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Proceedings of the National Academy of Sciences recent issues



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In This Issue [This Week in PNAS]

2017-08-22T09:15:27-07:00

Genetic engineering yields food crops in striking hues Engineered tomatoes produce red-violet betalain pigments. Betalains, which are a group of red and yellow plant pigments, are used as natural dyes in dairy, meat, and confectionery products, and as antioxidants in dietary supplements. Few edible plants yield commercial quantities of pure...



Edge effects in temperate forests subjected to high nitrogen deposition [Biological Sciences]

2017-08-22T09:15:27-07:00

Reinmann and Hutyra (1) measured an increase in aboveground forest growth and biomass at temperate oak forest edges (0–10 m) compared with the interior (20–30 m). When scaling their results up to the region of southern New England, they obtained an increase in aboveground carbon (C) uptake (13%) and C...



Reply to Remy et al.: Local and global limitations to forest productivity as mediators of biogeochemical response to forest edge effects [Biological Sciences]

2017-08-22T09:15:27-07:00

Despite the heavily fragmented nature of the world’s forests (1), the response of forest carbon (C) and nitrogen (N) dynamics to edge effects is understudied. Contrasting our findings that edge effects did not alter soil C and N storage of temperate forests within residential landscapes in New England (2), Remy...



QnAs with Alan Hastings [QnAs]

2017-08-22T09:15:27-07:00

Theoretical ecology uses conceptual and mathematical models, computer simulations, and data analysis to study ecological systems. Alan Hastings, a Distinguished Professor of Environmental Science and Policy at the University of California, Davis, has contributed significantly to the development of this field over the past four decades. Much of his research...



Profile of Nahum Sonenberg [Profile]

2017-08-22T09:15:27-07:00

Five years after the final shots of World War II rang out, a child and his father stood on the coast of the Mediterranean Sea. From their vantage point in a cemetery in the town of Jaffa, Israel, the boy gazed across the sea and envisioned stepping onto the sands...



Profile of Peidong Yang [Profile]

2017-08-22T09:15:27-07:00

In the fall of 2015, Peidong Yang, professor of chemistry at the University of California, Berkeley, received a phone call from the MacArthur Foundation. The caller asked if Yang was alone. Having just finished his lunch, Yang hurried to his office. The caller identified himself as the director of the...



Decoding ants’ olfactory system sheds light on the evolution of social communication [Evolution]

2017-08-22T09:15:27-07:00

Chemical communication is the primordial and possibly most efficient way of transmitting messages between living units (1). It has reached its apex in the “superorganisms” (2), for example in colonies of eusocial insects, such as honey bees (3). Colony survival and reproductive success rely on the chemical communication channel to...



Inflammation correlates with symptoms in chronic fatigue syndrome [Immunology and Inflammation]

2017-08-22T09:15:27-07:00

It is not unusual for patients who say they are sick to have normal results on standard laboratory testing. The physician often concludes that there is no “real” illness and that the patients’ symptoms likely stem from a psychological disorder. An alternative conclusion, often honored in the breach, is that...



Measuring the effects of farming on human skull morphology [Anthropology]

2017-08-22T09:15:27-07:00

Approximately 10,000 years ago, certain human groups began to rely on diets derived from domesticated plants and animals rather than acquiring wild sources of food via hunting, gathering, and foraging. This transition in subsistence economy occurred independently in several global regions, with particular starchy crops (e.g., wheat, barley, rice, maize,...



Pictures of the prologue to neurotransmitter release [Biophysics and Computational Biology]

2017-08-22T09:15:27-07:00

Membrane fusion and fission determine compartmentalization in eukaryotic cells and uptake or secretion of various molecular species. For example, a very rapid, tightly regulated, Ca2+-triggered fusion event releases neurotransmitters into the synaptic cleft (1). A long history of identifying and characterizing its essential components has allowed in vitro reconstitution, as...



Ballistic thermophoresis of adsorbates on free-standing graphene [Applied Physical Sciences]

2017-08-22T09:15:27-07:00

The textbook thermophoretic force which acts on a body in a fluid is proportional to the local temperature gradient. The same is expected to hold for the macroscopic drift behavior of a diffusive cluster or molecule physisorbed on a solid surface. The question we explore here is whether that is...



Janus dendrimersomes coassembled from fluorinated, hydrogenated, and hybrid Janus dendrimers as models for cell fusion and fission [Chemistry]

2017-08-22T09:15:27-07:00

A three-component system of Janus dendrimers (JDs) including hydrogenated, fluorinated, and hybrid hydrogenated–fluorinated JDs are reported to coassemble by film hydration at specific ratios into an unprecedented class of supramolecular Janus particles (JPs) denoted Janus dendrimersomes (JDSs). They consist of a dumbbell-shaped structure composed of an onion-like hydrogenated vesicle and...



Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood [Engineering]

2017-08-22T09:15:27-07:00

The ELISA is the mainstay for sensitive and quantitative detection of protein analytes. Despite its utility, ELISA is time-consuming, resource-intensive, and infrastructure-dependent, limiting its availability in resource-limited regions. Here, we describe a self-contained immunoassay platform (the “D4 assay”) that converts the sandwich immunoassay into a point-of-care test (POCT). The D4...



A study of problems encountered in Granger causality analysis from a neuroscience perspective [Statistics]

2017-08-22T09:15:27-07:00

Granger causality methods were developed to analyze the flow of information between time series. These methods have become more widely applied in neuroscience. Frequency-domain causality measures, such as those of Geweke, as well as multivariate methods, have particular appeal in neuroscience due to the prevalence of oscillatory phenomena and highly...



Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in Bacillus subtilis [Biochemistry]

2017-08-22T09:15:27-07:00

Bacterial sporulation allows starving cells to differentiate into metabolically dormant spores that can survive extreme conditions. Following asymmetric division, the mother cell engulfs the forespore, surrounding it with two bilayer membranes. During the engulfment process, an essential channel, the so-called feeding tube apparatus, is thought to cross both membranes to...



Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis [Biochemistry]

2017-08-22T09:15:27-07:00

Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, interfere with the efficiency and accuracy of DNA replication and transcription. However, the molecular mechanisms of DNA alkylation-induced transcriptional stalling and mutagenesis remain unknown. In this study, we systematically investigated how RNA polymerase II (pol II) recognizes and...



Histone phosphorylation by TRPM6’s cleaved kinase attenuates adȷacent arginine methylation to regulate gene expression [Biochemistry]

2017-08-22T09:15:27-07:00

TRPM6 and TRPM7 are members of the melastatin-related transient receptor potential (TRPM) subfamily of ion channels. Deletion of either gene in mice is embryonically lethal. TRPM6/7 are the only known examples of single polypeptides containing both an ion channel pore and a serine/threonine kinase (chanzyme). Here we show that the...



Self-organization process in newborn skin organoid formation inspires strategy to restore hair regeneration of adult cells [Cell Biology]

2017-08-22T09:15:27-07:00

Organoids made from dissociated progenitor cells undergo tissue-like organization. This in vitro self-organization process is not identical to embryonic organ formation, but it achieves a similar phenotype in vivo. This implies genetic codes do not specify morphology directly; instead, complex tissue architectures may be achieved through several intermediate layers of...



Zbtb7b engages the long noncoding RNA Blnc1 to drive brown and beige fat development and thermogenesis [Developmental Biology]

2017-08-22T09:15:27-07:00

Brown and beige adipocytes convert chemical energy into heat through uncoupled respiration to defend against cold stress. Beyond thermogenesis, brown and beige fats engage other metabolic tissues via secreted factors to influence systemic energy metabolism. How the protein and long noncoding RNA (lncRNA) regulatory networks act in concert to regulate...



Protein kinase C delta phosphorylates ecdysone receptor B1 to promote gene expression and apoptosis under 20-hydroxyecdysone regulation [Developmental Biology]

2017-08-22T09:15:27-07:00

The nuclear receptor EcRB1, which is activated by the insect steroid hormone 20-hydroxyecdysone (20E), is reportedly phosphorylated by a protein kinase after 20E induction. However, the protein kinase has not been identified, and the significance of EcRB1 phosphorylation is unclear. In this study, we identified a protein kinase C δ...



Genetic background-dependent role of Egr1 for eyelid development [Developmental Biology]

2017-08-22T09:15:27-07:00

EGR1 is an early growth response zinc finger transcription factor with broad actions, including in differentiation, mitogenesis, tumor suppression, and neuronal plasticity. Here we demonstrate that Egr1−/− mice on the C57BL/6 background have normal eyelid development, but back-crossing to BALB/c background for four or five generations resulted in defective eyelid...



miR-146a-Traf6 regulatory axis controls autoimmunity and myelopoiesis, but is dispensable for hematopoietic stem cell homeostasis and tumor suppression [Immunology and Inflammation]

2017-08-22T09:15:27-07:00

microRNA-146a (miR-146a) has been previously implicated as an essential molecular brake, preventing immune overreaction and malignant transformation by attenuating NF-κB signaling, putatively via repression of the Traf6 and Irak1 genes. The exact contribution of miR-146a–mediated silencing of these genes to the control of immune activation is currently unknown. Therefore, we...



Cytokine signature associated with disease severity in chronic fatigue syndrome patients [Immunology and Inflammation]

2017-08-22T09:15:27-07:00

Although some signs of inflammation have been reported previously in patients with myalgic encephalomyelitis or chronic fatigue syndrome (ME/CFS), the data are limited and contradictory. High-throughput methods now allow us to interrogate the human immune system for multiple markers of inflammation at a scale that was not previously possible. To...



Stress-inducible gene Atf3 in the noncancer host cells contributes to chemotherapy-exacerbated breast cancer metastasis [Medical Sciences]

2017-08-22T09:15:27-07:00

Chemotherapy is a double-edged sword. It is anticancer because of its cytotoxicity. Paradoxically, by increasing chemoresistance and cancer metastasis, it is also procancer. However, the underlying mechanisms for chemotherapy-induced procancer activities are not well understood. Here we describe the ability of paclitaxel (PTX), a frontline chemotherapeutic agent, to exacerbate metastasis...



Early cytoplasmic uncoating is associated with infectivity of HIV-1 [Microbiology]

2017-08-22T09:15:27-07:00

After fusion, HIV delivers its conical capsid into the cytoplasm. To release the contained reverse-transcribing viral genome, the capsid must disassemble in a process termed uncoating. Defining the kinetics, dynamics, and cellular location of uncoating of virions leading to infection has been confounded by defective, noninfectious particles and the stochastic...



Glycine receptor {alpha}3 and {alpha}2 subunits mediate tonic and exogenous agonist-induced currents in forebrain [Neuroscience]

2017-08-22T09:15:27-07:00

Neuronal inhibition can occur via synaptic mechanisms or through tonic activation of extrasynaptic receptors. In spinal cord, glycine mediates synaptic inhibition through the activation of heteromeric glycine receptors (GlyRs) composed primarily of α1 and β subunits. Inhibitory GlyRs are also found throughout the brain, where GlyR α2 and α3 subunit...



Adiponectin protects against development of metabolic disturbances in a PCOS mouse model [Physiology]

2017-08-22T09:15:27-07:00

Adiponectin, together with adipocyte size, is the strongest factor associated with insulin resistance in women with polycystic ovary syndrome (PCOS). This study investigates the causal relationship between adiponectin levels and metabolic and reproductive functions in PCOS. Prepubertal mice overexpressing adiponectin from adipose tissue (APNtg), adiponectin knockouts (APNko), and their wild-type...



Arabidopsis SH3P2 is an ubiquitin-binding protein that functions together with ESCRT-I and the deubiquitylating enzyme AMSH3 [Plant Biology]

2017-08-22T09:15:27-07:00

Clathrin-mediated endocytosis of plasma membrane proteins is an essential regulatory process that controls plasma membrane protein abundance and is therefore important for many signaling pathways, such as hormone signaling and biotic and abiotic stress responses. On endosomal sorting, plasma membrane proteins maybe recycled or targeted for vacuolar degradation, which is...



Flower-specific jasmonate signaling regulates constitutive floral defenses in wild tobacco [Plant Biology]

2017-08-22T09:15:27-07:00

Optimal defense (OD) theory predicts that within a plant, tissues are defended in proportion to their fitness value and risk of predation. The fitness value of leaves varies greatly and leaves are protected by jasmonate (JA)-inducible defenses. Flowers are vehicles of Darwinian fitness in flowering plants and are attacked by...



Urban sustainability in an age of enduring inequalities: Advancing theory and ecometrics for the 21st-century city [Social Sciences]

2017-08-22T09:15:27-07:00

The environmental fragility of cities under advanced urbanization has motivated extensive efforts to promote the sustainability of urban ecosystems and physical infrastructures. Less attention has been devoted to neighborhood inequalities and fissures in the civic infrastructure that potentially challenge social sustainability and the capacity of cities to collectively address environmental...



Inferring patterns of folktale diffusion using genomic data [Anthropology]

2017-08-22T09:15:27-07:00

Observable patterns of cultural variation are consistently intertwined with demic movements, cultural diffusion, and adaptation to different ecological contexts [Cavalli-Sforza and Feldman (1981) Cultural Transmission and Evolution: A Quantitative Approach; Boyd and Richerson (1985) Culture and the Evolutionary Process]. The quantitative study of gene–culture coevolution has focused in particular on...



Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany [Anthropology]

2017-08-22T09:15:27-07:00

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution...



Functional New World monkey oxytocin forms elicit an altered signaling profile and promotes parental care in rats [Anthropology]

2017-08-22T09:15:27-07:00

The neurohormone oxytocin is a key player in the modulation of reproductive and social behavioral traits, such as parental care. Recently, a correlation between different forms of oxytocin and behavioral phenotypes has been described in the New World Monkeys (NWMs). Here, we demonstrate that, compared with the Leu8OXT found in...



Changes in human skull morphology across the agricultural transition are consistent with softer diets in preindustrial farming groups [Anthropology]

2017-08-22T09:15:27-07:00

Agricultural foods and technologies are thought to have eased the mechanical demands of diet—how often or how hard one had to chew—in human populations worldwide. Some evidence suggests correspondingly worldwide changes in skull shape and form across the agricultural transition, although these changes have proved difficult to characterize at a...



Engineered gray mold resistance, antioxidant capacity, and pigmentation in betalain-producing crops and ornamentals [Applied Biological Sciences]

2017-08-22T09:15:27-07:00

Betalains are tyrosine-derived red-violet and yellow plant pigments known for their antioxidant activity, health-promoting properties, and wide use as food colorants and dietary supplements. By coexpressing three genes of the recently elucidated betalain biosynthetic pathway, we demonstrate the heterologous production of these pigments in a variety of plants, including three...



CRISPR-Cas9 vectors for genome editing and host engineering in the baculovirus-insect cell system [Applied Biological Sciences]

2017-08-22T09:15:27-07:00

The baculovirus–insect cell system (BICS) has been widely used to produce many different recombinant proteins for basic research and is being used to produce several biologics approved for use in human or veterinary medicine. Early BICS were technically complex and constrained by the relatively primordial nature of insect cell protein...



Dual-reporter SERS-based biomolecular assay with reduced false-positive signals [Applied Physical Sciences]

2017-08-22T09:15:27-07:00

We present a sensitive and quantitative protein detection assay that can efficiently distinguish between specific and nonspecific target binding. Our technique combines dual affinity reagents with surface-enhanced Raman spectroscopy (SERS) and chemometric analysis. We link one Raman reporter-tagged affinity reagent to gold nanoparticles and another to a gold film, such...



Cytotoxic protein from the mushroom Coprinus comatus possesses a unique mode for glycan binding and specificity [Biochemistry]

2017-08-22T09:15:27-07:00

Glycans possess significant chemical diversity; glycan binding proteins (GBPs) recognize specific glycans to translate their structures to functions in various physiological and pathological processes. Therefore, the discovery and characterization of novel GBPs and characterization of glycan–GBP interactions are significant to provide potential targets for therapeutic intervention of many diseases. Here,...



Identification of the Tau phosphorylation pattern that drives its aggregation [Biochemistry]

2017-08-22T09:15:27-07:00

Determining the functional relationship between Tau phosphorylation and aggregation has proven a challenge owing to the multiple potential phosphorylation sites and their clustering in the Tau sequence. We use here in vitro kinase assays combined with NMR spectroscopy as an analytical tool to generate well-characterized phosphorylated Tau samples and show...



Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase [Biochemistry]

2017-08-22T09:15:27-07:00

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



Molecular basis for the substrate specificity of quorum signal synthases [Biochemistry]

2017-08-22T09:15:27-07:00

In several Proteobacteria, LuxI-type enzymes catalyze the biosynthesis of acyl–homoserine lactones (AHL) signals using S-adenosyl–l-methionine and either cellular acyl carrier protein (ACP)-coupled fatty acids or CoA–aryl/acyl moieties as progenitors. Little is known about the molecular mechanism of signal biosynthesis, the basis for substrate specificity, or the rationale for donor specificity...



Phosphorylation of serine96 of histidine-rich calcium-binding protein by the Fam20C kinase functions to prevent cardiac arrhythmia [Biochemistry]

2017-08-22T09:15:27-07:00

Precise Ca cycling through the sarcoplasmic reticulum (SR), a Ca storage organelle, is critical for proper cardiac muscle function. This cycling initially involves SR release of Ca via the ryanodine receptor, which is regulated by its interacting proteins junctin and triadin. The sarco/endoplasmic reticulum Ca ATPase (SERCA) pump then refills...



Beyond icosahedral symmetry in packings of proteins in spherical shells [Biophysics and Computational Biology]

2017-08-22T09:15:27-07:00

The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral cage. In turn, this has inspired synthetic biologists to design de novo protein cages. We use...



Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE [Biophysics and Computational Biology]

2017-08-22T09:15:27-07:00

The lar operon in Lactobacillus plantarum encodes five Lar proteins (LarA/B/C/D/E) that collaboratively synthesize and incorporate a niacin-derived Ni-containing cofactor into LarA, an Ni-dependent lactate racemase. Previous studies have established that two molecules of LarE catalyze successive thiolation reactions by donating the sulfur atom of their exclusive cysteine residues to...



Chaperonin GroEL accelerates protofibril formation and decorates fibrils of the Het-s prion protein [Biophysics and Computational Biology]

2017-08-22T09:15:27-07:00

We have studied the interaction of the prototypical chaperonin GroEL with the prion domain of the Het-s protein using solution and solid-state NMR, electron and atomic force microscopies, and EPR. While GroEL accelerates Het-s protofibril formation by several orders of magnitude, the rate of appearance of fibrils is reduced. GroEL...



Morphologies of synaptic protein membrane fusion interfaces [Biophysics and Computational Biology]

2017-08-22T09:15:27-07:00

Neurotransmitter release is orchestrated by synaptic proteins, such as SNAREs, synaptotagmin, and complexin, but the molecular mechanisms remain unclear. We visualized functionally active synaptic proteins reconstituted into proteoliposomes and their interactions in a native membrane environment by electron cryotomography with a Volta phase plate for improved resolvability. The images revealed...



3.3 A structure of Niemann-Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport [Biophysics and Computational Biology]

2017-08-22T09:15:27-07:00

Niemann–Pick C1 (NPC1) and NPC2 proteins are indispensable for the export of LDL-derived cholesterol from late endosomes. Mutations in these proteins result in Niemann–Pick type C disease, a lysosomal storage disease. Despite recent reports of the NPC1 structure depicting its overall architecture, the function of its C-terminal luminal domain (CTD)...



Origins of coevolution between residues distant in protein 3D structures [Biophysics and Computational Biology]

2017-08-22T09:15:27-07:00

Residue pairs that directly coevolve in protein families are generally close in protein 3D structures. Here we study the exceptions to this general trend—directly coevolving residue pairs that are distant in protein structures—to determine the origins of evolutionary pressure on spatially distant residues and to understand the sources of error...



On the mechanism of long-range orientational order of fibroblasts [Cell Biology]

2017-08-22T09:15:27-07:00

Long-range alignment ordering of fibroblasts have been observed in the vicinity of cancerous tumors and can be recapitulated with in vitro experiments. However, the mechanisms driving their ordering are not understood. Here, we show that local collision-driven nematic alignment interactions among fibroblasts are insufficient to explain observed long-range alignment. One...



Electrocatalytic hydrogen evolution reaction activity comparable to platinum exhibited by the Ni/Ni(OH)2/graphite electrode [Chemistry]

2017-08-22T09:15:27-07:00

Electrochemical dual-pulse plating with sequential galvanostatic and potentiostatic pulses has been used to fabricate an electrocatalytically active Ni/Ni(OH)2/graphite electrode. This electrode design strategy to generate the Ni/Ni(OH)2 interface on graphite from Ni deposits is promising for electrochemical applications and has been used by us for hydrogen generation. The synergetic effect...



Redox variations in Mauna Kea lavas, the oxygen fugacity of the Hawaiian plume, and the role of volcanic gases in Earth’s oxygenation [Earth, Atmospheric, and Planetary Sciences]

2017-08-22T09:15:27-07:00

The behavior of C, H, and S in the solid Earth depends on their oxidation states, which are related to oxygen fugacity (fO2). Volcanic degassing is a source of these elements to Earth’s surface; therefore, variations in mantle fO2 may influence the fO2 at Earth’s surface. However, degassing can impact...



Stabilization of ammonia-rich hydrate inside icy planets [Earth, Atmospheric, and Planetary Sciences]

2017-08-22T09:15:27-07:00

The interior structure of the giant ice planets Uranus and Neptune, but also of newly discovered exoplanets, is loosely constrained, because limited observational data can be satisfied with various interior models. Although it is known that their mantles comprise large amounts of water, ammonia, and methane ices, it is unclear...



Electrical conductivity of SiO2 at extreme conditions and planetary dynamos [Earth, Atmospheric, and Planetary Sciences]

2017-08-22T09:15:27-07:00

Ab intio molecular dynamics simulations show that the electrical conductivity of liquid SiO2 is semimetallic at the conditions of the deep molten mantle of early Earth and super-Earths, raising the possibility of silicate dynamos in these bodies. Whereas the electrical conductivity increases uniformly with increasing temperature, it depends nonmonotonically on...



Science and Culture: Arctic photographers bring climate change into focus [Environmental Sciences]

2017-08-22T09:15:27-07:00

In 2009, a hunter shot a polar bear and carried it by dogsled about 750 meters to the town of Ittoqqortoormiit on the eastern coast of Greenland. Typically, the town’s hunters encounter polar bears on distant sea ice a couple of hours or even days from town. They skin their...



Global urban signatures of phenotypic change in animal and plant populations [Sustainability Science]

2017-08-22T09:15:27-07:00

Humans challenge the phenotypic, genetic, and cultural makeup of species by affecting the fitness landscapes on which they evolve. Recent studies show that cities might play a major role in contemporary evolution by accelerating phenotypic changes in wildlife, including animals, plants, fungi, and other organisms. Many studies of ecoevolutionary change...



Lampreys, the jawless vertebrates, contain only two ParaHox gene clusters [Evolution]

2017-08-22T09:15:27-07:00

ParaHox genes (Gsx, Pdx, and Cdx) are an ancient family of developmental genes closely related to the Hox genes. They play critical roles in the patterning of brain and gut. The basal chordate, amphioxus, contains a single ParaHox cluster comprising one member of each family, whereas nonteleost jawed vertebrates contain...



Complete overview of protein-inactivating sequence variations in 36 sequenced mouse inbred strains [Genetics]

2017-08-22T09:15:27-07:00

Mouse inbred strains remain essential in science. We have analyzed the publicly available genome sequences of 36 popular inbred strains and provide lists for each strain of protein-coding genes that acquired sequence variations that cause premature STOP codons, loss of STOP codons and single nucleotide polymorphisms, and short in-frame insertions...



Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality [Microbiology]

2017-08-22T09:15:27-07:00

Downstream metabolic events can contribute to the lethality of drugs or agents that interact with a primary cellular target. In bacteria, the production of reactive oxygen species (ROS) has been associated with the lethal effects of a variety of stresses including bactericidal antibiotics, but the relative contribution of this oxidative...



Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging [Microbiology]

2017-08-22T09:15:27-07:00

The emergence and spread of antibiotic-resistant bacteria are aggravated by incorrect prescription and use of antibiotics. A core problem is that there is no sufficiently fast diagnostic test to guide correct antibiotic prescription at the point of care. Here, we investigate if it is possible to develop a point-of-care susceptibility...



Noradrenergic activation of the basolateral amygdala maintains hippocampus-dependent accuracy of remote memory [Neuroscience]

2017-08-22T09:15:27-07:00

Emotional enhancement of memory by noradrenergic mechanisms is well-described, but the long-term consequences of such enhancement are poorly understood. Over time, memory traces are thought to undergo a neural reorganization, that is, a systems consolidation, during which they are, at least partly, transferred from the hippocampus to neocortical networks. This...



Arc restores juvenile plasticity in adult mouse visual cortex [Neuroscience]

2017-08-22T09:15:27-07:00

The molecular basis for the decline in experience-dependent neural plasticity over age remains poorly understood. In visual cortex, the robust plasticity induced in juvenile mice by brief monocular deprivation during the critical period is abrogated by genetic deletion of Arc, an activity-dependent regulator of excitatory synaptic modification. Here, we report...



MicroRNA-mediated disruption of dendritogenesis during a critical period of development influences cognitive capacity later in life [Neuroscience]

2017-08-22T09:15:27-07:00

The prenatal period of cortical development is important for the establishment of neural circuitry and functional connectivity of the brain; however, the molecular mechanisms underlying this process remain unclear. Here we report that disruption of the actin–cytoskeletal network in the developing mouse prefrontal cortex alters dendritic morphogenesis and synapse formation,...



Anomalous relaxation kinetics and charge-density-wave correlations in underdoped BaPb1-xBixO3 [Physics]

2017-08-22T09:15:27-07:00

Superconductivity often emerges in proximity of other symmetry-breaking ground states, such as antiferromagnetism or charge-density-wave (CDW) order. However, the subtle interrelation of these phases remains poorly understood, and in some cases even the existence of short-range correlations for superconducting compositions is uncertain. In such circumstances, ultrafast experiments can provide new...



Proteolytic cleavage and PKA phosphorylation of {alpha}1C subunit are not required for adrenergic regulation of CaV1.2 in the heart [Physiology]

2017-08-22T09:15:27-07:00

Calcium influx through the voltage-dependent L-type calcium channel (CaV1.2) rapidly increases in the heart during “fight or flight” through activation of the β-adrenergic and protein kinase A (PKA) signaling pathway. The precise molecular mechanisms of β-adrenergic activation of cardiac CaV1.2, however, are incompletely known, but are presumed to require phosphorylation...



High-precision chronology for Central American maize diversification from El Gigante rockshelter, Honduras [Plant Biology]

2017-08-22T09:15:27-07:00

The first steps toward maize (Zea mays subspecies mays) domestication occurred in the Balsas region of Mexico by ∼9,000 calendar years B.P. (cal B.P.), but it remains unclear when maize was productive enough to be a staple grain in the Americas. Molecular and microbotanical data provide a partial picture of...



Aquaporins facilitate hydrogen peroxide entry into guard cells to mediate ABA- and pathogen-triggered stomatal closure [Plant Biology]

2017-08-22T09:15:27-07:00

Stomatal movements are crucial for the control of plant water status and protection against pathogens. Assays on epidermal peels revealed that, similar to abscisic acid (ABA), pathogen-associated molecular pattern (PAMP) flg22 requires the AtPIP2;1 aquaporin to induce stomatal closure. Flg22 also induced an increase in osmotic water permeability (Pf) of...



Phototropin perceives temperature based on the lifetime of its photoactivated state [Plant Biology]

2017-08-22T09:15:27-07:00

Living organisms detect changes in temperature using thermosensory molecules. However, these molecules and/or their mechanisms for sensing temperature differ among organisms. To identify thermosensory molecules in plants, we investigated chloroplast positioning in response to temperature changes and identified a blue-light photoreceptor, phototropin, that is an essential regulator of chloroplast positioning....



Asymmetric percolation drives a double transition in sexual contact networks [Population Biology]

2017-08-22T09:15:27-07:00

Zika virus (ZIKV) exhibits unique transmission dynamics in that it is concurrently spread by a mosquito vector and through sexual contact. Due to the highly asymmetric durations of infectiousness between males and females—it is estimated that males are infectious for periods up to 10 times longer than females—we show that...



Hippocampal maturity promotes memory distinctiveness in childhood and adolescence [Psychological and Cognitive Sciences]

2017-08-22T09:15:27-07:00

Adaptive learning systems need to meet two complementary and partially conflicting goals: detecting regularities in the world versus remembering specific events. The hippocampus (HC) keeps a fine balance between computations that extract commonalities of incoming information (i.e., pattern completion) and computations that enable encoding of highly similar events into unique...



Stress promotes generalization of older but not recent threat memories [Psychological and Cognitive Sciences]

2017-08-22T09:15:27-07:00

Stress broadly affects the ability to regulate emotions and may contribute to generalization of threat-related behaviors to harmless stimuli. Behavioral generalization also tends to increase over time as memory precision for recent events gives way to more gist-like representations. Thus, acute stress coupled with a delay in time from a...



Bilingual infants control their languages as they listen [Psychological and Cognitive Sciences]

2017-08-22T09:15:27-07:00

Infants growing up in bilingual homes learn two languages simultaneously without apparent confusion or delay. However, the mechanisms that support this remarkable achievement remain unclear. Here, we demonstrate that infants use language-control mechanisms to preferentially activate the currently heard language during listening. In a naturalistic eye-tracking procedure, bilingual infants were...



Effects of maternal investment, temperament, and cognition on guide dog success [Psychological and Cognitive Sciences]

2017-08-22T09:15:27-07:00

A continuing debate in studies of social development in both humans and other animals is the extent to which early life experiences affect adult behavior. Also unclear are the relative contributions of cognitive skills (“intelligence”) and temperament for successful outcomes. Guide dogs are particularly suited to research on these questions....



Core Concept: Probing the phytobiome to advance agriculture [Sustainability Science]

2017-08-22T09:15:27-07:00

The Colorado potato beetle had Gary Felton stumped. Felton, an entomologist at Pennsylvania State University, has built his career on revealing how plants defend themselves against voracious insects. Plants often detect chemicals in an insect’s oral secretions and respond by producing proteins that wreak havoc on insect digestion and nutrient...



Emergence of a global science-business initiative for ocean stewardship [Sustainability Science]

2017-08-22T09:15:27-07:00

The ocean represents a fundamental source of micronutrients and protein for a growing world population. Seafood is a highly traded and sought after commodity on international markets, and is critically dependent on healthy marine ecosystems. A global trend of wild stocks being overfished and in decline, as well as multiple...



Marine reserves solve an important bycatch problem in fisheries [Sustainability Science]

2017-08-22T09:15:27-07:00

Management of the diverse fisheries of the world has had mixed success. While managing single species in data-rich environments has been largely effective, perhaps the greatest challenge facing fishery managers is how to deal with mixed stocks of fish with a range of life histories that reside in the same...



Sustainability in an urbanizing planet [Social Sciences]

2017-08-22T09:15:27-07:00

Sustainability science is use-inspired fundamental research that links knowledge to action such that meeting the needs of society can be balanced with sustaining the life support systems of the planet (1, 2). Nowhere is this action-oriented research needed more than in urban areas that are now home to more than...



Future urban land expansion and implications for global croplands [Sustainability Science]

2017-08-22T09:15:27-07:00

Urban expansion often occurs on croplands. However, there is little scientific understanding of how global patterns of future urban expansion will affect the world’s cultivated areas. Here, we combine spatially explicit projections of urban expansion with datasets on global croplands and crop yields. Our results show that urban expansion will...



Global scenarios of urban density and its impacts on building energy use through 2050 [Sustainability Science]

2017-08-22T09:15:27-07:00

Although the scale of impending urbanization is well-acknowledged, we have a limited understanding of how urban forms will change and what their impact will be on building energy use. Using both top-down and bottom-up approaches and scenarios, we examine building energy use for heating and cooling. Globally, the energy use...



Heterogeneity and scale of sustainable development in cities [Sustainability Science]

2017-08-22T09:15:27-07:00

Rapid worldwide urbanization is at once the main cause and, potentially, the main solution to global sustainable development challenges. The growth of cities is typically associated with increases in socioeconomic productivity, but it also creates strong inequalities. Despite a growing body of evidence characterizing these heterogeneities in developed urban areas,...



Air-quality implications of widespread adoption of cool roofs on ozone and particulate matter in southern California [Sustainability Science]

2017-08-22T09:15:27-07:00

The installation of roofing materials with increased solar reflectance (i.e., “cool roofs”) can mitigate the urban heat island effect and reduce energy use. In addition, meteorological changes, along with the possibility of enhanced UV reflection from these surfaces, can have complex impacts on ozone and PM2.5 concentrations. We aim to...



Landowner behavior can determine the success of conservation strategies for ecosystem migration under sea-level rise [Sustainability Science]

2017-08-22T09:15:27-07:00

The human aspects of conservation are often overlooked but will be critical for identifying strategies for biological conservation in the face of climate change. We surveyed the behavioral intentions of coastal landowners with respect to various conservation strategies aimed at facilitating ecosystem migration for tidal marshes. We found that several...



In This Issue [This Week in PNAS]

2017-08-15T10:30:28-07:00

Gecko evolution and human-caused isolation Common gecko of the Brazilian Cerrado. Image courtesy of Guilherme Santoro (Universidade de Brasília, Brasília, Brazil). Previous studies have found that human-caused ecosystem changes can drive rapid adaptive changes in local organisms. Mariana Eloy de Amorim et al. (pp. 8812–8816) explored how approximately 15 years...



Space radiobiology needs realistic hypotheses and relevant methodology [Biological Sciences]

2017-08-15T10:30:29-07:00

“If humans ever start to live permanently in space” and to verify whether assisted reproductive technology is safe in space, Wakayama et al. (1) maintained freeze-dried mouse spermatozoa in the International Space Station for 9 mo. While these authors are aware of the risks linked to space radiation, both their...



Reply to Ferlazzo and Foray: About the Space Pup project [Biological Sciences]

2017-08-15T10:30:29-07:00

We would like to thank Ferlazzo and Foray (1) for their very important comments and suggestions. We will keep in mind that “scientists should take particular care to justify their methodology and moderate their conclusions.” One concern of Ferlazzo and Foray (1) is that our control experiment entailed exposure to...



Disrupting the blood-brain barrier with focused ultrasound: Perspectives on inflammation and regeneration [Biological Sciences]

2017-08-15T10:30:29-07:00

Transcranial focused ultrasound (FUS) is promising for the treatment of neurological disorders, and the brain’s response to FUS requires full consideration for a safe translation to the clinic. The study by Kovacs et al. (1) provides insights into FUS-induced inflammatory changes that could be associated on the one hand with...



Reply to Silburt et al.: Concerning sterile inflammation following focused ultrasound and microbubbles in the brain [Biological Sciences]

2017-08-15T10:30:29-07:00

We thank Silburt et al. (1) for their comments on our article (2). The authors provide us with an opportunity to expand on sterile inflammation in the brain induced by pulsed focused ultrasound (pFUS) (3). pFUS with microbubbles (MB) resulting in blood–brain barrier disruption (BBBD) is accompanied by plasma protein...



QnAs with Daan Frenkel [QnAs]

2017-08-15T10:30:29-07:00

The self-assembly of biological molecules and systems is a common phenomenon in nature. Linear chains of protein molecules fold into functional 3D structures in one example of biological self-assembly (1). Computational scientist Daan Frenkel at the University of Cambridge seeks to explore how self-assembly might be applied to fields such...



QnAs with Luciana Borio [QnAs]

2017-08-15T10:30:29-07:00

Randomized controlled clinical trials (RCTs) are often held up as a touchstone for assessing the safety and efficacy of new drugs and vaccines. Because randomly assigning patients to either a control or intervention group renders the two groups comparable and reduces bias, RCTs have become the coin of the realm...



Profile of Bruce Western [Profiles]

2017-08-15T10:30:29-07:00

On a summer afternoon in the late 1990s in New York City’s Tompkins Square Park, sociologist Bruce Western and his colleague Katherine Beckett engaged in a conversation that would change the course of their research. At the time, Western studied the social programs of European welfare states. Against the backdrop...



Mercury, volcanism, and mass extinctions [Earth, Atmospheric, and Planetary Sciences]

2017-08-15T10:30:29-07:00

Understanding the causes and timings of mass extinctions are important for our understanding of the evolution of life on Earth and how major biogeochemical cycles have been and can be perturbed. Four of the five biggest mass extinctions (1) are associated with large igneous provinces (LIPS), which are the most...



Cytochrome c peroxidase facilitates the beneficial use of H2O2 in prokaryotes [Microbiology]

2017-08-15T10:30:29-07:00

A new exciting study reports the discovery of a beneficial function of H2O2 in bacteria (1). Khademian and Imlay show that Escherichia coli can use cytochrome c peroxidase (Ccp) as a respiratory enzyme, wherein H2O2 acts as an electron acceptor under anoxic conditions (Fig. 1A). This finding may impact our...



Role of clusterin in the brain vascular clearance of amyloid-{beta} [Neuroscience]

2017-08-15T10:30:29-07:00

Alzheimer’s disease (AD) is the most common form of dementia, characterized by neurovascular dysfunction, elevated brain parenchymal and vascular amyloid-β (Aβ) levels, tau pathology, and neuronal loss (1, 2). Faulty transvascular clearance of brain Aβ across the blood–brain barrier (BBB) plays an important role in Aβ accumulation in the brain,...



Crossover from band-like to thermally activated charge transport in organic transistors due to strain-induced traps [Applied Physical Sciences]

2017-08-15T10:30:29-07:00

The temperature dependence of the charge-carrier mobility provides essential insight into the charge transport mechanisms in organic semiconductors. Such knowledge imparts critical understanding of the electrical properties of these materials, leading to better design of high-performance materials for consumer applications. Here, we present experimental results that suggest that the inhomogeneous...



Quantitative time-resolved chemoproteomics reveals that stable O-GlcNAc regulates box C/D snoRNP biogenesis [Chemistry]

2017-08-15T10:30:29-07:00

O-linked GlcNAcylation (O-GlcNAcylation), a ubiquitous posttranslational modification on intracellular proteins, is dynamically regulated in cells. To analyze the turnover dynamics of O-GlcNAcylated proteins, we developed a quantitative time-resolved O-linked GlcNAc proteomics (qTOP) strategy based on metabolic pulse-chase labeling with an O-GlcNAc chemical reporter and stable isotope labeling with amino acids...



Impact of glacial/interglacial sea level change on the ocean nitrogen cycle [Earth, Atmospheric, and Planetary Sciences]

2017-08-15T10:30:29-07:00

The continental shelves are the most biologically dynamic regions of the ocean, and they are extensive worldwide, especially in the western North Pacific. Their area has varied dramatically over the glacial/interglacial cycles of the last million years, but the effects of this variation on ocean biological and chemical processes remain...



Factor-dependent archaeal transcription termination [Biochemistry]

2017-08-15T10:30:29-07:00

RNA polymerase activity is regulated by nascent RNA sequences, DNA template sequences, and conserved transcription factors. Transcription factors promoting initiation and elongation have been characterized in each domain, but transcription termination factors have been identified only in bacteria and eukarya. Here we describe euryarchaeal termination activity (Eta), the first archaeal...



Conformational and chemical selection by a trans-acting editing domain [Biochemistry]

2017-08-15T10:30:29-07:00

Molecular sieves ensure proper pairing of tRNAs and amino acids during aminoacyl-tRNA biosynthesis, thereby avoiding detrimental effects of mistranslation on cell growth and viability. Mischarging errors are often corrected through the activity of specialized editing domains present in some aminoacyl-tRNA synthetases or via single-domain trans-editing proteins. ProXp-ala is a ubiquitous...



Phospholipase A activity of adenylate cyclase toxin mediates translocation of its adenylate cyclase domain [Biochemistry]

2017-08-15T10:30:29-07:00

Adenylate cyclase toxin (ACT or CyaA) plays a crucial role in respiratory tract colonization and virulence of the whooping cough causative bacterium Bordetella pertussis. Secreted as soluble protein, it targets myeloid cells expressing the CD11b/CD18 integrin and on delivery of its N-terminal adenylate cyclase catalytic domain (AC domain) into the...



Homeostatic enhancement of sensory transduction [Biophysics and Computational Biology]

2017-08-15T10:30:29-07:00

Our sense of hearing boasts exquisite sensitivity, precise frequency discrimination, and a broad dynamic range. Experiments and modeling imply, however, that the auditory system achieves this performance for only a narrow range of parameter values. Small changes in these values could compromise hair cells’ ability to detect stimuli. We propose...



Time-resolved observation of protein allosteric communication [Biophysics and Computational Biology]

2017-08-15T10:30:29-07:00

Allostery represents a fundamental mechanism of biological regulation that is mediated via long-range communication between distant protein sites. Although little is known about the underlying dynamical process, recent time-resolved infrared spectroscopy experiments on a photoswitchable PDZ domain (PDZ2S) have indicated that the allosteric transition occurs on multiple timescales. Here, using...