Table Of Contents Page, PNAS Volume 106, Number 28

PNAS July 14, 2009

This Week in PNAS

Letters (Online Only)

Commentaries

Physical Sciences

Applied Mathematics

Networks describe a variety of interacting complex systems in social science, biology, and information technology. Usually the nodes of real networks are identified not only by their connections but also by some other characteristics. Examples of ...

Applied Physical Sciences

We study the relation at intraday level between serial correlation and volatility of the Standard and Poor (S&P) 500 stock index futures returns. At daily and weekly levels, serial correlation and volatility forecasts have been found to be negatively ...
An approach to quantitatively study vesicle dynamics as well as biologically-related micro-objects in a fluid flow, which is based on the combination of a dynamical trap and a control parameter, the ratio of the vorticity to the strain rate, is suggested. ...
Using electron spin resonance spectroscopy (ESR), we measure the rotational mobility of probe molecules highly diluted in deeply supercooled bulk water and negligibly constrained by the possible ice fraction. The mobility increases above the putative ...
The dendritic cell receptor DC-SIGN mediates pathogen recognition by binding to glycans characteristic of pathogen surfaces, including those found on HIV. Clustering of carbohydrate-binding sites in the receptor tetramer is believed to be critical for ...

Chemistry

High-pressure methods have been demonstrated to be efficient in providing new routes for the synthesis of materials of technological interest. In several molecular compounds, the drastic pressure conditions required for spontaneous transformations have ...
A chemicurrent is a flux of fast (kinetic energy ≳ 0.5−1.3 eV) metal electrons caused by moderately exothermic (1−3 eV) chemical reactions over high work function (4−6 eV) metal surfaces. In this report, the relation between chemicurrent and surface ...
We have shown recently that halogenated quinones could enhance the decomposition of hydroperoxides and formation of alkoxyl/hydroxyl radicals through a metal-independent mechanism. However, neither the proposed quinone enoxy radical intermediate, nor the ...
We introduce a concept to solve the structure of a microcrystalline material in the solid-state at natural abundance without access to distance constraints, using magic angle spinning (MAS) NMR spectroscopy in conjunction with X-ray powder diffraction and ...

Computer Sciences

Optimal choice of actions is a fundamental problem relevant to fields as diverse as neuroscience, psychology, economics, computer science, and control engineering. Despite this broad relevance the abstract setting is similar: we have an agent choosing ...

Engineering

The failure probability of engineering structures such as aircraft, bridges, dams, nuclear structures, and ships, as well as microelectronic components and medical implants, must be kept extremely low, typically <10−6. The safety factors needed to ensure ...

Geology

Fire has played an essential role in the development of human civilization. Most previous research suggests that frequent-fire regimes in the late Holocene were associated with intensification of human activities, especially agriculture development. Here, ...

Geophysics

The stratospheric CO2 oxygen isotope budget is thought to be governed primarily by the O(1D)+CO2 isotope exchange reaction. However, there is increasing evidence that other important physical processes may be occurring that standard isotopic tools have ...

Mathematics

We present a computer-aided, yet fully rigorous, proof of Ira Gessel's tantalizingly simply stated conjecture that the number of ways of walking 2n steps in the region x + y ≥ 0,y ≥ 0 of the square lattice with unit steps in the east, west, north, and ...

Physics

We compute, on a molecular basis, the viscosity of a deeply supercooled liquid at high shear rates. The viscosity is shown to decrease at growing shear rates, owing to an increase in the structural relaxation rate as caused by the shear. The onset of this ...
We explore the different local symmetries in colloidal glasses beyond the standard pair correlation analysis. Using our newly developed X-ray cross correlation analysis (XCCA) concept together with brilliant coherent X-ray sources, we have been able to ...
Capping proteins are among the most important regulatory proteins involved in controlling complicated stochastic dynamics of filopodia, which are dynamic finger-like protrusions used by eukaryotic motile cells to probe their environment and help guide ...

Social Sciences

Economic Sciences

We study the relation at intraday level between serial correlation and volatility of the Standard and Poor (S&P) 500 stock index futures returns. At daily and weekly levels, serial correlation and volatility forecasts have been found to be negatively ...

Psychology

A fundamental question in the study of cognition is whether memory strength varies continuously or whether memories sometimes fall below a threshold and fail completely. Previous studies examining this question have relied exclusively on 1 method—receiver ...

Social Sciences

In a series of experiments, we demonstrate that certain players of an economic game reject unfair offers even when this behavior increases rather than decreases inequity. A substantial proportion (30–40%, compared with 60–70% in the standard ultimatum ...

Biological Sciences

Applied Biological Sciences

The dendritic cell receptor DC-SIGN mediates pathogen recognition by binding to glycans characteristic of pathogen surfaces, including those found on HIV. Clustering of carbohydrate-binding sites in the receptor tetramer is believed to be critical for ...
Vector control is a key means of combating mosquito-borne diseases and the only tool available for tackling the transmission of dengue, a disease for which no vaccine, prophylaxis, or therapeutant currently exists. The most effective mosquito control ...
Phosphoinositide (PI) lipids are intracellular membrane signaling intermediates and effectors produced by localized PI kinase and phosphatase activities. Although many signaling roles of PI kinases have been identified in cultured cell lines, transgenic ...

Biochemistry

Archae possess unique biochemical systems quite distinct from the pathways present in eukaryotes and eubacteria. 7,8-Dimethyl-8-hydroxy-5deazaflavin (F0) and F420 are unique deazaflavin-containing coenzyme and methanogenic signature molecules, essential ...
Freshwater planarian flatworms possess uncanny regenerative capacities mediated by abundant and collectively totipotent adult stem cells. Key functions of these cells during regeneration and tissue homeostasis have been shown to depend on PIWI, a molecule ...
Human cells tolerate UV-induced cyclobutane pyrimidine dimers (CPD) by translesion DNA synthesis (TLS), carried out by DNA polymerase η, the POLH gene product. A deficiency in DNA polymerase η due to germ-line mutations in POLH causes the hereditary ...
Mutations in PKD1 and TRPP2 account for nearly all cases of autosomal dominant polycystic kidney disease (ADPKD). These 2 proteins form a receptor/ion channel complex on the cell surface. Using a combination of biochemistry, crystallography, and a single-...
IFNs λ1, λ2, and λ3, or type III IFNs, are recently identified cytokines distantly related to type I IFNs. Despite an early evolutionary divergence, the 2 types of IFNs display similar antiviral activities, and both are produced primarily in dendritic ...

Biophysics and Computational Biology

Capping proteins are among the most important regulatory proteins involved in controlling complicated stochastic dynamics of filopodia, which are dynamic finger-like protrusions used by eukaryotic motile cells to probe their environment and help guide ...
The prion protein (PrP) is responsible for a group of neurodegenerative diseases called the transmissible spongiform encephalopathies. The normal function of PrP has not yet been discovered, but indirect evidence suggests a linkage to its ability to bind ...
Many bacterial species swim by employing ion-driven molecular motors that power the rotation of helical filaments. Signals are transmitted to the motor from the external environment via the chemotaxis pathway. In bidirectional motors, the binding of ...
The insertion efficiency of transmembrane (TM) helices by the Sec61 translocon depends on helix amino acid composition, the positions of the amino acids within the helix, and helix length. We have used an in vitro expression system to examine ...
Many cell–cell adhesive events are mediated by the dimerization of cadherin proteins presented on apposing cell surfaces. Cadherin-mediated processes play a central role in the sorting of cells into separate tissues in vivo, but in vitro assays aimed at ...

Cell Biology

Glucose-regulated protein 94 (GRP94) is an endoplasmic reticulum (ER) chaperone for which only few client proteins and no cofactors are known and whose mode of action is unclear. To decipher the mode of GRP94 action in vivo, we exploited our finding that ...
Most kinases are capable of recognizing and phosphorylating peptides containing short, linear sequence motifs. To measure the activation state of many kinases from the same cell lysate, we created a multiplexed, mass-spectrometry-based in vitro kinase ...
Numerous studies focus on the tumor suppressor p53 as a protector of genomic stability, mediator of cell cycle arrest and apoptosis, and target of mutation in 50% of all human cancers. The vast majority of information on p53, its protein-interaction ...
View related content:

TRIMming p53 for ubiquitination

Developmental Biology

Stem cells, their niches, and their relationship to cancer are under intense investigation. Because tumors and metastases acquire self-renewing capacity, mechanisms for their establishment may involve cell–cell interactions similar to those between stem ...
Stem cell self-renewal is controlled by concerted actions of extrinsic niche signals and intrinsic factors in a variety of systems. Drosophila ovarian germline stem cells (GSCs) have been one of the most productive systems for identifying the factors ...

Ecology

Dust deposition to mountain snow cover, which has increased since the late 19th century, accelerates the rate of snowmelt by increasing the solar radiation absorbed by the snowpack. Snowmelt occurs earlier, but is decoupled from seasonal warming. Climate ...
From analysis of published global site biomass data (n = 136) from primary forests, we discovered (i) the world's highest known total biomass carbon density (living plus dead) of 1,867 tonnes carbon per ha (average value from 13 sites) occurs in ...
How biological diversity is generated and maintained is a fundamental question in ecology. Ecologists have delineated many mechanisms that can, in principle, favor species coexistence and hence maintain biodiversity. Most such coexistence mechanisms ...
Kangaroos are the world's most diverse group of herbivorous marsupials. Following late-Miocene intensification of aridity and seasonality, they radiated across Australia, becoming the continent's ecological equivalents of the artiodactyl ungulates ...

Environmental Sciences

The low-productivity South Pacific Gyre (SPG) is Earth's largest oceanic province. Its sediment accumulates extraordinarily slowly (0.1–1 m per million years). This sediment contains a living community that is characterized by very low biomass and very ...

Evolution

Commercial fisheries exert high mortalities on the stocks they exploit, and the consequent selection pressure leads to fisheries-induced evolution of growth rate, age and size at maturation, and reproductive output. Productivity and yields may decline as ...
FLOWERING LOCUS C (FLC) is a major regulator of flowering responses to seasonal environmental factors. Here, we document that FLC also regulates another major life-history transition-seed germination, and that natural variation at the FLC locus and in FLC ...

Genetics

We recently showed that the mammalian genome encodes >1,000 large intergenic noncoding (linc)RNAs that are clearly conserved across mammals and, thus, functional. Gene expression patterns have implicated these lincRNAs in diverse biological processes, ...

Immunology

Suppression by natural CD4+CD25+ regulatory T cells (Tregs) is one mechanism by which tolerance is maintained. However, the way in which Tregs mediate suppression is not well understood. Here, we show that secreted phospholipase A2 (sPLA2)-IID is ...
The β-1,3-glucan recognition protein (βGRP)/Gram-negative bacteria-binding protein 3 (GNBP3) is a crucial pattern-recognition receptor that specifically binds β-1,3-glucan, a component of fungal cell walls. It evokes innate immunity against fungi through ...
The cysteinyl leukotrienes (cys-LTs) are proinflammatory lipid mediators acting on the type 1 cys-LT receptor (CysLT1R) to mediate smooth muscle constriction and vascular permeability. GPR17, a G protein-coupled orphan receptor with homology to the P2Y ...

Medical Sciences

Trachealess (Trh) is a PAS domain transcription factor regulating Drosophila tracheogenesis. No other Trh homolog has been associated with a respiratory phenotype. Seeking homolog(s) regulating lung development, we screened murine genomic DNA using trh ...
A variety of mechanisms maintain the integrity of the genome in the face of cell stress. Cancer cell response to chemotherapeutic and radiation-induced DNA damage is mediated by multiple defense mechanisms including polo-like kinase 1 (Plk-1), protein ...
Idiopathic hypogonadotropic hypogonadism (IHH) is a condition characterized by failure to undergo puberty in the setting of low sex steroids and low gonadotropins. IHH is due to abnormal secretion or action of the master reproductive hormone gonadotropin-...

Microbiology

Pandemic influenza viruses cause significant mortality in humans. In the 20th century, 3 influenza viruses caused major pandemics: the 1918 H1N1 virus, the 1957 H2N2 virus, and the 1968 H3N2 virus. These pandemics were initiated by the introduction and ...
The negative-strand RNA viruses (NSRVs) are unique because their nucleocapsid, not the naked RNA, is the active template for transcription and replication. The viral polymerase of nonsegmented NSRVs contains a large polymerase catalytic subunit (L) and a ...
Because heme is a major iron-containing molecule in vertebrates, the ability to use heme-bound iron is a determining factor in successful infection by bacterial pathogens. Until today, all known enzymes performing iron extraction from heme did so through ...
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman's disease. Like other herpesviruses, KSHV establishes life-long latency in the human host with ...

Neuroscience

Optimal choice of actions is a fundamental problem relevant to fields as diverse as neuroscience, psychology, economics, computer science, and control engineering. Despite this broad relevance the abstract setting is similar: we have an agent choosing ...
GABA cell dysfunction in both schizophrenia (SZ) and bipolar disorder (BD) involves decreased GAD67 expression, although this change involves fundamentally different networks of genes in the 2 disorders. One gene that is common to these 2 networks is ...
Mammals evolved a potent fear-motivated defensive system capable of single-trial fear learning that shows no forgetting over the lifespan of the animal. The basolateral amygdala complex (BLA) is considered an essential component of this conditional fear ...
Recent work argues that similar network performance can result from highly variable sets of network parameters, raising the question of whether neuromodulation can be reliable across individuals with networks with different sets of synaptic strengths and ...
The human brain's capacity for cognitive function is thought to depend on coordinated activity in sparsely connected, complex networks organized over many scales of space and time. Recent work has demonstrated that human brain networks constructed from ...
Neocortical acetylcholine (ACH) release is known to enhance signal processing by increasing the amplitude and signal-to-noise ratio (SNR) of sensory responses. It is widely accepted that the larger sensory responses are caused by a persistent increase in ...
Evidence suggests that recovery from stroke damage results from the production of new synaptic pathways within surviving brain regions over weeks. To address whether brain function might redistribute more rapidly through preexisting pathways, we examined ...
Processing of speech and nonspeech sounds occurs bilaterally within primary auditory cortex and surrounding regions of the superior temporal gyrus; however, the manner in which these regions interact during speech and nonspeech processing is not well ...
Zif268 is a transcriptional regulator that plays a crucial role in maintenance of the late phases of hippocampal long-term potentiation (LTP) and consolidation of spatial memories. Because the hippocampal place cell system is essential for long-term ...
For vertebrate olfactory signal transduction, a calcium-activated chloride conductance serves as a major amplification step. However, the molecular identity of the olfactory calcium-activated chloride channel (CaCC) is unknown. Here we report a proteomic ...
Dominant-intermediate Charcot–Marie–Tooth neuropathy (DI-CMT) is characterized by axonal degeneration and demyelination of peripheral motor and sensory neurons. Three dominant mutations in the YARS gene, encoding tyrosyl-tRNA synthetase (TyrRS), have so ...
Cones show briefer light responses than rods and do not saturate even under very bright light. Using purified rod and cone homogenates, we measured the activity of guanylate cyclase (GC), an enzyme responsible for cGMP synthesis and therefore recovery of ...
Functional heterogeneity has been investigated for decades in the hippocampal region of the mammalian cerebral cortex, and evidence for vaguely defined “dorsal” and “ventral” regions is emerging. Direct evidence that hippocampal field CA1 displays clear ...

Physiology

Mice lacking the β1-subunit (gene, Kcnmb1; protein, BK-β1) of the large Ca-activated K channel (BK) are hypertensive. This phenotype is thought to result from diminished BK currents in vascular smooth muscle where BK-β1 is an ancillary subunit. However, ...

Plant Biology

Plant organs originate from meristems where stem cells are maintained to produce continuously daughter cells that are the source of different cell types. The cell cycle switch gene CCS52A, a substrate specific activator of the anaphase promoting complex/...

Sustainability Science

An increasing amount of investment has been devoted to protecting and restoring ecosystem services worldwide. The efficiency of conservation investments, including payments for ecosystem services (PES), has been found to be affected by biological, ...

Corrections

View the cover image for PNAS Vol.106; No.28
View the cover image for PNAS Vol.106; No.28

Cover image: Pictured is a section of cerebellum with phosphatidylinositol 4-kinase type 2α (green) in Purkinje cells, colocalized (yellow) with glial fibrillary acidic protein (red) in glia. Phosphoinositide (PI) kinase enzymes and the cognate phosphatases are vital to a range of cell functions in health and disease. Researchers found that PI 4-kinase 2α knockout mice develop movement disorders and other age-related deficiencies caused by late-onset degeneration of spinal cord axons in Purkinje cells. See the article by J. Paul Simons et al. on pages 11535–11539. Image by Stylianos Evangelou and J. Paul Simons

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