Table of Contents

Commentaries

Commentary:
- Douglas L. Black
A simple answer for a splicing conundrum
PNAS 2005 102:4927-4928; published online before print March 28, 2005, doi:10.1073/pnas.0501414102
- See companion article on page 5002 in issue 14 of volume 102
Commentary:
- Richard Horn
How ion channels sense membrane potential
PNAS 2005 102:4929-4930; published online before print March 28, 2005, doi:10.1073/pnas.0501640102
- See companion article on page 5020 in issue 14 of volume 102
Commentary:
- Diane E. Ullman,
- Anna E. Whitfield,
- and Thomas L. German
Thrips and tospoviruses come of age: Mapping determinants of insect transmission
PNAS 2005 102:4931-4932; published online before print March 28, 2005, doi:10.1073/pnas.0501341102
- See companion article on page 5168 in issue 14 of volume 102
Commentary:
- Ferric C. Fang
Sigma cascades in prokaryotic regulatory networks
PNAS 2005 102:4933-4934; published online before print March 28, 2005, doi:10.1073/pnas.0501417102
- See companion article on page 5162 in issue 14 of volume 102

In This Issue

In This Issue:
This Week in PNAS
PNAS 2005 102:4925-4926; doi:10.1073/iti1405102

Introduction

Introduction:
- Eric Davidson
- and Michael Levin
Gene Regulatory Networks Special Feature: Gene regulatory networks
PNAS 2005 102:4935; published online before print April 4, 2005, doi:10.1073/pnas.0502024102

Gene Regulatory Networks Special Feature

Perspective

Select this article
Gene Regulatory Networks Special Feature - Perspective:
- Michael Levine
- and Eric H. Davidson
Gene Regulatory Networks Special Feature: From the Cover: Gene regulatory networks for development
PNAS 2005 102:4936-4942; published online before print March 23, 2005, doi:10.1073/pnas.0408031102

Physical Sciences

Chemistry

Select this article
Physical Sciences - Chemistry:
- Jie Wang,
- Xiaoyun Chen,
- Matthew L. Clarke,
- and Zhan Chen
Detection of chiral sum frequency generation vibrational spectra of proteins and peptides at interfaces in situ
PNAS 2005 102:4978-4983; published online before print March 25, 2005, doi:10.1073/pnas.0501206102

Biological Sciences

Biochemistry

Select this article
Biological Sciences - Biochemistry:
- Erik W. Debler,
- Shuichiro Ito,
- Florian P. Seebeck,
- Andreas Heine,
- Donald Hilvert,
- and Ian A. Wilson
Structural origins of efficient proton abstraction from carbon by a catalytic antibody
PNAS 2005 102:4984-4989; published online before print March 23, 2005, doi:10.1073/pnas.0409207102
Select this article
Biological Sciences - Biochemistry:
- Shiwei Song,
- Zachary F. Pursell,
- William C. Copeland,
- Matthew J. Longley,
- Thomas A. Kunkel,
- and Christopher K. Mathews
DNA precursor asymmetries in mammalian tissue mitochondria and possible contribution to mutagenesis through reduced replication fidelity
PNAS 2005 102:4990-4995; published online before print March 22, 2005, doi:10.1073/pnas.0500253102
Select this article
Biological Sciences - Biochemistry:
- Eric S. Okerberg,
- Jiangyue Wu,
- Baohong Zhang,
- Babak Samii,
- Kelly Blackford,
- David T. Winn,
- Kevin R. Shreder,
- Jonathan J. Burbaum,
- and Matthew P. Patricelli
High-resolution functional proteomics by active-site peptide profiling
PNAS 2005 102:4996-5001; published online before print March 28, 2005, doi:10.1073/pnas.0501205102
Select this article
Biological Sciences - Biochemistry:
- El Chérif Ibrahim,
- Thomas D. Schaal,
- Klemens J. Hertel,
- Robin Reed,
- and Tom Maniatis
From the Cover: Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers
PNAS 2005 102:5002-5007; published online before print March 7, 2005, doi:10.1073/pnas.0500543102
- See commentary article on page 4927 in issue 14 of volume 102
Select this article
Biological Sciences - Biochemistry:
- Karl E. Hauschild,
- Renee E. Metzler,
- Hans-Dieter Arndt,
- Rocco Moretti,
- Marni Raffaelle,
- Peter B. Dervan,
- and Aseem Z. Ansari
Temperature-sensitive protein–DNA dimerizers
PNAS 2005 102:5008-5013; published online before print March 21, 2005, doi:10.1073/pnas.0501289102
Select this article
Biological Sciences - Biochemistry:
- Duhee Bang
- and Stephen B. H. Kent
His₆ tag-assisted chemical protein synthesis
PNAS 2005 102:5014-5019; published online before print March 22, 2005, doi:10.1073/pnas.0407648102

Biophysics

Select this article
Biological Sciences - Biophysics:
- Carlos Gonzalez,
- Francisco J. Morera,
- Eduardo Rosenmann,
- Osvaldo Alvarez,
- and Ramon Latorre
S3b amino acid residues do not shuttle across the bilayer in voltage-dependent Shaker K⁺ channels
PNAS 2005 102:5020-5025; published online before print March 17, 2005, doi:10.1073/pnas.0501051102
- See commentary article on page 4929 in issue 14 of volume 102
Select this article
Biological Sciences - Biophysics:
- Hanqiao Feng,
- Zheng Zhou,
- and Yawen Bai
A protein folding pathway with multiple folding intermediates at atomic resolution
PNAS 2005 102:5026-5031; published online before print March 25, 2005, doi:10.1073/pnas.0501372102
Select this article
Biological Sciences - Biophysics:
- Dan McElheny,
- Jason R. Schnell,
- Jonathan C. Lansing,
- H. Jane Dyson,
- and Peter E. Wright
Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis
PNAS 2005 102:5032-5037; published online before print March 28, 2005, doi:10.1073/pnas.0500699102
Select this article
Biological Sciences - Biophysics:
- Maia V. Vinogradova,
- Deborah B. Stone,
- Galina G. Malanina,
- Christina Karatzaferi,
- Roger Cooke,
- Robert A. Mendelson,
- and Robert J. Fletterick
Ca²⁺-regulated structural changes in troponin
PNAS 2005 102:5038-5043; published online before print March 22, 2005, doi:10.1073/pnas.0408882102

Cell Biology

Select this article
Biological Sciences - Cell Biology:
- Garrett J. DeYulia, Jr.,
- Juan M. Cárcamo,
- Oriana Bórquez-Ojeda,
- Christopher C. Shelton,
- and David W. Golde
Hydrogen peroxide generated extracellularly by receptor–ligand interaction facilitates cell signaling
PNAS 2005 102:5044-5049; published online before print March 28, 2005, doi:10.1073/pnas.0501154102
Select this article
Biological Sciences - Cell Biology:
- Guenter Albrecht-Buehler
A long-range attraction between aggregating 3T3 cells mediated by near-infrared light scattering
PNAS 2005 102:5050-5055; published online before print March 24, 2005, doi:10.1073/pnas.0407763102
Select this article
Biological Sciences - Cell Biology:
- Yaron Pereg,
- Dganit Shkedy,
- Petra de Graaf,
- Erik Meulmeester,
- Marina Edelson-Averbukh,
- Mogjiborahman Salek,
- Sharon Biton,
- Amina F. A. S. Teunisse,
- Wolf D. Lehmann,
- Aart G. Jochemsen,
- and Yosef Shiloh
Phosphorylation of Hdmx mediates its Hdm2- and ATM-dependent degradation in response to DNA damage
PNAS 2005 102:5056-5061; published online before print March 23, 2005, doi:10.1073/pnas.0408595102

Developmental Biology

Select this article
Biological Sciences - Developmental Biology - Gene Regulatory Networks Special Feature:
- Tetsuya Koide,
- Tadayoshi Hayata,
- and Ken W. Y. Cho
Gene Regulatory Networks Special Feature: Xenopus as a model system to study transcriptional regulatory networks
PNAS 2005 102:4943-4948; published online before print March 28, 2005, doi:10.1073/pnas.0408125102
Select this article
Biological Sciences - Developmental Biology - Gene Regulatory Networks Special Feature:
- Harinder Singh,
- Kay L. Medina,
- and Jagan M. R. Pongubala
Gene Regulatory Networks Special Feature: Contingent gene regulatory networks and B cell fate specification
PNAS 2005 102:4949-4953; published online before print March 23, 2005, doi:10.1073/pnas.0500480102
Select this article
Biological Sciences - Developmental Biology - Gene Regulatory Networks Special Feature:
- Sorin Istrail
- and Eric H. Davidson
Gene Regulatory Networks Special Feature: Logic functions of the genomic cis-regulatory code
PNAS 2005 102:4954-4959; published online before print March 23, 2005, doi:10.1073/pnas.0409624102
Select this article
Biological Sciences - Developmental Biology - Gene Regulatory Networks Special Feature:
- Amanda Ochoa-Espinosa,
- Gozde Yucel,
- Leah Kaplan,
- Adam Pare,
- Noel Pura,
- Adam Oberstein,
- Dmitri Papatsenko,
- and Stephen Small
Gene Regulatory Networks Special Feature: The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila
PNAS 2005 102:4960-4965; published online before print March 25, 2005, doi:10.1073/pnas.0500373102
Select this article
Biological Sciences - Developmental Biology - Gene Regulatory Networks Special Feature:
- Dmitri Papatsenko
- and Michael Levine
Gene Regulatory Networks Special Feature: Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo
PNAS 2005 102:4966-4971; published online before print March 28, 2005, doi:10.1073/pnas.0409414102
Select this article
Biological Sciences - Developmental Biology - Gene Regulatory Networks Special Feature:
- Takao Inoue,
- Minqin Wang,
- Ted O. Ririe,
- Jolene S. Fernandes,
- and Paul W. Sternberg
Gene Regulatory Networks Special Feature: Transcriptional network underlying Caenorhabditis elegans vulval development
PNAS 2005 102:4972-4977; published online before print March 4, 2005, doi:10.1073/pnas.0408122102
Select this article
Biological Sciences - Developmental Biology:
- Byeong S. Yoon,
- Dmitry A. Ovchinnikov,
- Isaac Yoshii,
- Yuji Mishina,
- Richard R. Behringer,
- and Karen M. Lyons
Bmpr1a and Bmpr1b have overlapping functions and are essential for chondrogenesis in vivo
PNAS 2005 102:5062-5067; published online before print March 21, 2005, doi:10.1073/pnas.0500031102
Select this article
Biological Sciences - Developmental Biology:
- Susie B. Corley,
- Rosemary Carpenter,
- Lucy Copsey,
- and Enrico Coen
Floral asymmetry involves an interplay between TCP and MYB transcription factors in Antirrhinum
PNAS 2005 102:5068-5073; published online before print March 24, 2005, doi:10.1073/pnas.0501340102

Ecology

Select this article
Biological Sciences - Ecology:
- Paul Alan Cox,
- Sandra Anne Banack,
- Susan J. Murch,
- Ulla Rasmussen,
- Georgia Tien,
- Robert Richard Bidigare,
- James S. Metcalf,
- Louise F. Morrison,
- Geoffrey A. Codd,
- and Birgitta Bergman
Diverse taxa of cyanobacteria produce β-N-methylamino-l-alanine, a neurotoxic amino acid
PNAS 2005 102:5074-5078; published online before print April 4, 2005, doi:10.1073/pnas.0501526102
Select this article
Biological Sciences - Ecology:
- Michael Kaspari
Global energy gradients and size in colonial organisms: Worker mass and worker number in ant colonies
PNAS 2005 102:5079-5083; published online before print March 23, 2005, doi:10.1073/pnas.0407827102

Evolution

Select this article
Biological Sciences - Evolution:
- Alejandro P. Rooney
- and Todd J. Ward
Evolution of a large ribosomal RNA multigene family in filamentous fungi: Birth and death of a concerted evolution paradigm
PNAS 2005 102:5084-5089; published online before print March 22, 2005, doi:10.1073/pnas.0409689102
Select this article
Biological Sciences - Evolution:
- K. Praveen Karanth,
- Thomas Delefosse,
- Berthe Rakotosamimanana,
- Thomas J. Parsons,
- and Anne D. Yoder
Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates
PNAS 2005 102:5090-5095; published online before print March 22, 2005, doi:10.1073/pnas.0408354102

Genetics

Select this article
Biological Sciences - Genetics:
- Samir M. Hamdan,
- Boriana Marintcheva,
- Timothy Cook,
- Seung-Joo Lee,
- Stanley Tabor,
- and Charles C. Richardson
A unique loop in T7 DNA polymerase mediates the binding of helicase-primase, DNA binding protein, and processivity factor
PNAS 2005 102:5096-5101; published online before print March 28, 2005, doi:10.1073/pnas.0501637102
Select this article
Biological Sciences - Genetics:
- Hartmut Geiger,
- Gabriela Rennebeck,
- and Gary Van Zant
Regulation of hematopoietic stem cell aging in vivo by a distinct genetic element
PNAS 2005 102:5102-5107; published online before print March 23, 2005, doi:10.1073/pnas.0408654102

Immunology

Select this article
Biological Sciences - Immunology:
- C. J. Drakeley,
- P. H. Corran,
- P. G. Coleman,
- J. E. Tongren,
- S. L. R. McDonald,
- I. Carneiro,
- R. Malima,
- J. Lusingu,
- A. Manjurano,
- W. M. M. Nkya,
- M. M. Lemnge,
- J. Cox,
- H. Reyburn,
- and E. M. Riley
Estimating medium- and long-term trends in malaria transmission by using serological markers of malaria exposure
PNAS 2005 102:5108-5113; published online before print March 25, 2005, doi:10.1073/pnas.0408725102
Select this article
Biological Sciences - Immunology:
- Jelena S. Bezbradica,
- Timothy Hill,
- Aleksandar K. Stanic,
- Luc Van Kaer,
- and Sebastian Joyce
Commitment toward the natural T (iNKT) cell lineage occurs at the CD4⁺8⁺ stage of thymic ontogeny
PNAS 2005 102:5114-5119; published online before print March 25, 2005, doi:10.1073/pnas.0408449102
Select this article
Biological Sciences - Immunology:
- Sreyashi Basu
- and Pramod Srivastava
Immunological role of neuronal receptor vanilloid receptor 1 expressed on dendritic cells
PNAS 2005 102:5120-5125; published online before print March 25, 2005, doi:10.1073/pnas.0407780102
Select this article
Biological Sciences - Immunology:
- Yisong Y. Wan
- and Richard A. Flavell
Identifying Foxp3-expressing suppressor T cells with a bicistronic reporter
PNAS 2005 102:5126-5131; published online before print March 28, 2005, doi:10.1073/pnas.0501701102
Select this article
Biological Sciences - Immunology:
- Xiaoren Tang,
- Deborah Levy Marciano,
- Susan E. Leeman,
- and Salomon Amar
LPS induces the interaction of a transcription factor, LPS-induced TNF-α factor, and STAT6(B) with effects on multiple cytokines
PNAS 2005 102:5132-5137; published online before print March 25, 2005, doi:10.1073/pnas.0501159102
Select this article
Biological Sciences - Immunology:
- Estelle Bettelli,
- Maryam Dastrange,
- and Mohamed Oukka
Foxp3 interacts with nuclear factor of activated T cells and NF-κB to repress cytokine gene expression and effector functions of T helper cells
PNAS 2005 102:5138-5143; published online before print March 24, 2005, doi:10.1073/pnas.0501675102
Select this article
Biological Sciences - Immunology:
- Danijela Koppers-Lalic,
- Eric A. J. Reits,
- Maaike E. Ressing,
- Andrea D. Lipinska,
- Rupert Abele,
- Joachim Koch,
- Marisa Marcondes Rezende,
- Pieter Admiraal,
- Daphne van Leeuwen,
- Krystyna Bienkowska-Szewczyk,
- Thomas C. Mettenleiter,
- Frans A. M. Rijsewijk,
- Robert Tampé,
- Jacques Neefjes,
- and Emmanuel J. H. J. Wiertz
Varicelloviruses avoid T cell recognition by UL49.5-mediated inactivation of the transporter associated with antigen processing
PNAS 2005 102:5144-5149; published online before print March 25, 2005, doi:10.1073/pnas.0501463102

Medical Sciences

Select this article

Biological Sciences - Medical Scienc

FROM THE COVER

A simple answer for a splicing conundrum

How ion channels sense membrane potential

Thrips and tospoviruses come of age: Mapping determinants of insect transmission

Sigma cascades in prokaryotic regulatory networks

This Week in PNAS

Gene Regulatory Networks Special Feature: Gene regulatory networks

Gene Regulatory Networks Special Feature: From the Cover: Gene regulatory networks for development

Detection of chiral sum frequency generation vibrational spectra of proteins and peptides at interfaces in situ

Structural origins of efficient proton abstraction from carbon by a catalytic antibody

DNA precursor asymmetries in mammalian tissue mitochondria and possible contribution to mutagenesis through reduced replication fidelity

High-resolution functional proteomics by active-site peptide profiling

From the Cover: Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers

Temperature-sensitive protein–DNA dimerizers

His6 tag-assisted chemical protein synthesis

S3b amino acid residues do not shuttle across the bilayer in voltage-dependent Shaker K+ channels

A protein folding pathway with multiple folding intermediates at atomic resolution

Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis

Ca2+-regulated structural changes in troponin

Hydrogen peroxide generated extracellularly by receptor–ligand interaction facilitates cell signaling

A long-range attraction between aggregating 3T3 cells mediated by near-infrared light scattering

Phosphorylation of Hdmx mediates its Hdm2- and ATM-dependent degradation in response to DNA damage

Gene Regulatory Networks Special Feature: Xenopus as a model system to study transcriptional regulatory networks

Gene Regulatory Networks Special Feature: Contingent gene regulatory networks and B cell fate specification

Gene Regulatory Networks Special Feature: Logic functions of the genomic cis-regulatory code

Gene Regulatory Networks Special Feature: The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila

Gene Regulatory Networks Special Feature: Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo

Gene Regulatory Networks Special Feature: Transcriptional network underlying Caenorhabditis elegans vulval development

Bmpr1a and Bmpr1b have overlapping functions and are essential for chondrogenesis in vivo

Floral asymmetry involves an interplay between TCP and MYB transcription factors in Antirrhinum

Diverse taxa of cyanobacteria produce β-N-methylamino-l-alanine, a neurotoxic amino acid

Global energy gradients and size in colonial organisms: Worker mass and worker number in ant colonies

Evolution of a large ribosomal RNA multigene family in filamentous fungi: Birth and death of a concerted evolution paradigm

Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates

A unique loop in T7 DNA polymerase mediates the binding of helicase-primase, DNA binding protein, and processivity factor

Regulation of hematopoietic stem cell aging in vivo by a distinct genetic element

Estimating medium- and long-term trends in malaria transmission by using serological markers of malaria exposure

Commitment toward the natural T (iNKT) cell lineage occurs at the CD4+8+ stage of thymic ontogeny

Immunological role of neuronal receptor vanilloid receptor 1 expressed on dendritic cells

Identifying Foxp3-expressing suppressor T cells with a bicistronic reporter

LPS induces the interaction of a transcription factor, LPS-induced TNF-α factor, and STAT6(B) with effects on multiple cytokines

Foxp3 interacts with nuclear factor of activated T cells and NF-κB to repress cytokine gene expression and effector functions of T helper cells

Varicelloviruses avoid T cell recognition by UL49.5-mediated inactivation of the transporter associated with antigen processing

His₆ tag-assisted chemical protein synthesis

S3b amino acid residues do not shuttle across the bilayer in voltage-dependent Shaker K⁺ channels

Ca²⁺-regulated structural changes in troponin

Commitment toward the natural T (iNKT) cell lineage occurs at the CD4⁺8⁺ stage of thymic ontogeny