith, Ken Alibek, Robert C. Liddington, Alex Y. Strongin, and Maurizio Pellecchia
Efficient synthetic inhibitors of anthrax lethal factor
PNAS 2005 102: 9499-9504; published online before print June 27 2005, 10.1073/pnas.0502733102 [Abstract] [Full Text] [Figures Only] [PDF] OPEN ACCESS ARTICLE  

Yong Li, Mihwa Choi, Kelly Suino, Amanda Kovach, Jennifer Daugherty, Steven A. Kliewer, and H. Eric Xu
Structural and biochemical basis for selective repression of the orphan nuclear receptor liver receptor homolog 1 by small heterodimer partner
PNAS 2005 102: 9505-9510; published online before print June 23 2005, 10.1073/pnas.0501204102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information] OPEN ACCESS ARTICLE  

Biophysics

Huajian Gao, Wendong Shi, and Lambert B. Freund
From The Cover: Mechanics of receptor-mediated endocytosis
PNAS 2005 102: 9469-9474; published online before print June 22 2005, 10.1073/pnas.0503879102 [Abstract] [Full Text] [Figures Only] [PDF]  
See Commentary on page 9997

Xiaoman Li and Wing H. Wong
Sampling motifs on phylogenetic trees
PNAS 2005 102: 9481-9486; published online before print June 27 2005, 10.1073/pnas.0501620102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information] OPEN ACCESS ARTICLE  

Satoshi Habuchi, Ryoko Ando, Peter Dedecker, Wendy Verheijen, Hideaki Mizuno, Atsushi Miyawaki, and Johan Hofkens
From The Cover: Reversible single-molecule photoswitching in the GFP-like fluorescent protein Dronpa
PNAS 2005 102: 9511-9516; published online before print June 22 2005, 10.1073/pnas.0500489102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information] OPEN ACCESS ARTICLE  
See Commentary on page 9433

Beat P. Kramer and Martin Fussenegger
Hysteresis in a synthetic mammalian gene network
PNAS 2005 102: 9517-9522; published online before print June 22 2005, 10.1073/pnas.0500345102 [Abstract] [Full Text] [Figures Only] [PDF]  

Cell Biology

Enzo Di Iorio, Vanessa Barbaro, Alessandro Ruzza, Diego Ponzin, Graziella Pellegrini, and Michele De Luca
Isoforms of {Delta}Np63 and the migration of ocular limbal cells in human corneal regeneration
PNAS 2005 102: 9523-9528; published online before print June 27 2005, 10.1073/pnas.0503437102 [Abstract] [Full Text] [Figures Only] [PDF]  

Christopher J. Bakal, Dina Finan, José LaRose, Clark D. Wells, Gerald Gish, Sarang Kulkarni, Paulo DeSepulveda, Andrew Wilde, and Robert Rottapel
The Rho GTP exchange factor Lfc promotes spindle assembly in early mitosis
PNAS 2005 102: 9529-9534; published online before print June 23 2005, 10.1073/pnas.0504190102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Figures] OPEN ACCESS ARTICLE  

Ecology

J. S. Weitz, H. Hartman, and S. A. Levin
Coevolutionary arms races between bacteria and bacteriophage
PNAS 2005 102: 9535-9540; published online before print June 23 2005, 10.1073/pnas.0504062102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Text]  

Evolution

Guy Sella and Aaron E. Hirsh
The application of statistical physics to evolutionary biology
PNAS 2005 102: 9541-9546; published online before print June 24 2005, 10.1073/pnas.0501865102 [Abstract] [Full Text] [PDF] [Supporting Information]  

Kevin J. Peterson and Nicholas J. Butterfield
From The Cover: Origin of the Eumetazoa: Testing ecological predictions of molecular clocks against the Proterozoic fossil record
PNAS 2005 102: 9547-9552; published online before print June 27 2005, 10.1073/pnas.0503660102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Appendices]  

Genetics

Olof H. Sundin, Gregory S. Leppert, Eduardo D. Silva, Jun-Ming Yang, Sharola Dharmaraj, Irene H. Maumenee, Luisa Coutinho Santos, Cameron F. Parsa, Elias I. Traboulsi, Karl W. Broman, Cathy DiBernardo, Janet S. Sunness, Jeffrey Toy, and Ethan M. Weinberg
Extreme hyperopia is the result of null mutations in MFRP, which encodes a Frizzled-related protein
PNAS 2005 102: 9553-9558; published online before print June 23 2005, 10.1073/pnas.0501451102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  

Nicolas E. Buchler, Ulrich Gerland, and Terence Hwa
Nonlinear protein degradation and the function of genetic circuits
PNAS 2005 102: 9559-9564; published online before print June 22 2005, 10.1073/pnas.0409553102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  

Melissa R. Thomas and Erin K. O'Shea
An intracellular phosphate buffer filters transient fluctuations in extracellular phosphate levels
PNAS 2005 102: 9565-9570; published online before print June 22 2005, 10.1073/pnas.0501122102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information] OPEN ACCESS ARTICLE  

Immunology

Christopher A. Klebanoff, Luca Gattinoni, Parizad Torabi-Parizi, Keith Kerstann, Adela R. Cardones, Steven E. Finkelstein, Douglas C. Palmer, Paul A. Antony, Sam T. Hwang, Steven A. Rosenberg, Thomas A. Waldmann, and Nicholas P. Restifo
Central memory self/tumor-reactive CD8+ T cells confer superior antitumor immunity compared with effector memory T cells
PNAS 2005 102: 9571-9576; published online before print June 24 2005, 10.1073/pnas.0503726102 [Abstract] [Full Text] [Figures Only] [PDF]  

Jared C. Roach, Gustavo Glusman, Lee Rowen, Amardeep Kaur, Maureen K. Purcell, Kelly D. Smith, Leroy E. Hood, and Alan Aderem
The evolution of vertebrate Toll-like receptors
PNAS 2005 102: 9577-9582; published online before print June 23 2005, 10.1073/pnas.0502272102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  

R. Pacheco, J. M. Martinez-Navio, M. Lejeune, N. Climent, H. Oliva, J. M. Gatell, T. Gallart, J. Mallol, C. Lluis, and R. Franco
CD26, adenosine deaminase, and adenosine receptors mediate costimulatory signals in the immunological synapse
PNAS 2005 102: 9583-9588; published online before print June 27 2005, 10.1073/pnas.0501050102 [Abstract] [Full Text] [Figures Only] [PDF]  

Rachel M. McLoughlin, Brendan J. Jenkins, Dianne Grail, Anwen S. Williams, Ceri A. Fielding, Clare R. Parker, Matthias Ernst, Nicholas Topley, and Simon A. Jones
IL-6 trans-signaling via STAT3 directs T cell infiltration in acute inflammation
PNAS 2005 102: 9589-9594; published online before print June 23 2005, 10.1073/pnas.0501794102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  

Cassandra E. Smith, Todd N. Eagar, Jack L. Strominger, and Stephen D. Miller
Differential induction of IgE-mediated anaphylaxis after soluble vs. cell-bound tolerogenic peptide therapy of autoimmune encephalomyelitis
PNAS 2005 102: 9595-9600; published online before print June 27 2005, 10.1073/pnas.0504131102 [Abstract] [Full Text] [Figures Only] [PDF]  

Medical Sciences

Nicole Comtesse, Andrea Zippel, Sascha Walle, Dominik Monz, Christina Backes, Ulrike Fischer, Jens Mayer, Nicole Ludwig, Andreas Hildebrandt, Andreas Keller, Wolf-Ingo Steudel, Hans-Peter Lenhof, and Eckart Meese
Complex humoral immune response against a benign tumor: Frequent antibody response against specific antigens as diagnostic targets
PNAS 2005 102: 9601-9606; published online before print June 27 2005, 10.1073/pnas.0500404102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  

Xander H. T. Wehrens, Stephan E. Lehnart, Steven Reiken, Roel van der Nagel, Raymond Morales, Jie Sun, Zhenzhuang Cheng, Shi-Xiang Deng, Leon J. de Windt, Donald W. Landry, and Andrew R. Marks
Enhancing calstabin binding to ryanodine receptors improves cardiac and skeletal muscle function in heart failure
PNAS 2005 102: 9607-9612; published online before print June 22 2005, 10.1073/pnas.0500353102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  

Sherif F. Louis, Bart J. Vermolen, Yuval Garini, Ian T. Young, Amanda Guffei, Zelda Lichtensztejn, Fabien Kuttler, Tony C. Y. Chuang, Sharareh Moshir, Virginie Mougey, Alice Y. C. Chuang, Paul Donald Kerr, Thierry Fest, Petra Boukamp, and Sabine Mai
c-Myc induces chromosomal rearrangements through telomere and chromosome remodeling in the interphase nucleus
PNAS 2005 102: 9613-9618; published online before print June 27 2005, 10.1073/pnas.0407512102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  

B. G. Williams, R. Granich, L. S. Chauhan, N. S. Dharmshaktu, and C. Dye
The impact of HIV/AIDS on the control of tuberculosis in India
PNAS 2005 102: 9619-9624; published online before print June 23 2005, 10.1073/pnas.0501615102 [Abstract] [Full Text] [Figures Only] [PDF] OPEN ACCESS ARTICLE  

Giovanni Tonon, Kwok-Kin Wong, Gautam Maulik, Cameron Brennan, Bin Feng, Yunyu Zhang, Deepak B. Khatry, Alexei Protopopov, Mingjian James You, Andrew J. Aguirre, Eric S. Martin, Zhaohui Yang, Hongbin Ji, Lynda Chin, and Ronald A. DePinho
High-resolution genomic profiles of human lung cancer
PNAS 2005 102: 9625-9630; published online before print June 27 2005, 10.1073/pnas.0504126102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information] OPEN ACCESS ARTICLE  

Qingfeng Yang, Wei Huang, Catherine Jozwik, Yong Lin, Mirta Glasman, Hung Caohuy, Meera Srivastava, Dominic Esposito, William Gillette, James Hartley, and Harvey B. Pollard
Cardiac glycosides inhibit TNF-{alpha}/NF-{kappa}B signaling by blocking recruitment of TNF receptor-associated death domain to the TNF receptor
PNAS 2005 102: 9631-9636; published online before print June 27 2005, 10.1073/pnas.0504097102 [Abstract] [Full Text] [Figures Only] [PDF] OPEN ACCESS ARTICLE  

Yves Sabbagh, Thomas O. Carpenter, and Marie B. Demay
Hypophosphatemia leads to rickets by impairing caspase-mediated apoptosis of hypertrophic chondrocytes
PNAS 2005 102: 9637-9642; published online before print June 23 2005, 10.1073/pnas.0502249102 [Abstract] [Full Text] [Figures Only] [PDF]  

Weiguo Shu, Julie Y. Cho, Yuhui Jiang, Minhua Zhang, Donald Weisz, Gregory A. Elder, James Schmeidler, Rita De Gasperi, Miguel A. Gama Sosa, Donald Rabidou, Anthony C. Santucci, Daniel Perl, Edward Morrisey, and Joseph D. Buxbaum
Altered ultrasonic vocalization in mice with a disruption in the Foxp2 gene
PNAS 2005 102: 9643-9648; published online before print June 27 2005, 10.1073/pnas.0503739102 [Abstract] [Full Text] [Figures Only] [PDF] OPEN ACCESS ARTICLE  

Alex C. Minella, Markus Welcker, and Bruce E. Clurman
Ras activity regulates cyclin E degradation by the Fbw7 pathway
PNAS 2005 102: 9649-9654; published online before print June 24 2005, 10.1073/pnas.0503677102 [Abstract] [Full Text] [Figures Only] [PDF]  

Hideshi Ishii, Taeko Inageta, Koshi Mimori, Toshiyuki Saito, Hiroki Sasaki, Masaharu Isobe, Masaki Mori, Carlo M. Croce, Kay Huebner, Keiya Ozawa, and Yusuke Furukawa
Frag1, a homolog of alternative replication factor C subunits, links replication stress surveillance with apoptosis
PNAS 2005 102: 9655-9660; published online before print June 27 2005, 10.1073/pnas.0504222102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  

Microbiology

Kazuyuki Yokoyama, Hideaki Higashi, Susumu Ishikawa, Yumiko Fujii, Satoshi Kondo, Hiroyuki Kato, Takeshi Azuma, Akihiro Wada, Toshiya Hirayama, Hiroyuki Aburatani, and Masanori Hatakeyama
Functional antagonism between Helicobacter pylori CagA and vacuolating toxin VacA in control of the NFAT signaling pathway in gastric epithelial cells
PNAS 2005 102: 9661-9666; published online before print June 24 2005, 10.1073/pnas.0502529102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Tables]  

Anthony Griffiths and Donald M. Coen
An unusual internal ribosome entry site in the herpes simplex virus thymidine kinase gene
PNAS 2005 102: 9667-9672; published online before print June 22 2005, 10.1073/pnas.0504132102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  

Neuroscience

Michael D. Fox, Abraham Z. Snyder, Justin L. Vincent, Maurizio Corbetta, David C. Van Essen, and Marcus E. Raichle
From The Cover: The human brain is intrinsically organized into dynamic, anticorrelated functional networks
PNAS 2005 102: 9673-9678; published online before print June 23 2005, 10.1073/pnas.0504136102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Figures] OPEN ACCESS ARTICLE  

Daniel H. O'Connor, Gayle M. Wittenberg, and Samuel S.-H. Wang
Graded bidirectional synaptic plasticity is composed of switch-like unitary events
PNAS 2005 102: 9679-9684; published online before print June 27 2005, 10.1073/pnas.0502332102 [Abstract] [Full Text] [Figures Only] [PDF]  

Michael I. Miller, M. Faisal Beg, Can Ceritoglu, and Craig Stark
Increasing the power of functional maps of the medial temporal lobe by using large deformation diffeomorphic metric mapping
PNAS 2005 102: 9685-9690; published online before print June 24 2005, 10.1073/pnas.0503892102 [Abstract] [Full Text] [Figures Only] [PDF]  

Eunsung Junn, Hiroyuki Taniguchi, Byeong Seon Jeong, Xin Zhao, Hidenori Ichijo, and M. Maral Mouradian
Interaction of DJ-1 with Daxx inhibits apoptosis signal-regulating kinase 1 activity and cell death
PNAS 2005 102: 9691-9696; published online before print June 27 2005, 10.1073/pnas.0409635102 [Abstract] [Full Text] [Figures Only] [PDF]  

Masahiro Yamaguchi and Kensaku Mori
Critical period for sensory experience-dependent survival of newly generated granule cells in the adult mouse olfactory bulb
PNAS 2005 102: 9697-9702; published online before print June 23 2005, 10.1073/pnas.0406082102 [Abstract] [Full Text] [Figures Only] [PDF] OPEN ACCESS ARTICLE  

Plant Biology

Leor Williams, Cristel C. Carles, Karen S. Osmont, and Jennifer C. Fletcher
A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes
PNAS 2005 102: 9703-9708; published online before print June 24 2005, 10.1073/pnas.0504029102 [Abstract] [Full Text] [Figures Only] [PDF]  

Thomas J. Avenson, Jeffrey A. Cruz, Atsuko Kanazawa, and David M. Kramer
Regulating the proton budget of higher plant photosynthesis
PNAS 2005 102: 9709-9713; published online before print June 22 2005, 10.1073/pnas.0503952102 [Abstract] [Full Text] [Figures Only] [PDF]  

Population Biology

Natalia L. Komarova and Dominik Wodarz
Drug resistance in cancer: Principles of emergence and prevention
PNAS 2005 102: 9714-9719; published online before print June 24 2005, 10.1073/pnas.0501870102 [Abstract] [Full Text] [Figures Only] [PDF] [Supporting Information]  

CORRECTIONS

Correction for Shen et al., Scanning the human proteome for calmodulin-binding proteins, PNAS 2005 102:5969-5974 [Extract] [Full Text] [PDF]  

errata for Cox et al., Diverse taxa of cyanobacteria produce {beta}-N-methylamino-L-alanine, a neurotoxic amino acid, PNAS 2005 102:5074-5078 [Extract] [Full Text] [PDF]  

errata for Davis et al., Recombinant NY-ESO-1 protein with ISCOMATRIX adjuvant induces broad integrated antibody and CD4+ and CD8+ T cell responses in humans, PNAS 2004 101:10697-10702 [Extract] [Full Text] [PDF]  

Correction for Miura et al., The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses, PNAS 2005 102:7760-7765 [Extract] [Full Text] [PDF]  

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