Table Of Contents Page, PNAS Volume 109, Number 10

PNAS March 6, 2012

This Week in PNAS

Letters (Online Only)

QnAs

Retrospective

Commentaries

PNAS Plus (Author Summaries and Research Articles)

Biological Sciences – Biochemistry

Transcription regulation by steroid hormones, vitamin derivatives, and metabolites is mediated by nuclear receptors (NRs), which play an important role in ligand-dependent gene expression and human health. NRs function as homodimers or heterodimers and ...

Biological Sciences – Biophysics and Computational Biology

The regulation of cell shape is a common challenge faced by organisms across all biological kingdoms. In nearly all bacteria, cell shape is determined by the architecture of the peptidoglycan cell wall, a macromolecule consisting of glycan strands ...

Biological Sciences – Genetics

Photoreceptor cell death accompanying many retinal degenerative disorders results in irreversible loss of vision in humans. However, the precise molecular pathway that executes cell death is not known. Our results from a Drosophila model of retinal ...

Biological Sciences – Immunology

The protein kinases Akt1, Akt2, and Akt3 possess nonredundant signaling properties, few of which have been investigated. Here, we present evidence for an Akt1-dependent pathway that controls interferon (IFN)-regulated gene expression and antiviral ...

Critical Perspectives on Historical Collapse Special Feature (free online)

Introduction

Historical collapse of ancient states or civilizations has raised new awareness about its possible relevance to current issues of sustainability, in the context of global change. This Special Feature examines 12 case studies of societies under stress, of ...

Perspective

PerspectiveFebruary 27, 2012Inaugural ArticleFrom the Cover

Collapse, environment, and society

Historical collapse of ancient states poses intriguing social-ecological questions, as well as potential applications to global change and contemporary strategies for sustainability. Five Old World case studies are developed to identify interactive inputs,...

Research Articles

Climatic forcing during the Younger Dryas (∼12.9–11.5 ky B.P.) event has become the theoretical basis to explain the origins of agricultural lifestyles in the Levant by suggesting a failure of foraging societies to adjust. This explanation however, does ...
Getting at the Maya Collapse has both temporal and geographic dimensions, because it occurred over centuries and great distances. This requires a wide range of research sites and proxy records, ranging from lake cores to geomorphic evidence, such as ...
Episodes of population loss and cultural change, including the famous Classic Collapse, punctuated the long course of Maya civilization. In many cases, these downturns in the fortunes of individual sites and entire regions included significant ...
Norse Greenland has been seen as a classic case of maladaptation by an inflexible temperate zone society extending into the arctic and collapse driven by climate change. This paper, however, recognizes the successful arctic adaptation achieved in Norse ...
In debates on societal collapse, Iceland occupies a position of precarious survival, defined by not becoming extinct, like Norse Greenland, but having endured, sometimes by the narrowest of margins. Classic decline narratives for late medieval to early ...
Concerns about global warming, degradation of fragile ecosystems, and environmental and societal collapse have increased interest for lessons and/or solutions for today's environmental issues. Popular writers have turned to a classic degradation thesis of ...
Civilization collapse scenarios highlight what for some are worrying parallels between past case studies and societies under threat from apparently unprecedented global environmental and climate change today. Archive-based studies of socio-economic ...

Physical Sciences

Applied Mathematics

We consider a simplified model of a social network in which individuals have one of two opinions (called 0 and 1) and their opinions and the network connections coevolve. Edges are picked at random. If the two connected individuals hold different opinions ...

Applied Physical Sciences

Cavitation, known as the formation of vapor bubbles when liquids are under tension, is of great interest both in condensed matter science as well as in diverse applications such as botany, hydraulic engineering, and medicine. Although widely studied in ...
The physical property investigation (like transport measurements) and ultimate application of the topological insulators usually involve surfaces that are exposed to ambient environment (1 atm and room temperature). One critical issue is how the ...
Microorganisms play pivotal functions in the trophic dynamics and biogeochemistry of aquatic ecosystems. Their concentrations and activities often peak at localized hotspots, an important example of which are pycnoclines, where water density increases ...

Chemistry

Structuring over many length scales is a design strategy widely used in Nature to create materials with unique functional properties. We here present a comprehensive analysis of an adult sea urchin spine, and in revealing a complex, hierarchical structure,...
Protein-protein and protein-ligand interactions are ubiquitous in a biological cell. Here, we report a comprehensive study of the distribution of protein-ligand interaction sites, namely ligand-binding pockets, around protein-protein interfaces where ...

Engineering

The nature of certain clinical samples (tissue biopsies, fluids) or the subjects themselves (pediatric subjects, neonates) often constrain the number of cells available to evaluate the breadth of functional T-cell responses to infections or therapeutic ...

Mathematics

The spectral bound, s(αA + βV), of a combination of a resolvent positive linear operator A and an operator of multiplication V, was shown by Kato to be convex in
cover
. Kato's result is shown here to imply, through an elementary “dual convexity” lemma, that s(...

Physics

Much of our enjoyment of music comes from its balance of predictability and surprise. Musical pitch fluctuations follow a 1/f power law that precisely achieves this balance. Musical rhythms, especially those of Western classical music, are considered ...

Social Sciences

Anthropology

Climatic forcing during the Younger Dryas (∼12.9–11.5 ky B.P.) event has become the theoretical basis to explain the origins of agricultural lifestyles in the Levant by suggesting a failure of foraging societies to adjust. This explanation however, does ...

Economic Sciences

Analysis of data from the American Life Panel shows that in the presidential election of 2008 and in multiple statewide elections in 2010, citizens exhibited large differences in their expectations of election outcomes. Expectations were strongly ...

Environmental Sciences

Climate change and water availability in the Middle East are important in understanding human adaptive capacities in the face of long-term environmental changes. The key role of water availability for sedentary and nomad populations in these arid to ...

Psychological and Cognitive Sciences

The present study explores the dramatic projection of one's own views onto those of Jesus among conservative and liberal American Christians. In a large-scale survey, the relevant views that each group attributed to a contemporary Jesus differed almost as ...
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Profile of Lee D. Ross

Much of our enjoyment of music comes from its balance of predictability and surprise. Musical pitch fluctuations follow a 1/f power law that precisely achieves this balance. Musical rhythms, especially those of Western classical music, are considered ...

Sustainability Science

Getting at the Maya Collapse has both temporal and geographic dimensions, because it occurred over centuries and great distances. This requires a wide range of research sites and proxy records, ranging from lake cores to geomorphic evidence, such as ...
Episodes of population loss and cultural change, including the famous Classic Collapse, punctuated the long course of Maya civilization. In many cases, these downturns in the fortunes of individual sites and entire regions included significant ...
Norse Greenland has been seen as a classic case of maladaptation by an inflexible temperate zone society extending into the arctic and collapse driven by climate change. This paper, however, recognizes the successful arctic adaptation achieved in Norse ...
In debates on societal collapse, Iceland occupies a position of precarious survival, defined by not becoming extinct, like Norse Greenland, but having endured, sometimes by the narrowest of margins. Classic decline narratives for late medieval to early ...
Concerns about global warming, degradation of fragile ecosystems, and environmental and societal collapse have increased interest for lessons and/or solutions for today's environmental issues. Popular writers have turned to a classic degradation thesis of ...
Civilization collapse scenarios highlight what for some are worrying parallels between past case studies and societies under threat from apparently unprecedented global environmental and climate change today. Archive-based studies of socio-economic ...

Biological Sciences

Agricultural Sciences

We postulated that a synergistic combination of two innate immune functions, pathogen surface recognition and lysis, in a protein chimera would lead to a robust class of engineered antimicrobial therapeutics for protection against pathogens. In support of ...

Anthropology

It is generally understood that foxtail millet and broomcorn millet were initially domesticated in Northern China where they eventually became the dominant plant food crops. The rarity of older archaeological sites and archaeobotanical work in the region, ...

Applied Biological Sciences

Structuring over many length scales is a design strategy widely used in Nature to create materials with unique functional properties. We here present a comprehensive analysis of an adult sea urchin spine, and in revealing a complex, hierarchical structure,...

Biochemistry

Transcription regulation by steroid hormones, vitamin derivatives, and metabolites is mediated by nuclear receptors (NRs), which play an important role in ligand-dependent gene expression and human health. NRs function as homodimers or heterodimers and ...
Antibody conjugates are widely used as diagnostics and imaging reagents. However, many such conjugates suffer losses in sensitivity and specificity due to nonspecific labeling techniques. We have developed methodology to site-specifically conjugate ...
Multimeric AAA ATPases represent a structurally homologous yet functionally diverse family of proteins. The essential and highly abundant hexameric AAA ATPase p97 is perhaps the best studied AAA protein, playing an essential role in various important ...
Von Willebrand factor (VWF) is a large, multimeric plasma glycoprotein that critically mediates hemostasis at sites of vascular injury. Very large VWF multimers have the greatest thrombogenic activity, which is attenuated by cleavage in the A2 domain by ...
Protein synthesis on the ribosome requires translational GTPase factors to bind to the ribosome in the GTP-bound form, take individual actions that are coupled with GTP hydrolysis, and dissociate, usually in the GDP-bound form. The multiple copies of the ...
Eukarya and, more recently, some bacteria have been shown to rely on a cytoskeleton-based apparatus to drive chromosome segregation. In contrast, the factors and mechanisms underpinning this fundamental process are underexplored in archaea, the third ...
Syndapin I (PACSIN 1) is a synaptically enriched membrane tubulating protein that plays important roles in activity-dependent bulk endocytosis and neuronal morphogenesis. While syndapin I is an in vitro phosphoprotein, it is not known to be phosphorylated ...
Chemoreceptor arrays are supramolecular transmembrane machines of unknown structure that allow bacteria to sense their surroundings and respond by chemotaxis. We have combined X-ray crystallography of purified proteins with electron cryotomography of ...
To gain insight into mechanisms controlling SRY (sex determining region Y)-box 2 (Sox2) protein activity in mouse embryonic stem cells (ESCs), the endogenous Sox2 gene was tagged with FLAG/Hemagglutinin (HA) sequences by homologous recombination. Sox2 ...
Activation of p53 target genes for tumor suppression depends on the stress-specific regulation of transcriptional coactivator complexes. Strap (stress-responsive activator of p300) is activated upon DNA damage by ataxia telangiectasia mutated (ATM) and ...

Biophysics and Computational Biology

The regulation of cell shape is a common challenge faced by organisms across all biological kingdoms. In nearly all bacteria, cell shape is determined by the architecture of the peptidoglycan cell wall, a macromolecule consisting of glycan strands ...
Protein-protein and protein-ligand interactions are ubiquitous in a biological cell. Here, we report a comprehensive study of the distribution of protein-ligand interaction sites, namely ligand-binding pockets, around protein-protein interfaces where ...
A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the ...
Recently, the role of force in cellular processes has become more evident, and now with advances in force spectroscopy, the response of proteins to force can be directly studied. Such studies have found that native proteins are brittle, and thus not very ...
Mint adaptor proteins bind to the amyloid precursor protein (APP) and regulate APP processing associated with Alzheimer’s disease; however, the molecular mechanisms underlying Mint regulation in APP binding and processing remain unclear. Biochemical, ...

Cell Biology

Heme is an iron-coordinated porphyrin that is universally essential as a protein cofactor for fundamental cellular processes, such as electron transport in the respiratory chain, oxidative stress response, or redox reactions in various metabolic pathways. ...
Epac1 is a cAMP-regulated guanine nucleotide exchange factor for the small G protein Rap. Upon cAMP binding, Epac1 undergoes a conformational change that results in its release from autoinhibition. In addition, cAMP induces the translocation of Epac1 from ...
The coxsackie and adenovirus receptor (CAR) plays key roles in epithelial barrier function at the tight junction, a localization guided in part by a tyrosine-based basolateral sorting signal, 318YNQV321. Sorting motifs of this type are known to route ...
Cyclin-dependent kinase 1 (Cdk1) is an archetypical kinase and a central regulator that drives cells through G2 phase and mitosis. Knockouts of Cdk2, Cdk3, Cdk4, or Cdk6 have resulted in viable mice, but the in vivo functions of Cdk1 have not been fully ...

Developmental Biology

Two mechanisms that play important roles in cell fate decisions are control of a “core transcriptional network” and repression of alternative transcriptional programs by antagonizing transcription factors. Whether these two mechanisms operate together is ...
Full limb regeneration is a property that seems to be restricted to urodele amphibians. Here we found that Polypterus, the most basal living ray-finned fish, regenerates its pectoral lobed fins with a remarkable accuracy. Pectoral Polypterus fins are ...
The Drosophila R7 photoreceptor provides an excellent model system with which to study how cells receive and “decode” signals that specify cell fate. R7 is specified by the combined actions of the receptor tyrosine kinase (RTK) and Notch (N) signaling ...
A disintegrin and metalloproteinase 3 (ADAM3) is a sperm membrane protein critical for both sperm migration from the uterus into the oviduct and sperm primary binding to the zona pellucida (ZP). Here we show that the testis-specific protein disulfide ...

Environmental Sciences

Microorganisms play pivotal functions in the trophic dynamics and biogeochemistry of aquatic ecosystems. Their concentrations and activities often peak at localized hotspots, an important example of which are pycnoclines, where water density increases ...
Climate change and water availability in the Middle East are important in understanding human adaptive capacities in the face of long-term environmental changes. The key role of water availability for sedentary and nomad populations in these arid to ...

Evolution

Behaviors are challenging to reconstruct for extinct species, particularly the nature and origins of acoustic communication. Here we unravel the song of Archaboilus musicus Gu, Engel and Ren sp. nov., a 165 million year old stridulating katydid. From the ...
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Choristers of the Jurassic

Organismal fitness depends on the ability of gene networks to function robustly in the face of environmental and genetic perturbations. Understanding the mechanisms of this stability is one of the key aims of modern systems biology. Dissecting the basis ...

Genetics

Photoreceptor cell death accompanying many retinal degenerative disorders results in irreversible loss of vision in humans. However, the precise molecular pathway that executes cell death is not known. Our results from a Drosophila model of retinal ...

Immunology

The protein kinases Akt1, Akt2, and Akt3 possess nonredundant signaling properties, few of which have been investigated. Here, we present evidence for an Akt1-dependent pathway that controls interferon (IFN)-regulated gene expression and antiviral ...
The nature of certain clinical samples (tissue biopsies, fluids) or the subjects themselves (pediatric subjects, neonates) often constrain the number of cells available to evaluate the breadth of functional T-cell responses to infections or therapeutic ...
Immature thymocytes expressing autoreactive T-cell receptors (TCR) can adopt differing cell fates: clonal deletion by apoptosis or deviation into alternative lineages such as FoxP3+ regulatory T cells (Treg). We revisited the role of the transcription ...
Dendritic cells (DCs) are pivotal for the development of experimental autoimmune encephalomyelitis (EAE). However, the mechanisms by which they control disease remain to be determined. This study demonstrates that expression of CC chemokine receptor 4 (...
Nonhomologous end joining (NHEJ), a major pathway of DNA double-strand break (DSB) repair, is required during lymphocyte development to resolve the programmed DSBs generated during Variable, Diverse, and Joining [V(D)J] recombination. XRCC4-like factor (...
Tolerance to self-antigens present in apoptotic cells is critical to maintain immune-homeostasis and prevent systemic autoimmunity. However, mechanisms that sustain self-tolerance are poorly understood. Here we show that systemic administration of ...

Medical Sciences

For prevention of Streptococcus pneumoniae (pneumococcus) infections in infancy, protein-conjugated capsular polysaccharide vaccines provide serotype-specific, antibody-mediated immunity but do not cover all of the 90+ capsule serotypes. Therefore, ...
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QnAs with Porter W. Anderson, Jr.

Diabetes is a pathological condition characterized by relative insulin deficiency, persistent hyperglycemia, and, consequently, diffuse micro- and macrovascular disease. One therapeutic strategy is to amplify insulin-secretion capacity by increasing the ...
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Stem cells and diabetes

Although ovarian cancer is the most lethal gynecologic malignancy in women, little is known about how the cancer initiates and metastasizes. In the last decade, new evidence has challenged the dogma that the ovary is the main source of this cancer. The ...
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Nonovarian origins of ovarian cancer

Tissue factor pathway inhibitor (TFPI) blocks thrombin generation via the extrinsic blood coagulation pathway. Because the severe bleeding in patients with hemophilia occurs from deficiency of intrinsic blood coagulation pathway factor VIII or IX, ...
Lifelong self-renewal of the adult intestinal epithelium requires the activity of stem cells located in mucosal crypts. Lgr5 and Bmi1 are two molecular markers of crypt-cell populations that replenish all lineages over time and hence function as stem ...

Microbiology

A common challenge in pathogen discovery by deep sequencing approaches is to recognize viral or subviral pathogens in samples of diseased tissue that share no significant homology with a known pathogen. Here we report a homology-independent approach for ...
Recent isolation of a novel swine-origin influenza A H3N2 variant virus [A(H3N2)v] from humans in the United States has raised concern over the pandemic potential of these viruses. Here, we analyzed the virulence, transmissibility, and receptor-binding ...
Bacteria have evolved a variety of mechanisms for developing community-based biofilms. These bacterial aggregates are of clinical importance, as they are a major source of recurrent disease. Bacterial surface fibers (pili) permit adherence to biotic and ...
In response to environmental stresses, the mammalian serine threonine kinases PERK, GCN2, HRI, and PKR phosphorylate the regulatory serine 51 of the eukaryotic translation initiation factor 2α (eIF2α) to inhibit global protein synthesis. Plasmodium, the ...
Genetic variation is critical in microbial immune evasion and drug resistance, but variation has rarely been studied in complex heterogeneous communities such as the human microbiome. To begin to study natural variation, we analyzed DNA viruses present in ...

Neuroscience

How the brain translates changes in internal metabolic state or perceived food quality into alterations in feeding behavior remains poorly understood. Studies in Drosophila larvae have yielded information about neuropeptides and circuits that promote ...
Glycogen synthase kinase 3β (GSK3β) inhibitors, especially the mood stabilizer lithium chloride, are also used as neuroprotective or anti-inflammatory agents. We studied the influence of LiCl on the remyelination of peripheral nerves. We showed that the ...
The default mode network (DMN) in humans has been suggested to support a variety of cognitive functions and has been implicated in an array of neuropsychological disorders. However, its function(s) remains poorly understood. We show that rats possess a ...
Multiple stimulation protocols have been found to be effective in changing synaptic efficacy by inducing long-term potentiation or depression. In many of those protocols, increases in postsynaptic calcium concentration have been shown to play a crucial ...

Physiology

Cardiomyocyte contraction and relaxation are controlled by Ca2+ handling, which can be regulated to meet demand. Indeed, major reduction in sarcoplasmic reticulum (SR) function in mice with Serca2 knockout (KO) is compensated by enhanced plasmalemmal Ca2+ ...

Plant Biology

The transcription factor WUSCHEL (WUS) acts from a well-defined domain within the Arabidopsis thaliana shoot apical meristem (SAM) to maintain a stem cell niche. A negative-feedback loop involving the CLAVATA (CLV) signaling pathway regulates the number ...
Whole, fertile plants of Silene stenophylla Ledeb. (Caryophyllaceae) have been uniquely regenerated from maternal, immature fruit tissue of Late Pleistocene age using in vitro tissue culture and clonal micropropagation. The fruits were excavated in ...

Population Biology

The spectral bound, s(αA + βV), of a combination of a resolvent positive linear operator A and an operator of multiplication V, was shown by Kato to be convex in
cover
. Kato's result is shown here to imply, through an elementary “dual convexity” lemma, that s(...

Sustainability Science

Almost one-quarter of the world's population has basic energy needs that are not being met. Efforts to increase renewable energy resources in developing countries where per capita energy availability is low are needed. Herein, we examine integrated dual ...

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