Table Of Contents Page, PNAS Volume 109, Number 26

PNAS June 26, 2012

This Week in PNAS

Letters (Online Only)

QnAs

Commentaries

Perspective

Despite its enormous cost, large-scale carbon capture and storage (CCS) is considered a viable strategy for significantly reducing CO2 emissions associated with coal-based electrical power generation and other industrial sources of CO2 [Intergovernmental ...

Physical Sciences

Applied Mathematics

While analyzing all available protein structures for the presence of knots and slipknots, we detected a strict conservation of complex knotting patterns within and between several protein families despite their large sequence divergence. Because protein ...
The advent of transformation optics and metamaterials has made possible devices producing extreme effects on wave propagation. Here we describe a class of invisible reservoirs and amplifiers for waves, which we refer to as Schrödinger hats. The unifying ...

Applied Physical Sciences

The mathematical theory of compressed sensing (CS) asserts that one can acquire signals from measurements whose rate is much lower than the total bandwidth. Whereas the CS theory is now well developed, challenges concerning hardware implementations of CS-...
The platinum-based chemotherapy is the standard treatment for several types of cancer. However, cancer cells often become refractory with time and most patients with serious cancers die of drug resistance. Recently, we have discovered a unique ...
Integrated physiological systems, such as the cardiac and the respiratory system, exhibit complex dynamics that are further influenced by intrinsic feedback mechanisms controlling their interaction. To probe how the cardiac and the respiratory system ...
Nanostructured materials based on colloidal particles embedded in a polymer network are used in a variety of applications ranging from nanocomposite rubbers to organic-inorganic hybrid solar cells. Further, polymer-network-mediated colloidal interactions ...
Swollen elastomer liquid crystals undergo significant deformations by application of an electric field perpendicular to their alignment axis, as shown in experiments by Urayama et al. [Urayama K, Honda S, Takigawa T (2006) Macromolecules 39:1943–1949]. ...
X-ray grating interferometry is a coherent imaging technique that bears tremendous potential for three-dimensional tomographic imaging of soft biological tissue and other specimens whose details exhibit very weak absorption contrast. It is intrinsically ...
Uranium and plutonium’s 5f electrons are tenuously poised between strongly bonding with ligand spd-states and residing close to the nucleus. The unusual properties of these elements and their compounds (e.g., the six different allotropes of elemental ...
Nature offers exciting examples for functional wetting properties based on superhydrophobicity, such as the self-cleaning surfaces on plant leaves and trapped air on immersed insect surfaces allowing underwater breathing. They inspire biomimetic ...

Chemistry

Fluorescent small molecules have become indispensable tools for biomedical research along with the rapidly developing optical imaging technology. We report here a neural stem cell specific boron-dipyrromethane (BODIPY) derivative compound of designation ...
Melanin is a ubiquitous biological pigment found in bacteria, fungi, plants, and animals. It has a diverse range of ecological and biochemical functions, including display, evasion, photoprotection, detoxification, and metal scavenging. To date, evidence ...
The dissociative chemisorption of water is an important step in many heterogeneous catalytic processes. Here, the mode selectivity of this process was examined quantum mechanically on a realistic potential energy surface determined by fitting planewave ...
Proton transfer (PT) through and across aqueous interfaces is a fundamental process in chemistry and biology. Notwithstanding its importance, it is not generally realized that interfacial PT is quite different from conventional PT in bulk water. Here we ...
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Many chemical models of dense interstellar clouds predict that the majority of gas-phase elemental nitrogen should be present as N2, with an abundance approximately five orders of magnitude less than that of hydrogen. As a homonuclear diatomic molecule, N...
In this work we show how hydrodynamic forces can be used to locally trap molecules in a supported lipid bilayer (SLB). The method uses the hydrodynamic drag forces arising from a flow through a conical pipette with a tip radius of 1–1.5 μm, placed ...

Earth, Atmospheric, and Planetary Sciences

The collapse of the Bronze Age Harappan, one of the earliest urban civilizations, remains an enigma. Urbanism flourished in the western region of the Indo-Gangetic Plain for approximately 600 y, but since approximately 3,900 y ago, the total settled area ...
Global climate carbon-cycle models predict acceleration of soil organic carbon losses to the atmosphere with warming, but the size of this feedback is poorly known. The temperature sensitivity of soil carbon decomposition is commonly determined by ...
Compressional wave velocity-density (VP - ρ) relations of candidate Fe alloys at relevant pressure-temperature conditions of the Earth’s core are critically needed to evaluate the composition, seismic signatures, and geodynamics of the planet’s remotest ...

Engineering

Tumor invasion and metastasis are strongly regulated by biophysical interactions between tumor cells and the extracellular matrix (ECM). While the influence of ECM stiffness on cell migration, adhesion, and contractility has been extensively studied in 2D ...

Environmental Sciences

Diatoms are responsible for ∼40% of marine primary production and are key players in global carbon cycling. There is mounting evidence that diatom growth is influenced by cobalamin (vitamin B12) availability. This cobalt-containing micronutrient is only ...
Declining CO2 over the Cretaceous has been suggested as an evolutionary driver of the high leaf vein densities (7–28 mm mm−2) that are unique to the angiosperms throughout all of Earth history. Photosynthetic modeling indicated the link between high vein ...

Physics

During spontaneous imbibition, a wetting liquid is drawn into a porous medium by capillary forces. In systems with comparable pore length and diameter, such as paper and sand, the front of the propagating liquid forms a continuous interface. Sections of ...
Typically one expects that the intervals between consecutive occurrences of a particular behavior will have a characteristic time scale around which most observations are centered. Surprisingly, the timing of many diverse behaviors from human ...

Social Sciences

Anthropology

Telomeres are repeating DNA sequences at the ends of chromosomes that protect and buffer genes from nucleotide loss as cells divide. Telomere length (TL) shortens with age in most proliferating tissues, limiting cell division and thereby contributing to ...

Economic Sciences

The birth and explosive growth of mobile money in Kenya has provided economists with an opportunity to study the evolution and impact of a new financial system. Mobile money is an innovation that allows individuals to store, send, and receive money on ...

Environmental Sciences

The collapse of the Bronze Age Harappan, one of the earliest urban civilizations, remains an enigma. Urbanism flourished in the western region of the Indo-Gangetic Plain for approximately 600 y, but since approximately 3,900 y ago, the total settled area ...
Across diverse ecosystems, greater climatic variability tends to increase wildfire size, particularly in Australia, where alternating wet–dry cycles increase vegetation growth, only to leave a dry overgrown landscape highly susceptible to fire spread. ...

Political Sciences

Jared Diamond’s Guns, Germs, and Steel [Diamond J, (1997) Guns, Germs, and Steel (WW Norton, NY)] has provided a scientific foundation for answering basic questions, such as why Eurasians colonized the global South and not the other way around, and why ...

Psychological and Cognitive Sciences

The two-player Iterated Prisoner’s Dilemma game is a model for both sentient and evolutionary behaviors, especially including the emergence of cooperation. It is generally assumed that there exists no simple ultimatum strategy whereby one player can ...

Biological Sciences

Agricultural Sciences

The endocrine regulation of vertebrate reproduction is achieved by the coordinated actions of several peptide neurohormones, tachykinin among them. To study the evolutionary conservation and physiological functions of neurokinin B (NKB), we identified ...
Evolution of pest resistance reduces the efficacy of insecticidal proteins from Bacillus thuringiensis (Bt) used in sprays or in transgenic crops. Although several pests have evolved resistance to Bt crops in the field, information about the genetic basis ...
Sorghum, an ancient old-world cereal grass, is the dietary staple of over 500 million people in more than 30 countries in the tropics and semitropics. Its C4 photosynthesis, drought resistance, wide adaptation, and high nutritional value hold the promise ...

Anthropology

Across diverse ecosystems, greater climatic variability tends to increase wildfire size, particularly in Australia, where alternating wet–dry cycles increase vegetation growth, only to leave a dry overgrown landscape highly susceptible to fire spread. ...
Reconstructing the origin and early evolutionary history of anthropoid primates (monkeys, apes, and humans) is a current focus of paleoprimatology. Although earlier hypotheses frequently supported an African origin for anthropoids, recent discoveries of ...

Applied Biological Sciences

MicroRNA-155 (miR-155) is an oncogenic microRNA that regulates several pathways involved in cell division and immunoregulation. It is overexpressed in numerous cancers, is often correlated with poor prognosis, and is thus a key target for future ...
The conversion of recalcitrant plant-derived cellulosic biomass into biofuels is dependent on highly efficient cellulase systems that produce near-quantitative levels of soluble saccharides. Similar to other fungal and bacterial cellulase systems, the ...

Biochemistry

The way nature evolves and sculpts materials using proteins inspires new approaches to materials engineering but is still not completely understood. Here, we present a cell-free synthetic biological platform to advance studies of biologically synthesized ...
The pharmacologically important tropane alkaloids have a scattered distribution among angiosperm families, like many other groups of secondary metabolites. To determine whether tropane alkaloids have evolved repeatedly in different lineages or arise from ...
Deficiency of glycosaminoglycan (GAG) degradation causes a subclass of lysosomal storage disorders called mucopolysaccharidoses (MPSs), many of which present with severe neuropathology. Critical steps in the degradation of the GAG heparan sulfate remain ...
The IFN family of cytokines operates a frontline defense against pathogens and neoplastic cells in vivo by controlling the expression of several genes. The death-associated protein kinase 1 (DAPK1), an IFN-γ–induced enzyme, controls cell cycle, apoptosis, ...
Mutations in human leucine-rich-repeat kinase 2 (LRRK2) have been found to be the most frequent cause of late-onset Parkinson disease. Here we show that Dictyostelium discoideum Roco4 is a suitable model to study the structural and biochemical ...

Biophysics and Computational Biology

While analyzing all available protein structures for the presence of knots and slipknots, we detected a strict conservation of complex knotting patterns within and between several protein families despite their large sequence divergence. Because protein ...
Egr-1 is an inducible transcription factor that recognizes 9-bp target DNA sites via three zinc finger domains and activates genes in response to cellular stimuli such as synaptic signals and vascular stresses. Using spectroscopic and computational ...
Signal transduction proteins such as bacterial sensor histidine kinases, designed to transition between multiple conformations, are often ruled by unstable transient interactions making structural characterization of all functional states difficult. This ...
The platinum-based chemotherapy is the standard treatment for several types of cancer. However, cancer cells often become refractory with time and most patients with serious cancers die of drug resistance. Recently, we have discovered a unique ...
In this work we show how hydrodynamic forces can be used to locally trap molecules in a supported lipid bilayer (SLB). The method uses the hydrodynamic drag forces arising from a flow through a conical pipette with a tip radius of 1–1.5 μm, placed ...
Tumor invasion and metastasis are strongly regulated by biophysical interactions between tumor cells and the extracellular matrix (ECM). While the influence of ECM stiffness on cell migration, adhesion, and contractility has been extensively studied in 2D ...
We introduce a theoretical framework that exploits the ever-increasing genomic sequence information for protein structure prediction. Structure-based models are modified to incorporate constraints by a large number of non-local contacts estimated from ...
Structural fluctuations of a protein are essential for a protein to function and fold. By using molecular dynamics (MD) simulations of the model α/β protein VA3 in its native state, the coupling between the main-chain (MC) motions [represented by coarse-...
Living cells respond to mechanical forces applied to their outer membrane through processes referred to as “mechanosensation”. Faced with hypotonic shock, to circumvent cell lysis, bacteria open large solute-passing channels to reduce the osmotic pressure ...
Computational design is a test of our understanding of enzyme catalysis and a means of engineering novel, tailor-made enzymes. While the de novo computational design of catalytically efficient enzymes remains a challenge, designed enzymes may comprise ...
Actin filaments play a fundamental role in cell mechanics: assembled into networks by a large number of partners, they ensure cell integrity, deformability, and migration. Here we focus on the mechanics of the dense branched network found at the leading ...

Cell Biology

Fluorescent small molecules have become indispensable tools for biomedical research along with the rapidly developing optical imaging technology. We report here a neural stem cell specific boron-dipyrromethane (BODIPY) derivative compound of designation ...
Fe-S clusters are critical prosthetic groups for proteins involved in various critical biological processes. Before being transferred to recipient apo-proteins, Fe-S clusters are assembled on the highly conserved scaffold protein Isu, the abundance of ...
The newly discovered Ca2+-activated Cl channel (CaCC), Anoctamin 1 (Ano1 or TMEM16A), has been implicated in vital physiological functions including epithelial fluid secretion, gut motility, and smooth muscle tone. Overexpression of Ano1 in HEK cells or ...
Regulation of actin dynamics is key to many cell physiological processes, ranging from protrusion formation and control of cell shape to cellular motility, endocytosis, and vesicle movement. The actin-related protein (ARP)2/3 complex is a major actin ...
The microenvironment of the cochlea is maintained by the barrier between the systemic circulation and the fluids inside the stria vascularis. However, the mechanisms that control the permeability of the intrastrial fluid–blood barrier remain largely ...

Ecology

Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a “holy grail” in microbiology. This work describes a highly sensitive, broadly applicable, and cost-effective approach that allows metabolic profiling of ...
Although the impacts of the loss of biodiversity on ecosystem functioning are well established, the importance of the loss of biodiversity relative to other human-caused drivers of environmental change remains uncertain. Results of 11 experiments show ...
Fast-growing forests such as tropical secondary forests can accumulate large amounts of carbon (C), and thereby play an important role in the atmospheric CO2 balance. Because nitrogen (N) cycling is inextricably linked with C cycling, the question becomes:...

Environmental Sciences

Global climate carbon-cycle models predict acceleration of soil organic carbon losses to the atmosphere with warming, but the size of this feedback is poorly known. The temperature sensitivity of soil carbon decomposition is commonly determined by ...
Diatoms are responsible for ∼40% of marine primary production and are key players in global carbon cycling. There is mounting evidence that diatom growth is influenced by cobalamin (vitamin B12) availability. This cobalt-containing micronutrient is only ...

Evolution

Telomeres are repeating DNA sequences at the ends of chromosomes that protect and buffer genes from nucleotide loss as cells divide. Telomere length (TL) shortens with age in most proliferating tissues, limiting cell division and thereby contributing to ...
Declining CO2 over the Cretaceous has been suggested as an evolutionary driver of the high leaf vein densities (7–28 mm mm−2) that are unique to the angiosperms throughout all of Earth history. Photosynthetic modeling indicated the link between high vein ...
The two-player Iterated Prisoner’s Dilemma game is a model for both sentient and evolutionary behaviors, especially including the emergence of cooperation. It is generally assumed that there exists no simple ultimatum strategy whereby one player can ...
Phenotypes tend to remain relatively constant in natural populations, suggesting a limit to trait evolution. Although stationary phenotypes suggest stabilizing selection, directional selection is more commonly reported. However, selection on phenotypes ...
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including pathway ...
Iron/sulfur cluster (ISC)-containing proteins are essential components of cells. In most eukaryotes, Fe/S clusters are synthesized by the mitochondrial ISC machinery, the cytosolic iron/sulfur assembly system, and, in photosynthetic species, a plastid ...
Prions are infectious proteins that cause fatal diseases in mammals. Prions have also been found in fungi, but studies on their role in nature are scarce. The proposed biological function of fungal prions is debated and varies from detrimental to benign ...

Genetics

Studies of the familial Parkinson disease-related proteins PINK1 and Parkin have demonstrated that these factors promote the fragmentation and turnover of mitochondria following treatment of cultured cells with mitochondrial depolarizing agents. Whether ...
Small RNAs (sRNAs) are hypothesized to contribute to hybrid vigor because they maintain genome integrity, contribute to genetic diversity, and control gene expression. We used Illumina sequencing to assess how sRNA populations vary between two maize ...
The cyclin-dependent kinase Cdc28 is the master regulator of the cell cycle in Saccharomyces cerevisiae. Cdc28 initiates the cell cycle by activating cell-cycle–specific transcription factors that switch on a transcriptional program during late G1 phase. ...

Immunology

Analysis of the molecular etiologies of SCID has led to important insights into the control of immune cell development. Most cases of SCID result from either X-linked or autosomal recessive inheritance of mutations in a known causative gene. However, in ...
An imbalance of commensal bacteria and their gene products underlies mucosal and, in particular, gastrointestinal inflammation and a predisposition to cancer. Lactobacillus species have received considerable attention as examples of beneficial microbiota. ...
The mechanisms by which regulatory T cells (Tregs) suppress autoantibody production are unclear. Here we have addressed this question using transgenic mice expressing model antigens in the kidney. We report that Tregs were essential and sufficient to ...
T cells spend the majority of their time perusing lymphoid organs in search of cognate antigen presented by antigen presenting cells (APCs) and then quickly recirculate through the bloodstream to another lymph node. Therefore, regulation of a T-cell ...
The NLRP3 inflammasome is a multiprotein complex consisting of three kinds of proteins, NLRP3, ASC, and pro-caspase-1, and plays a role in sensing pathogens and danger signals in the innate immune system. The NLRP3 inflammasome is thought to be involved ...
The synthetic double-stranded RNA poly(I:C) is commonly used as an adjuvant to boost CD8 T-cell function; however, polyinosinic:polycytidylic acid [poly(I:C)] can also suppress autoimmune disease. The mechanism by which a single adjuvant achieves two ...
Langerhans cells (LCs) are skin-resident dendritic cells (DC) located in the epidermis that migrate to skin-draining lymph nodes during the steady state and in response to inflammatory stimuli. TGF-β1 is a critical immune regulator that is highly ...
The lectin pathway of complement activation is an important component of the innate immune defense. The initiation complexes of the lectin pathway consist of a recognition molecule and associated serine proteases. Until now the autoactivating mannose-...

Medical Sciences

Infarction occurs when myocardial perfusion is interrupted for prolonged periods of time. Short episodes of ischemia and reperfusion protect against tissue injury when the heart is subjected to a subsequent prolonged ischemic episode, a phenomenon known ...
Patched (Ptc), the main receptor for Sonic Hedghog, is a tumor suppressor. Ptc has been shown to be a dependence receptor, and as such triggers apoptosis in the absence of its ligand. This apoptosis induction occurs through the recruitment by the Ptc ...
Infection by carcinogenic human papillomaviruses (HPV) results in precancers [cervical intraepithelial neoplasia (CIN)] and cancers near the ectoendocervical squamocolumnar (SC) junction of the cervix. However, the specific cells targeted by HPV have not ...
Human aging cannot be fully understood in terms of the constrained genetic setting. Epigenetic drift is an alternative means of explaining age-associated alterations. To address this issue, we performed whole-genome bisulfite sequencing (WGBS) of newborn ...
It has been hypothesized that respiration defects caused by accumulation of pathogenic mitochondrial DNA (mtDNA) mutations and the resultant overproduction of reactive oxygen species (ROS) or lactates are responsible for aging and age-associated disorders,...

Microbiology

Cerebral malaria is the most deadly manifestation of infection with Plasmodium falciparum. The pathology of cerebral malaria is characterized by the accumulation of infected erythrocytes (IEs) in the microvasculature of the brain caused by parasite ...
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Molecular basis of severe malaria

Cerebral malaria (CM) is a deadly complication of Plasmodium falciparum infection, but specific interactions involved in cerebral homing of infected erythrocytes (IEs) are poorly understood. In this study, P. falciparum-IEs were characterized for binding ...
View related content:

Molecular basis of severe malaria

The clinical outcome of Plasmodium falciparum infections ranges from asymptomatic parasitemia to severe malaria syndromes associated with high mortality. The virulence of P. falciparum infections is associated with the type of P. falciparum erythrocyte ...
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Molecular basis of severe malaria

We describe a directed genome-engineering approach that combines genome-wide methods for mapping genes to traits [Warner JR, Reeder PJ, Karimpour-Fard A, Woodruff LBA, Gill RT (2010) Nat Biotechnol 28:856–862] with strategies for rapidly creating ...
The regulation of iron homeostasis is essential for most organisms, because iron is required for a variety of conserved biochemical processes, yet can be toxic at high concentrations. Upon experiencing iron starvation in vitro, the obligate intracellular ...
Beneficial microbe functions range from host dietary supplementation to development and maintenance of host immune system. In mammals, newborn progeny are quickly colonized with a symbiotic fauna that is provisioned in mother’s milk and that closely ...
Detection of pathogenic nucleic acids is essential for mammalian innate immunity. IFN-inducible protein IFI16 has emerged as a critical sensor for detecting pathogenic DNA, stimulating both type I IFN and proinflammatory responses. Despite being ...

Neuroscience

Typically one expects that the intervals between consecutive occurrences of a particular behavior will have a characteristic time scale around which most observations are centered. Surprisingly, the timing of many diverse behaviors from human ...
Using diffusion tensor imaging, several recent studies have shown that training results in changes in white matter efficiency as measured by fractional anisotropy (FA). In our work, we found that a form of mindfulness meditation, integrative body–mind ...
It is believed that neural representations of recent experiences become reactivated during sleep, and that this process serves to stabilize associated memories in long-term memory. Here, we initiated this reactivation process for specific memories during ...
Elevating Akt activation is an obvious clinical strategy to prevent progressive neuronal death in neurological diseases. However, this endeavor has been hindered because of the lack of specific Akt activators. Here, from a cell-based high-throughput ...

Physiology

Integrated physiological systems, such as the cardiac and the respiratory system, exhibit complex dynamics that are further influenced by intrinsic feedback mechanisms controlling their interaction. To probe how the cardiac and the respiratory system ...
Many age-related diseases are known to elicit protein misfolding and aggregation. Whereas environmental stressors, such as temperature, oxidative stress, and osmotic stress, can also damage proteins, it is not known whether aging and the environment ...

Plant Biology

The plant hormone abscisic acid (ABA) is produced in response to abiotic stresses and mediates stomatal closure in response to drought via recently identified ABA receptors (pyrabactin resistance/regulatory component of ABA receptor; PYR/RCAR). SLAC1 ...

Psychological and Cognitive Sciences

As the visual world changes, its representation in our consciousness must be constantly updated. Given that the external changes are continuous, it appears plausible that conscious updating is continuous as well. Alternatively, this updating could be ...

Systems Biology

A fundamental problem in meta-analysis is how to systematically combine information from multiple statistical tests to rigorously evaluate a single overarching hypothesis. This problem occurs in systems biology when attempting to map genomic attributes to ...

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