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Preview: Proceedings of the National Academy of Sciences recent issues

Proceedings of the National Academy of Sciences recent issues



Proceedings of the National Academy of Sciences RSS feed -- recent issues



 



In This Issue [This Week in PNAS]

2017-03-28T08:30:46-07:00

Bison invasion of North America Modern American bison. Image courtesy of the Government of Yukon. The arrival of bison in North America from Asia was an ecologically significant event, causing a major upheaval within the established large mammal community. The timing of the first bison arrival in North America remains...



Relevance of the alternate conductance states of anthrax toxin channel [Biological Sciences]

2017-03-28T08:30:47-07:00

In their recent article in PNAS, Das and Krantz (1) attempt to relate the previously described (2, 3) alternate conductance substate of the anthrax toxin protective antigen (PA63) channel to the allosteric helix compression model (4). Although we do not intend to discuss the differences between this model and the...



Reply to Yamini and Nestorovich: Alternate clamped states of the anthrax toxin protective antigen channel [Biological Sciences]

2017-03-28T08:30:47-07:00

Yamini and Nestorovich (1) recently commented on our article in PNAS (2). In their letter, they weigh in on two issues with the previously reported (3, 4) alternate conductance substate of the protective antigen (PA) translocase channel. The first point they raised was whether the conductance substate was a clamped...



QnAs with Marcia McNutt [QnAs]

2017-03-28T08:30:46-07:00

When geophysicist Marcia McNutt learned that she had been nominated to stand for election as president of the National Academy of Sciences (NAS), she modestly pointed out to the selection committee that, although she felt honored, she was surprised to be chosen from a pool of what were surely far...



George Klein: 1925-2016 [Retrospectives]

2017-03-28T08:30:46-07:00

George Klein, famous cancer biologist and acclaimed writer on matters of science, human responsibility, and the human condition, decorated by innumerable awards, honorary doctorates and other honors, elected member of this Academy and many other learned societies, including the Royal Swedish Academy of Sciences and the American Philosophical Society, and...



Manipulating molecules with quantum light [Chemistry]

2017-03-28T08:30:46-07:00

It was first realized by Purcell (1) that the spontaneous emission rate of a quantum system can be enhanced or suppressed by placing it in a resonant radiofrequency cavity. Spontaneous emission as it was first theoretically described by Einstein (2) is not a pure property of matter. It is described...



Can self-awareness be taught? Monkeys pass the mirror test—again [Psychological and Cognitive Sciences]

2017-03-28T08:30:46-07:00

“Mirrors,” she said, “are never to be trusted.” Neil Gaiman, Coraline The ability to recognize oneself in the mirror is often held as evidence of self-awareness. However, children under the age of 2 y and most animals do not behave as if their mirrored reflection represents their own face or...



Rationally designed PPAR{delta}-specific agonists and their therapeutic potential for metabolic syndrome [Chemistry]

2017-03-28T08:30:46-07:00

The peroxisome proliferator-activated receptor (PPAR) family of nuclear receptors regulates a wide variety of lipid-related genes, including those responsible for adipose differentiation, cholesterol metabolism, and lipid metabolism and transport. There are three different PPAR nuclear receptors, with different localizations and specializations. PPARα is primarily expressed in the liver, heart, kidney,...



Collaboration, conflict, and disconnect between psychologists and economists [Psychological and Cognitive Sciences]

2017-03-28T08:30:46-07:00

In PNAS, Bruine de Bruin and Fischhoff (1) describe two collaborations of psychologists and economists in which they made the central contributions by psychologists. In both cases, the objective was to design survey questions that measure in probabilistic terms the expectations that individuals hold for future events. They judged both...



Glass transition imminent, resistance is futile [Applied Physical Sciences]

2017-03-28T08:30:46-07:00

The immense variety of glassy materials around us makes it is easy to get caught up in excessive detail when thinking about the structural glass transition. For decades, there have been only a few attempts to describe covalently bonded, molecular, and metallic glasses on the same footing, so different do...



Effect of material flexibility on the thermodynamics and kinetics of hydrophobically induced evaporation of water [Applied Physical Sciences]

2017-03-28T08:30:47-07:00

The evaporation of water induced by confinement between hydrophobic surfaces has received much attention due to its suggested functional role in numerous biophysical phenomena and its importance as a general mechanism of hydrophobic self-assembly. Although much progress has been made in understanding the basic physics of hydrophobically induced evaporation, a...



Electron transfer between anatase TiO2 and an O2 molecule directly observed by atomic force microscopy [Chemistry]

2017-03-28T08:30:47-07:00

Activation of molecular oxygen is a key step in converting fuels into energy, but there is precious little experimental insight into how the process proceeds at the atomic scale. Here, we show that a combined atomic force microscopy/scanning tunneling microscopy (AFM/STM) experiment can both distinguish neutral O2 molecules in the...



Structural basis for specific ligation of the peroxisome proliferator-activated receptor {delta} [Chemistry]

2017-03-28T08:30:47-07:00

The peroxisome proliferator-activated receptor (PPAR) family comprises three subtypes: PPARα, PPARγ, and PPARδ. PPARδ transcriptionally modulates lipid metabolism and the control of energy homeostasis; therefore, PPARδ agonists are promising agents for treating a variety of metabolic disorders. In the present study, we develop a panel of rationally designed PPARδ agonists....



Biological regulation of atmospheric chemistry en route to planetary oxygenation [Earth, Atmospheric, and Planetary Sciences]

2017-03-28T08:30:47-07:00

Emerging evidence suggests that atmospheric oxygen may have varied before rising irreversibly ∼2.4 billion years ago, during the Great Oxidation Event (GOE). Significantly, however, pre-GOE atmospheric aberrations toward more reducing conditions—featuring a methane-derived organic-haze—have recently been suggested, yet their occurrence, causes, and significance remain underexplored. To examine the role of...



Optimal run-and-tumble-based transportation of a Janus particle with active steering [Physics]

2017-03-28T08:30:47-07:00

Although making artificial micrometric swimmers has been made possible by using various propulsion mechanisms, guiding their motion in the presence of thermal fluctuations still remains a great challenge. Such a task is essential in biological systems, which present a number of intriguing solutions that are robust against noisy environmental conditions...



Cross-cousin marriage among the Yanomamo shows evidence of parent-offspring conflict and mate competition between brothers [Anthropology]

2017-03-28T08:30:47-07:00

Marriage in many traditional societies often concerns the institutionalized exchange of reproductive partners among groups of kin. Such exchanges most often involve cross-cousins—marriage with the child of a parent’s opposite-sex sibling—but it is unclear who benefits from these exchanges. Here we analyze the fitness consequences of marrying relatives among the...



Morphological features of IFN-{gamma}-stimulated mesenchymal stromal cells predict overall immunosuppressive capacity [Applied Biological Sciences]

2017-03-28T08:30:47-07:00

Human mesenchymal stromal cell (MSC) lines can vary significantly in their functional characteristics, and the effectiveness of MSC-based therapeutics may be realized by finding predictive features associated with MSC function. To identify features associated with immunosuppressive capacity in MSCs, we developed a robust in vitro assay that uses principal-component analysis...



Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism [Biochemistry]

2017-03-28T08:30:47-07:00

Vertebrate rhodopsin (Rh) contains 11-cis-retinal as a chromophore to convert light energy into visual signals. On absorption of light, 11-cis-retinal is isomerized to all-trans-retinal, constituting a one-way reaction that activates transducin (Gt) followed by chromophore release. Here we report that bovine Rh, regenerated instead with a six-carbon-ring retinal chromophore featuring...



Phytosphingosine degradation pathway includes fatty acid {alpha}-oxidation reactions in the endoplasmic reticulum [Biochemistry]

2017-03-28T08:30:47-07:00

Although normal fatty acids (FAs) are degraded via β-oxidation, unusual FAs such as 2-hydroxy (2-OH) FAs and 3-methyl-branched FAs are degraded via α-oxidation. Phytosphingosine (PHS) is one of the long-chain bases (the sphingolipid components) and exists in specific tissues, including the epidermis and small intestine in mammals. In the degradation...



Structure-guided SCHEMA recombination generates diverse chimeric channelrhodopsins [Biochemistry]

2017-03-28T08:30:47-07:00

Integral membrane proteins (MPs) are key engineering targets due to their critical roles in regulating cell function. In engineering MPs, it can be extremely challenging to retain membrane localization capability while changing other desired properties. We have used structure-guided SCHEMA recombination to create a large set of functionally diverse chimeras...



Multisite aggregation of p53 and implications for drug rescue [Biochemistry]

2017-03-28T08:30:47-07:00

Protein aggregation is involved in many diseases. Often, a unique aggregation-prone sequence polymerizes to form regular fibrils. Many oncogenic mutants of the tumor suppressor p53 rapidly aggregate but form amorphous fibrils. A peptide surrounding Ile254 is proposed to be the aggregation-driving sequence in cells. We identified several different aggregating sites...



Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity [Biophysics and Computational Biology]

2017-03-28T08:30:47-07:00

Intrinsically disordered proteins (IDPs) that lack a unique 3D structure and comprise a large fraction of the human proteome play important roles in numerous cellular functions. Prostate-Associated Gene 4 (PAGE4) is an IDP that acts as a potentiator of the Activator Protein-1 (AP-1) transcription factor. Homeodomain-Interacting Protein Kinase 1 (HIPK1)...



Bacterial proteostasis balances energy and chaperone utilization efficiently [Biophysics and Computational Biology]

2017-03-28T08:30:47-07:00

Chaperones are protein complexes that help to fold and disaggregate a cell’s proteins. It is not understood how four major chaperone systems of Escherichia coli work together in proteostasis: the recognition, sorting, folding, and disaggregating of the cell’s many different proteins. Here, we model this machine. We combine extensive data...



Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis [Biophysics and Computational Biology]

2017-03-28T08:30:47-07:00

Proteins have evolved to perform diverse cellular functions, from serving as reaction catalysts to coordinating cellular propagation and development. Frequently, proteins do not exert their full potential as monomers but rather undergo concerted interactions as either homo-oligomers or with other proteins as hetero-oligomers. The experimental study of such protein complexes...



Fission yeast myosin I facilitates PI(4,5)P2-mediated anchoring of cytoplasmic dynein to the cortex [Cell Biology]

2017-03-28T08:30:47-07:00

Several key processes in the cell, such as vesicle transport and spindle positioning, are mediated by the motor protein cytoplasmic dynein, which produces force on the microtubule. For the functions that require movement of the centrosome and the associated nuclear material, dynein needs to have a stable attachment at the...



Toll pathway is required for wound-induced expression of barrier repair genes in the Drosophila epidermis [Developmental Biology]

2017-03-28T08:30:47-07:00

The epidermis serves as a protective barrier in animals. After epidermal injury, barrier repair requires activation of many wound response genes in epidermal cells surrounding wound sites. Two such genes in Drosophila encode the enzymes dopa decarboxylase (Ddc) and tyrosine hydroxylase (ple). In this paper we explore the involvement of...



AMPK blocks starvation-inducible transgenerational defects in Caenorhabditis elegans [Developmental Biology]

2017-03-28T08:30:48-07:00

Life history events, such as traumatic stress, illness, or starvation, can influence us through molecular changes that are recorded in a pattern of characteristic chromatin modifications. These modifications are often associated with adaptive adjustments in gene expression that can persist throughout the lifetime of the organism, or even span multiple...



Injury-stimulated and self-restrained BMP signaling dynamically regulates stem cell pool size during Drosophila midgut regeneration [Developmental Biology]

2017-03-28T08:30:48-07:00

Many adult organs rely on resident stem cells to maintain homeostasis. Upon injury, stem cells increase proliferation, followed by lineage differentiation to replenish damaged cells. Whether stem cells also change division mode to transiently increase their population size as part of a regenerative program and, if so, what the underlying...



Hormone and receptor interplay in the regulation of mosquito lipid metabolism [Developmental Biology]

2017-03-28T08:30:48-07:00

Mosquitoes transmit devastating human diseases because they need vertebrate blood for egg development. Metabolism in female mosquitoes is tightly coupled with blood meal-mediated reproduction, which requires an extremely high level of energy consumption. Functional analysis has shown that major genes encoding for enzymes involved in lipid metabolism (LM) in the...



Multitrait successional forest dynamics enable diverse competitive coexistence [Ecology]

2017-03-28T08:30:48-07:00

To explain diversity in forests, niche theory must show how multiple plant species coexist while competing for the same resources. Although successional processes are widespread in forests, theoretical work has suggested that differentiation in successional strategy allows only a few species stably to coexist, including only a single shade tolerant....



Osmolality/salinity-responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fish [Evolution]

2017-03-28T08:30:48-07:00

Fish respond to salinity stress by transcriptional induction of many genes, but the mechanism of their osmotic regulation is unknown. We developed a reporter assay using cells derived from the brain of the tilapia Oreochromis mossambicus (OmB cells) to identify osmolality/salinity-responsive enhancers (OSREs) in the genes of O. mossambicus. Genomic...



Loss of LMOD1 impairs smooth muscle cytocontractility and causes megacystis microcolon intestinal hypoperistalsis syndrome in humans and mice [Genetics]

2017-03-28T08:30:48-07:00

Megacystis microcolon intestinal hypoperistalsis syndrome (MMIHS) is a congenital visceral myopathy characterized by severe dilation of the urinary bladder and defective intestinal motility. The genetic basis of MMIHS has been ascribed to spontaneous and autosomal dominant mutations in actin gamma 2 (ACTG2), a smooth muscle contractile gene. However, evidence suggesting...



Cathepsin S is the maȷor activator of the psoriasis-associated proinflammatory cytokine IL-36{gamma} [Immunology and Inflammation]

2017-03-28T08:30:48-07:00

The proinflammatory cytokine IL-36γ is highly expressed in epithelial cells and is a pivotal mediator of epithelial inflammation. In particular, IL-36γ is strongly associated with the inflammatory skin disease psoriasis. As with other IL-1 cytokines, IL-36γ is expressed as an inactive precursor and must be processed by specific proteases to...



Receptor Mincle promotes skin allergies and is capable of recognizing cholesterol sulfate [Immunology and Inflammation]

2017-03-28T08:30:48-07:00

Sterile (noninfected) inflammation underlies the pathogenesis of many widespread diseases, such as allergies and autoimmune diseases. The evolutionarily conserved innate immune system is considered to play a key role in tissue injury recognition and the subsequent development of sterile inflammation; however, the underlying molecular mechanisms are not yet completely understood....



Inhibition of atherogenesis by the COP9 signalosome subunit 5 in vivo [Immunology and Inflammation]

2017-03-28T08:30:48-07:00

Constitutive photomorphogenesis 9 (COP9) signalosome 5 (CSN5), an isopeptidase that removes neural precursor cell-expressed, developmentally down-regulated 8 (NEDD8) moieties from cullins (thus termed “deNEDDylase”) and a subunit of the cullin-RING E3 ligase-regulating COP9 signalosome complex, attenuates proinflammatory NF-κB signaling. We previously showed that CSN5 is up-regulated in human atherosclerotic arteries....



Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells [Immunology and Inflammation]

2017-03-28T08:30:48-07:00

T-cell exhaustion is a progressive loss of effector function and memory potential due to persistent antigen exposure, which occurs in chronic viral infections and cancer. Here we investigate the relation between gene expression and chromatin accessibility in CD8+ tumor-infiltrating lymphocytes (TILs) that recognize a model tumor antigen and have features...



Mouse cytomegalovirus M36 and M45 death suppressors cooperate to prevent inflammation resulting from antiviral programmed cell death pathways [Microbiology]

2017-03-28T08:30:48-07:00

The complex interplay between caspase-8 and receptor-interacting protein (RIP) kinase RIP 3 (RIPK3) driving extrinsic apoptosis and necroptosis is not fully understood. Murine cytomegalovirus triggers both apoptosis and necroptosis in infected cells; however, encoded inhibitors of caspase-8 activity (M36) and RIP3 signaling (M45) suppress these antiviral responses. Here, we report...



Eliciting probabilistic expectations: Collaborations between psychologists and economists [Psychological and Cognitive Sciences]

2017-03-28T08:30:46-07:00

We describe two collaborations in which psychologists and economists provided essential support on foundational projects in major research programs. One project involved eliciting adolescents’ expectations regarding significant future life events affecting their psychological and economic development. The second project involved eliciting consumers’ expectations regarding inflation, a potentially vital input to...



New Middle Pleistocene hominin cranium from Gruta da Aroeira (Portugal) [Anthropology]

2017-03-28T08:30:46-07:00

The Middle Pleistocene is a crucial time period for studying human evolution in Europe, because it marks the appearance of both fossil hominins ancestral to the later Neandertals and the Acheulean technology. Nevertheless, European sites containing well-dated human remains associated with an Acheulean toolkit remain scarce. The earliest European hominin...



Topological knots and links in proteins [Applied Mathematics]

2017-03-28T08:30:46-07:00

Twenty years after their discovery, knots in proteins are now quite well understood. They are believed to be functionally advantageous and provide extra stability to protein chains. In this work, we go one step further and search for links—entangled structures, more complex than knots, which consist of several components. We...



Overcoming catastrophic forgetting in neural networks [Applied Mathematics]

2017-03-28T08:30:47-07:00

The ability to learn tasks in a sequential fashion is crucial to the development of artificial intelligence. Until now neural networks have not been capable of this and it has been widely thought that catastrophic forgetting is an inevitable feature of connectionist models. We show that it is possible to...



Eradicating catastrophic collapse in interdependent networks via reinforced nodes [Applied Physical Sciences]

2017-03-28T08:30:46-07:00

In interdependent networks, it is usually assumed, based on percolation theory, that nodes become nonfunctional if they lose connection to the network giant component. However, in reality, some nodes, equipped with alternative resources, together with their connected neighbors can still be functioning after disconnected from the giant component. Here, we...



Computational investigation of surface freezing in a molecular model of water [Applied Physical Sciences]

2017-03-28T08:30:46-07:00

Water freezes in a wide variety of low-temperature environments, from meteors and atmospheric clouds to soil and biological cells. In nature, ice usually nucleates at or near interfaces, because homogenous nucleation in the bulk can only be observed at deep supercoolings. Although the effect of proximal surfaces on freezing has...



Dynamic cross-correlations between entangled biofilaments as they diffuse [Applied Physical Sciences]

2017-03-28T08:30:46-07:00

Entanglement in polymer and biological physics involves a state in which linear interthreaded macromolecules in isotropic liquids diffuse in a spatially anisotropic manner beyond a characteristic mesoscopic time and length scale (tube diameter). The physical reason is that linear macromolecules become transiently localized in directions transverse to their backbone but...



Real space renormalization group theory of disordered models of glasses [Applied Physical Sciences]

2017-03-28T08:30:46-07:00

We develop a real space renormalization group analysis of disordered models of glasses, in particular of the spin models at the origin of the random first-order transition theory. We find three fixed points, respectively, associated with the liquid state, with the critical behavior, and with the glass state. The latter...



Core Concept: Unraveling the enigma of fast radio bursts [Astronomy]

2017-03-28T08:30:46-07:00

The mystery began in 2007, when astrophysicist Duncan Lorimer and his undergraduate physics student were combing through archival data from the Parkes Observatory in Australia. After a month of analysis, the two noticed something unusual: an extreme burst from 2001 that briefly became one of the brightest radio objects in...



Distinct recognition of complement iC3b by integrins {alpha}X{beta}2 and {alpha}M{beta}2 [Biochemistry]

2017-03-28T08:30:46-07:00

Recognition by the leukocyte integrins αXβ2 and αMβ2 of complement iC3b-opsonized targets is essential for effector functions including phagocytosis. The integrin-binding sites on iC3b remain incompletely characterized. Here, we describe negative-stain electron microscopy and biochemical studies of αXβ2 and αMβ2 in complex with iC3b. Despite high homology, the two integrins...



Persistence of the mitochondrial permeability transition in the absence of subunit c of human ATP synthase [Biochemistry]

2017-03-28T08:30:46-07:00

The permeability transition in human mitochondria refers to the opening of a nonspecific channel, known as the permeability transition pore (PTP), in the inner membrane. Opening can be triggered by calcium ions, leading to swelling of the organelle, disruption of the inner membrane, and ATP synthesis, followed by cell death....



Ligand-induced allostery in the interaction of the Pseudomonas aeruginosa heme binding protein with heme oxygenase [Biophysics and Computational Biology]

2017-03-28T08:30:46-07:00

A heme-dependent conformational rearrangement of the C-terminal domain of heme binding protein (PhuS) is required for interaction with the iron-regulated heme oxygenase (HemO). Herein, we further investigate the underlying mechanism of this conformational rearrangement and its implications for heme transfer via site-directed mutagenesis, resonance Raman (RR), hydrogen–deuterium exchange MS (HDX-MS)...



Steady-state EB cap size fluctuations are determined by stochastic microtubule growth and maturation [Biophysics and Computational Biology]

2017-03-28T08:30:46-07:00

Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively...



Conserved role for Gga proteins in phosphatidylinositol 4-kinase localization to the trans-Golgi network [Cell Biology]

2017-03-28T08:30:46-07:00

Phosphoinositides serve as key membrane determinants for assembly of clathrin coat proteins that drive formation of clathrin-coated vesicles. At the trans-Golgi network (TGN), phosphatidylinositol 4-phosphate (PtdIns4P) plays important roles in recruitment of two major clathrin adaptors, Gga (Golgi-localized, gamma-adaptin ear homology, Arf-binding) proteins and the AP-1 (assembly protein-1) complex. The...



Parasitophorous vacuole poration precedes its rupture and rapid host erythrocyte cytoskeleton collapse in Plasmodium falciparum egress [Cell Biology]

2017-03-28T08:30:46-07:00

In the asexual blood stages of malarial infection, merozoites invade erythrocytes and replicate within a parasitophorous vacuole to form daughter cells that eventually exit (egress) by sequential rupture of the vacuole and erythrocyte membranes. The current model is that PKG, a malarial cGMP-dependent protein kinase, triggers egress, activating malarial proteases...



Diagnosis of prostate cancer by desorption electrospray ionization mass spectrometric imaging of small metabolites and lipids [Chemistry]

2017-03-28T08:30:46-07:00

Accurate identification of prostate cancer in frozen sections at the time of surgery can be challenging, limiting the surgeon’s ability to best determine resection margins during prostatectomy. We performed desorption electrospray ionization mass spectrometry imaging (DESI-MSI) on 54 banked human cancerous and normal prostate tissue specimens to investigate the spatial...



Volatile secondary metabolites as aposematic olfactory signals and defensive weapons in aquatic environments [Chemistry]

2017-03-28T08:30:47-07:00

Olfaction is considered a distance sense; hence, aquatic olfaction is thought to be mediated only by molecules dissolved in water. Here, we challenge this view by showing that shrimp and fish can recognize the presence of hydrophobic olfactory cues by a “tactile” form of chemoreception. We found that odiferous furanosesquiterpenes...



Storage and release of hydrogen cyanide in a chelicerate (Oribatula tibialis) [Chemistry]

2017-03-28T08:30:47-07:00

Cyanogenesis denotes a chemical defensive strategy where hydrogen cyanide (HCN, hydrocyanic or prussic acid) is produced, stored, and released toward an attacking enemy. The high toxicity and volatility of HCN requires both chemical stabilization for storage and prevention of accidental self-poisoning. The few known cyanogenic animals are exclusively mandibulate arthropods...



Experimental comparison of two quantum computing architectures [Computer Sciences]

2017-03-28T08:30:46-07:00

We run a selection of algorithms on two state-of-the-art 5-qubit quantum computers that are based on different technology platforms. One is a publicly accessible superconducting transmon device (www.research.ibm.com/ibm-q) with limited connectivity, and the other is a fully connected trapped-ion system. Even though the two systems have different native quantum interactions,...



Specific deletion of LKB1/Stk11 in the Mullerian duct mesenchyme drives hyperplasia of the periurethral stroma and tumorigenesis in male mice [Developmental Biology]

2017-03-28T08:30:46-07:00

Nearly all older men will experience lower urinary tract symptoms associated with benign prostatic hyperplasia (BPH), the etiology of which is not well understood. We have generated Stk11CKO mice by conditional deletion of the liver kinase B1 (LKB1) tumor suppressor gene, Stk11 (serine threonine kinase 11), in the fetal Müllerian...



Pacific North American circulation pattern links external forcing and North American hydroclimatic change over the past millennium [Earth, Atmospheric, and Planetary Sciences]

2017-03-28T08:30:46-07:00

Land and sea surface temperatures, precipitation, and storm tracks in North America and the North Pacific are controlled to a large degree by atmospheric variability associated with the Pacific North American (PNA) pattern. The modern instrumental record indicates a trend toward a positive PNA phase in recent decades, which has...



Sediment supply controls equilibrium channel geometry in gravel rivers [Earth, Atmospheric, and Planetary Sciences]

2017-03-28T08:30:46-07:00

In many gravel-bedded rivers, floods that fill the channel banks create just enough shear stress to move the median-sized gravel particles on the bed surface (D50). Because this observation is common and is supported by theory, the coincidence of bankfull flow and the incipient motion of D50 has become a...



Deep-sea coral evidence for lower Southern Ocean surface nitrate concentrations during the last ice age [Earth, Atmospheric, and Planetary Sciences]

2017-03-28T08:30:46-07:00

The Southern Ocean regulates the ocean’s biological sequestration of CO2 and is widely suspected to underpin much of the ice age decline in atmospheric CO2 concentration, but the specific changes in the region are debated. Although more complete drawdown of surface nutrients by phytoplankton during the ice ages is supported...



Fossil and genomic evidence constrains the timing of bison arrival in North America [Earth, Atmospheric, and Planetary Sciences]

2017-03-28T08:30:47-07:00

The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry...



Flowering phenology shifts in response to biodiversity loss [Ecology]

2017-03-28T08:30:47-07:00

Observational studies and experimental evidence agree that rising global temperatures have altered plant phenology—the timing of life events, such as flowering, germination, and leaf-out. Other large-scale global environmental changes, such as nitrogen deposition and altered precipitation regimes, have also been linked to changes in flowering times. Despite our increased understanding...



Inner Workings: SMART collars help track and conserve wildlife [Engineering]

2017-03-28T08:30:46-07:00

Caleb Bryce drops into a ravine and tucks into the shadows. The dry foliage bursts into confetti as a puma careens up the opposite bank, hounds wailing close behind. Bryce and other scientists leap in pursuit. The big cat skirts a meadow and vaults into a fir tree. Wide-eyed, she...



Wettability effect on nanoconfined water flow [Engineering]

2017-03-28T08:30:46-07:00

Understanding and controlling the flow of water confined in nanopores has tremendous implications in theoretical studies and industrial applications. Here, we propose a simple model for the confined water flow based on the concept of effective slip, which is a linear sum of true slip, depending on a contact angle,...



Transcriptional landscape of the human cell cycle [Genetics]

2017-03-28T08:30:47-07:00

Steady-state gene expression across the cell cycle has been studied extensively. However, transcriptional gene regulation and the dynamics of histone modification at different cell-cycle stages are largely unknown. By applying a combination of global nuclear run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and histone-modification Chip sequencing (ChIP-seq), we depicted a comprehensive...



Gentamicin B1 is a minor gentamicin component with major nonsense mutation suppression activity [Genetics]

2017-03-28T08:30:47-07:00

Nonsense mutations underlie about 10% of rare genetic disease cases. They introduce a premature termination codon (PTC) and prevent the formation of full-length protein. Pharmaceutical gentamicin, a mixture of several related aminoglycosides, is a frequently used antibiotic in humans that can induce PTC readthrough and suppress nonsense mutations at high...



Modulating IgG effector function by Fc glycan engineering [Immunology and Inflammation]

2017-03-28T08:30:47-07:00

IgG antibodies contain a conserved N-glycosylation site on the Fc domain to which a complex, biantennary glycan is attached. The fine structures of this glycan modulate antibody effector functions by affecting the binding affinity of the Fc to diverse Fc receptor family members. For example, core fucosylation significantly decreases antibody-dependent...



Genetic variation in chromosome Y regulates susceptibility to influenza A virus infection [Immunology and Inflammation]

2017-03-28T08:30:47-07:00

Males of many species, ranging from humans to insects, are more susceptible than females to parasitic, fungal, bacterial, and viral infections. One mechanism that has been proposed to account for this difference is the immunocompetence handicap model, which posits that the greater infectious disease burden in males is due to...



Small molecule selectively suppresses MYC transcription in cancer cells [Medical Sciences]

2017-03-28T08:30:47-07:00

Stauprimide is a staurosporine analog that promotes embryonic stem cell (ESC) differentiation by inhibiting nuclear localization of the MYC transcription factor NME2, which in turn results in down-regulation of MYC transcription. Given the critical role the oncogene MYC plays in tumor initiation and maintenance, we explored the potential of stauprimide...



B vitamins attenuate the epigenetic effects of ambient fine particles in a pilot human intervention trial [Medical Sciences]

2017-03-28T08:30:47-07:00

Acute exposure to fine particle (PM2.5) induces DNA methylation changes implicated in inflammation and oxidative stress. We conducted a crossover trial to determine whether B-vitamin supplementation averts such changes. Ten healthy adults blindly received a 2-h, controlled-exposure experiment to sham under placebo, PM2.5 (250 μg/m3) under placebo, and PM2.5 (250...



Selective dietary supplementation in early postpartum is associated with high resilience against depressed mood [Medical Sciences]

2017-03-28T08:30:47-07:00

Medical research is moving toward prevention strategies during prodromal states. Postpartum blues (PPB) is often a prodromal state for postpartum depression (PPD), with severe PPB strongly associated with an elevated risk for PPD. The most common complication of childbearing, PPD has a prevalence of 13%, but there are no widespread...



Host immunity to Plasmodium falciparum and the assessment of emerging artemisinin resistance in a multinational cohort [Microbiology]

2017-03-28T08:30:47-07:00

Artemisinin-resistant falciparum malaria, defined by a slow-clearance phenotype and the presence of kelch13 mutants, has emerged in the Greater Mekong Subregion. Naturally acquired immunity to malaria clears parasites independent of antimalarial drugs. We hypothesized that between- and within-population variations in host immunity influence parasite clearance after artemisinin treatment and the...



Patterns of coordinated cortical remodeling during adolescence and their associations with functional specialization and evolutionary expansion [Neuroscience]

2017-03-28T08:30:47-07:00

During adolescence, the human cortex undergoes substantial remodeling to support a rapid expansion of behavioral repertoire. Accurately quantifying these changes is a prerequisite for understanding normal brain development, as well as the neuropsychiatric disorders that emerge in this vulnerable period. Past accounts have demonstrated substantial regional heterogeneity in patterns of...



Tunable moire bands and strong correlations in small-twist-angle bilayer graphene [Physics]

2017-03-28T08:30:46-07:00

According to electronic structure theory, bilayer graphene is expected to have anomalous electronic properties when it has long-period moiré patterns produced by small misalignments between its individual layer honeycomb lattices. We have realized bilayer graphene moiré crystals with accurately controlled twist angles smaller than 1° and studied their properties using...



Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model [Physics]

2017-03-28T08:30:46-07:00

A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a...



Deep melting reveals liquid structural memory and anomalous ferromagnetism in bismuth [Physics]

2017-03-28T08:30:46-07:00

As an archetypal semimetal with complex and anisotropic Fermi surface and unusual electric properties (e.g., high electrical resistance, large magnetoresistance, and giant Hall effect), bismuth (Bi) has played a critical role in metal physics. In general, Bi displays diamagnetism with a high volumetric susceptibility (∼10−4). Here, we report unusual ferromagnetism...



Electron-hole asymmetry of the topological surface states in strained HgTe [Physics]

2017-03-28T08:30:46-07:00

Topological insulators are a new class of materials with an insulating bulk and topologically protected metallic surface states. Although it is widely assumed that these surface states display a Dirac-type dispersion that is symmetric above and below the Dirac point, this exact equivalence across the Fermi level has yet to...



Monostable superrepellent materials [Physics]

2017-03-28T08:30:46-07:00

Superrepellency is an extreme situation where liquids stay at the tops of rough surfaces, in the so-called Cassie state. Owing to the dramatic reduction of solid/liquid contact, such states lead to many applications, such as antifouling, droplet manipulation, hydrodynamic slip, and self-cleaning. However, superrepellency is often destroyed by impalement transitions...



In vivo diagnostics of early abiotic plant stress response via Raman spectroscopy [Physics]

2017-03-28T08:30:46-07:00

Development of a phenotyping platform capable of noninvasive biochemical sensing could offer researchers, breeders, and producers a tool for precise response detection. In particular, the ability to measure plant stress in vivo responses is becoming increasingly important. In this work, a Raman spectroscopic technique is developed for high-throughput stress phenotyping...



BRASSINOSTEROID INSENSITIVE2 negatively regulates cellulose synthesis in Arabidopsis by phosphorylating cellulose synthase 1 [Plant Biology]

2017-03-28T08:30:47-07:00

The deposition of cellulose is a defining aspect of plant growth and development, but regulation of this process is poorly understood. Here, we demonstrate that the protein kinase BRASSINOSTEROID INSENSITIVE2 (BIN2), a key negative regulator of brassinosteroid (BR) signaling, can phosphorylate Arabidopsis cellulose synthase A1 (CESA1), a subunit of the...



Noncanonical role of Arabidopsis COP1/SPA complex in repressing BIN2-mediated PIF3 phosphorylation and degradation in darkness [Plant Biology]

2017-03-28T08:30:47-07:00

The E3 ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) has been known to mediate key signaling factors for degradation via the ubiquitin/26S proteasome pathway in both plants and animals. Here, we report a noncanonical function of Arabidopsis COP1, the central repressor of photomorphogenesis, in the form of a COP1/ SUPPRESSOR of phyA-105...



Correction for Nielsen et al., Opinion: Gender diversity leads to better science [Correction]

2017-03-28T08:30:48-07:00

OPINION Correction for “Opinion: Gender diversity leads to better science,” by Mathias Wullum Nielsen, Sharla Alegria, Love Börjeson, Henry Etzkowitz, Holly J. Falk-Krzesinski, Aparna Joshi, Erin Leahey, Laurel Smith-Doerr, Anita Williams Woolley, and Londa Schiebinger, which appeared in issue 8, February 21, 2017, of Proc Natl Acad Sci USA (114:1740–1742;...



Correction for Koop, Crystals creeping out of cracks [Correction]

2017-03-28T08:30:48-07:00

COMMENTARY Correction for “Crystals creeping out of cracks,” by Thomas Koop, which appeared in issue 5, January 31, 2017, of Proc Natl Acad Sci USA (114:797–799; first published January 19, 2017; 10.1073/pnas.1620084114). The author notes that panel E in Fig. 1 appeared incorrectly. The corrected figure and its legend appear...



Correction for Sethna et al., Insights into immune system development and function from mouse T-cell repertoires [Correction]

2017-03-28T08:30:48-07:00

BIOPHYSICS AND COMPUTATIONAL BIOLOGY Correction for “Insights into immune system development and function from mouse T-cell repertoires,” by Zachary Sethna, Yuval Elhanati, Chrissy S. Dudgeon, Curtis G. Callan Jr., Arnold J. Levine, Thierry Mora, and Aleksandra M. Walczak, which appeared in issue 9, February 28, 2017, of Proc Natl Acad...



Correction for Hou et al., Homeostatic regulation of AMPA receptor expression at single hippocampal synapses [Correction]

2017-03-28T08:30:48-07:00

NEUROSCIENCE Correction for “Homeostatic regulation of AMPA receptor expression at single hippocampal synapses,” by Qingming Hou, Dawei Zhang, Larissa Jarzylo, Richard L. Huganir, and Heng-Ye Man, which appeared in issue 2, January 15, 2008, of Proc Natl Acad Sci USA (105:775–780; first published January 3, 2008; 10.1073/pnas.0706447105). The authors note...



In This Issue [This Week in PNAS]

2017-03-21T09:13:07-07:00

Enhanced vision may have enabled evolutionary shift from water to land Enlarged eyes may have aided vertebrates’ shift from water to land. The origin of limbs in the evolutionary foray of vertebrates from water to land has long claimed researchers’ interest, but the role of vision in this momentous transition,...



On the role of Mitofusin 2 in endoplasmic reticulum-mitochondria tethering [Biological Sciences]

2017-03-21T09:13:08-07:00

The recent paper by Naon et al. (1) claims that their new data “definitively” prove the role of Mitofusin 2 (Mfn2) as an endoplasmic reticulum (ER)–mitochondria tether, supporting their original proposal (2) and arguing against evidence presented by ourselves and others (3–6) suggesting that Mfn2 is a negative regulator of...



Reply to Filadi et al.: Does Mitofusin 2 tether or separate endoplasmic reticulum and mitochondria? [Biological Sciences]

2017-03-21T09:13:08-07:00

We thank Filadi et al. for their comments (1) on our paper (2), where we address whether the discrepancies between their paper (3) and our original discovery of Mitofusin (Mfn) 2 as an endoplasmic reticulum (ER)–mitochondria tether (4) resulted from: (i) clonal effects of chronic Mfn2 ablation, (ii) proximity measurement...



Does influenza drive absolute humidity? [Biological Sciences]

2017-03-21T09:13:08-07:00

Multiple lines of evidence suggest that absolute humidity and school terms affect the timing of influenza epidemics, although the contributions of these and other factors are still unresolved (1–5). In PNAS, Deyle et al. (6) applied convergent cross-mapping (CCM) to measure the impact of environmental variables on influenza activity. The...



Reply to Baskerville and Cobey: Misconceptions about causation with synchrony and seasonal drivers [Biological Sciences]

2017-03-21T09:13:08-07:00

Baskerville and Cobey (1) caution against convergent cross-mapping (CCM) as a test for causation. However, their argument is based on an incorrect application of CCM arising from misconceptions about causation with synchrony. As stated in Deyle et al. (2), it is widely believed that there is synchrony between flu incidence...



Stephen Fienberg: Superman of statistics [Retrospectives]

2017-03-21T09:13:07-07:00

Stephen E. Fienberg died on December 14, 2016 after a 4-year battle with cancer. He was husband to Joyce, father to Anthony and Howard, grandfather to six, brother to Lorne, mentor, teacher, and a prolific researcher. Most of all, he was a tireless promoter of the idea that the field...



The depressed brain in Parkinson's disease: Implications for an inflammatory biomarker [Neuroscience]

2017-03-21T09:13:07-07:00

The Need for a Biomarker in Parkinson's Disease Parkinson’s disease (PD) is an increasingly prevalent neurodegenerative disorder currently diagnosed solely on the presence of motor symptoms (i.e., tremor, rigidity, bradykinesia, and postural instability) and their response to dopamine replacement therapy. A major unmet need is the limited number and failure...



Glucagon antagonism in islet cell proliferation [Physiology]

2017-03-21T09:13:07-07:00

The peptide hormones insulin and glucagon (gcg) are inextricably linked in the normal control of glucose homeostasis and in the dysregulated glucose homeostasis that defines diabetes mellitus. Pancreatic islets secrete both insulin and gcg in a manner that is tightly juxtaposed. β Cells secrete insulin, a peptide hormone that promotes...



Keeping the nitrogen-fixation dream alive [Microbiology]

2017-03-21T09:13:07-07:00

The conversion of inert N2 gas to a metabolically tractable form, such as ammonia, is called nitrogen fixation. In biology, nitrogen fixation is a highly oxygen-sensitive process restricted to a select group of diverse microorganisms, often collectively referred to as diazotrophs, or “nitrogen eaters.” The sparse availability of fixed nitrogen,...



Self-interrupted synthesis of sterically hindered aliphatic polyamide dendrimers [Chemistry]

2017-03-21T09:13:08-07:00

2,2-Bis(azidomethyl)propionic acid was prepared in four steps and 85% yield from the commercially available 2,2-bis(hydroxymethyl)propionic acid and used as the starting building block for the divergent, convergent, and double-stage convergent–divergent iterative methods for the synthesis of dendrimers and dendrons containing ethylenediamine (EDA), piperazine (PPZ), and methyl 2,2-bis(aminomethyl)propionate (COOMe) cores. These...



Determining climate effects on US total agricultural productivity [Earth, Atmospheric, and Planetary Sciences]

2017-03-21T09:13:08-07:00

The sensitivity of agricultural productivity to climate has not been sufficiently quantified. The total factor productivity (TFP) of the US agricultural economy has grown continuously for over half a century, with most of the growth typically attributed to technical change. Many studies have examined the effects of local climate on...



Multisensor-integrated organs-on-chips platform for automated and continual in situ monitoring of organoid behaviors [Engineering]

2017-03-21T09:13:08-07:00

Organ-on-a-chip systems are miniaturized microfluidic 3D human tissue and organ models designed to recapitulate the important biological and physiological parameters of their in vivo counterparts. They have recently emerged as a viable platform for personalized medicine and drug screening. These in vitro models, featuring biomimetic compositions, architectures, and functions, are...



Entanglement of quantum clocks through gravity [Physics]

2017-03-21T09:13:08-07:00

In general relativity, the picture of space–time assigns an ideal clock to each world line. Being ideal, gravitational effects due to these clocks are ignored and the flow of time according to one clock is not affected by the presence of clocks along nearby world lines. However, if time is...



Deep-sea vent phage DNA polymerase specifically initiates DNA synthesis in the absence of primers [Biochemistry]

2017-03-21T09:13:08-07:00

A DNA polymerase is encoded by the deep-sea vent phage NrS-1. NrS-1 has a unique genome organization containing genes that are predicted to encode a helicase and a single-stranded DNA (ssDNA)-binding protein. The gene for an unknown protein shares weak homology with the bifunctional primase–polymerases (prim–pols) from archaeal plasmids but...



Arsenic trioxide targets MTHFD1 and SUMO-dependent nuclear de novo thymidylate biosynthesis [Biochemistry]

2017-03-21T09:13:08-07:00

Arsenic exposure increases risk for cancers and is teratogenic in animal models. Here we demonstrate that small ubiquitin-like modifier (SUMO)- and folate-dependent nuclear de novo thymidylate (dTMP) biosynthesis is a sensitive target of arsenic trioxide (As2O3), leading to uracil misincorporation into DNA and genome instability. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) and...