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Preview: Proceedings of the National Academy of Sciences current issue

Proceedings of the National Academy of Sciences current issue



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In This Issue [This Week in PNAS]

2016-11-29T08:48:07-08:00

Tuberculosis evolution and armed conflict M. tuberculosis. Image courtesy of Flickr/National Institute of Allergy and Infectious Diseases. Lineage 2 (L2) of Mycobacterium tuberculosis is spreading globally and has been associated with accelerated disease progression and increased drug resistance. Vegard Eldholm et al. (pp. 13881–13886) reconstructed the evolutionary history of an...



QnAs with Steven A. Balbus [QnAs]

2016-11-29T08:48:07-08:00

In early 2016, Oxford University astrophysicist Steven Balbus was filling in for a colleague, teaching a course on general relativity. Although not an expert in relativity before the course, Balbus felt growing admiration for Albert Einstein’s century-old theory. In February, during the course, Balbus and others around the world heard...



QnAs with Gerald M. Rubin [QnAs]

2016-11-29T08:48:07-08:00

On a rolling meadow along the Potomac, in a suburb of Washington, DC, stands the sprawling embodiment of a bold idea born more than a decade ago. Designed by the Uruguay-born architect Rafael Viñoly, the serpentine structure—glass walls, macadam-gray facade, and gleaming floors terraced into a grassy landscape—was built to...



Profile of Peter A. Jones [Profiles]

2016-11-29T08:48:07-08:00

Van Andel Research Institute chief scientific officer Peter A. Jones, who was born in Cape Town, South Africa, recalls a challenge he received after traveling to Los Angeles in 1973. “Shortly after I arrived in the [United States], I met Charles Heidelberger, who was a giant in cancer research and...



Homogeneous nucleation: Patching the way from the macroscopic to the nanoscopic description [Applied Physical Sciences]

2016-11-29T08:48:07-08:00

How and when does water ‘‘fracture’’? In other words, how and when does a small cavity, or nucleus, form that does not heal but grows to macroscopic size, thus becoming a bubble? This question is important in various areas of technology and nature, affecting, for example, the ability of tall...



Multistep crystallization processes: How not to make perfect single crystals [Chemistry]

2016-11-29T08:48:07-08:00

The beauty of snowflakes originates from the very different ways the ice crystals grow in different environments (1, 2). The amazing variety of snowflake crystal shapes occurs despite the fact that the crystalline structure of snow is always the same: the thermodynamic equilibrium shape is a simple hexagonal crystal. Therefore,...



Baby birds do not always tell the truth [Evolution]

2016-11-29T08:48:07-08:00

A parent bird carries prey to its nest and is met by chicks opening their colorful mouths, stretching their necks and bodies upward, and vocalizing enthusiastically (Fig. 1). At first glance, these active and noisy displays seem remarkably inconsistent with expectations that dependent nestlings ought to divert their energy to...



Pandemic influenza and socioeconomic disparities: Lessons from 1918 Chicago [Medical Sciences]

2016-11-29T08:48:07-08:00

The 1918 “Spanish” influenza pandemic holds a particular place in medical history; it wiped out an estimated ∼1% of the global population, or ∼20–50 million deaths worldwide, and earned the dubious honor of being coined the “mother of all pandemics” (1). Fortunately, important strides have been made in elucidating the...



Lifestyle chemistries from phones for individual profiling [Chemistry]

2016-11-29T08:48:08-08:00

Imagine a scenario where personal belongings such as pens, keys, phones, or handbags are found at an investigative site. It is often valuable to the investigative team that is trying to trace back the belongings to an individual to understand their personal habits, even when DNA evidence is also available....



Unreasonable effectiveness of learning neural networks: From accessible states and robust ensembles to basic algorithmic schemes [Computer Sciences]

2016-11-29T08:48:08-08:00

In artificial neural networks, learning from data is a computationally demanding task in which a large number of connection weights are iteratively tuned through stochastic-gradient-based heuristic processes over a cost function. It is not well understood how learning occurs in these systems, in particular how they avoid getting trapped in...



Tissue-scale, personalized modeling and simulation of prostate cancer growth [Engineering]

2016-11-29T08:48:08-08:00

Recently, mathematical modeling and simulation of diseases and their treatments have enabled the prediction of clinical outcomes and the design of optimal therapies on a personalized (i.e., patient-specific) basis. This new trend in medical research has been termed “predictive medicine.” Prostate cancer (PCa) is a major health problem and an...



Life cycle greenhouse gas emissions and freshwater consumption associated with Bakken tight oil [Sustainability Science]

2016-11-29T08:48:08-08:00

In recent years, hydraulic fracturing and horizontal drilling have been applied to extract crude oil from tight reservoirs, including the Bakken formation. There is growing interest in understanding the greenhouse gas (GHG) emissions associated with the development of tight oil. We conducted a life cycle assessment of Bakken crude using...



The emergence of longevous populations [Social Sciences]

2016-11-29T08:48:08-08:00

The human lifespan has traversed a long evolutionary and historical path, from short-lived primate ancestors to contemporary Japan, Sweden, and other longevity frontrunners. Analyzing this trajectory is crucial for understanding biological and sociocultural processes that determine the span of life. Here we reveal a fundamental regularity. Two straight lines describe...



Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor [Biochemistry]

2016-11-29T08:48:08-08:00

Ring-shaped hexameric helicases and translocases support essential DNA-, RNA-, and protein-dependent transactions in all cells and many viruses. How such systems coordinate ATPase activity between multiple subunits to power conformational changes that drive the engagement and movement of client substrates is a fundamental question. Using the Escherichia coli Rho transcription...



Two familial ALS proteins function in prevention/repair of transcription-associated DNA damage [Cell Biology]

2016-11-29T08:48:08-08:00

Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron dysfunction disease that leads to paralysis and death. There is currently no established molecular pathogenesis pathway. Multiple proteins involved in RNA processing are linked to ALS, including FUS and TDP43, and we propose a disease mechanism in which loss of function...



Notch1 controls development of the extravillous trophoblast lineage in the human placenta [Developmental Biology]

2016-11-29T08:48:08-08:00

Development of the human placenta and its different epithelial trophoblasts is crucial for a successful pregnancy. Besides fusing into a multinuclear syncytium, the exchange surface between mother and fetus, progenitors develop into extravillous trophoblasts invading the maternal uterus and its spiral arteries. Migration into these vessels promotes remodelling and, as...



Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape [Developmental Biology]

2016-11-29T08:48:08-08:00

Vertebrate Hox genes encode transcription factors operating during the development of multiple organs and structures. However, the evolutionary mechanism underlying this remarkable pleiotropy remains to be fully understood. Here, we show that Hoxd8 and Hoxd9, two genes of the HoxD complex, are transcribed during mammary bud (MB) development. However, unlike...



Origins of the current seventh cholera pandemic [Evolution]

2016-11-29T08:48:08-08:00

Vibrio cholerae has caused seven cholera pandemics since 1817, imposing terror on much of the world, but bacterial strains are currently only available for the sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in Indonesia, but did not originate directly from the classical biotype sixth-pandemic...



Evolution of directional hearing in moths via conversion of bat detection devices to asymmetric pressure gradient receivers [Evolution]

2016-11-29T08:48:08-08:00

Small animals typically localize sound sources by means of complex internal connections and baffles that effectively increase time or intensity differences between the two ears. However, some miniature acoustic species achieve directional hearing without such devices, indicating that other mechanisms have evolved. Using 3D laser vibrometry to measure tympanum deflection,...



Transposon mutagenesis identifies genes that cooperate with mutant Pten in breast cancer progression [Genetics]

2016-11-29T08:48:08-08:00

Triple-negative breast cancer (TNBC) has the worst prognosis of any breast cancer subtype. To better understand the genetic forces driving TNBC, we performed a transposon mutagenesis screen in a phosphatase and tensin homolog (Pten) mutant mice and identified 12 candidate trunk drivers and a much larger number of progression genes....



Density of immunogenic antigens does not explain the presence or absence of the T-cell-inflamed tumor microenvironment in melanoma [Immunology and Inflammation]

2016-11-29T08:48:08-08:00

Melanoma metastases can be categorized by gene expression for the presence of a T-cell–inflamed tumor microenvironment, which correlates with clinical efficacy of immunotherapies. T cells frequently recognize mutational antigens corresponding to nonsynonymous somatic mutations (NSSMs), and in some cases shared differentiation or cancer–testis antigens. Therapies are being pursued to trigger...



Association of PD-1/PD-L axis expression with cytolytic activity, mutational load, and prognosis in melanoma and other solid tumors [Immunology and Inflammation]

2016-11-29T08:48:08-08:00

Programmed cell death protein-1 (PD-1)/programmed death ligand-1 (PD-L1) checkpoint blockade has led to remarkable and durable objective responses in a number of different tumor types. A better understanding of factors associated with the PD-1/PD-L axis expression is desirable, as it informs their potential role as prognostic and predictive biomarkers and...



Trypanosoma brucei metabolite indolepyruvate decreases HIF-1{alpha} and glycolysis in macrophages as a mechanism of innate immune evasion [Immunology and Inflammation]

2016-11-29T08:48:08-08:00

The parasite Trypanasoma brucei causes African trypanosomiasis, known as sleeping sickness in humans and nagana in domestic animals. These diseases are a major burden in the 36 sub-Saharan African countries where the tsetse fly vector is endemic. Untreated trypanosomiasis is fatal and the current treatments are stage-dependent and can be...



Tethered IL-15 augments antitumor activity and promotes a stem-cell memory subset in tumor-specific T cells [Immunology and Inflammation]

2016-11-29T08:48:08-08:00

Adoptive immunotherapy retargeting T cells to CD19 via a chimeric antigen receptor (CAR) is an investigational treatment capable of inducing complete tumor regression of B-cell malignancies when there is sustained survival of infused cells. T-memory stem cells (TSCM) retain superior potential for long-lived persistence, but challenges exist in manufacturing this...



In vivo amelioration of endogenous antitumor autoantibodies via low-dose P4N through the LTA4H/activin A/BAFF pathway [Immunology and Inflammation]

2016-11-29T08:48:08-08:00

Cancer progression is associated with the development of antitumor autoantibodies in patients’ sera. Although passive treatment with antitumor antibodies has exhibited remarkable therapeutic efficacy, inhibitory effects on tumor progression by endogenous antitumor autoantibodies (EAAs) have been limited. In this study, we show that P4N, a derivative of the plant lignan...



Heparanase is required for activation and function of macrophages [Medical Sciences]

2016-11-29T08:48:08-08:00

The emerging role of heparanase in tumor initiation, growth, metastasis, and chemoresistance is well recognized and is encouraging the development of heparanase inhibitors as anticancer drugs. Unlike the function of heparanase in cancer cells, very little attention has been given to heparanase contributed by cells composing the tumor microenvironment. Here...



Role of nucleotide-binding oligomerization domain 1 (NOD1) and its variants in human cytomegalovirus control in vitro and in vivo [Microbiology]

2016-11-29T08:48:08-08:00

Induction of nucleotide-binding oligomerization domain 2 (NOD2) and downstream receptor-interacting serine/threonine-protein kinase 2 (RIPK2) by human cytomegalovirus (HCMV) is known to up-regulate antiviral responses and suppress virus replication. We investigated the role of nucleotide-binding oligomerization domain 1 (NOD1), which also signals through RIPK2, in HCMV control. NOD1 activation by Tri-DAP...



VEGF preconditioning leads to stem cell remodeling and attenuates age-related decay of adult hippocampal neurogenesis [Neuroscience]

2016-11-29T08:48:08-08:00

Several factors are known to enhance adult hippocampal neurogenesis but a factor capable of inducing a long-lasting neurogenic enhancement that attenuates age-related neurogenic decay has not been described. Here, we studied hippocampal neurogenesis following conditional VEGF induction in the adult brain and showed that a short episode of VEGF exposure...



Circadian rhythms identified in Caenorhabditis elegans by in vivo long-term monitoring of a bioluminescent reporter [Neuroscience]

2016-11-29T08:48:08-08:00

Circadian rhythms are based on endogenous clocks that allow organisms to adjust their physiology and behavior by entrainment to the solar day and, in turn, to select the optimal times for most biological variables. Diverse model systems—including mice, flies, fungi, plants, and bacteria—have provided important insights into the mechanisms of...



Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript [Plant Biology]

2016-11-29T08:48:08-08:00

Seed dormancy is one of the most crucial process transitions in a plant’s life cycle. Its timing is tightly controlled by the expression level of the Delay of Germination 1 gene (DOG1). DOG1 is the major quantitative trait locus for seed dormancy in Arabidopsis and has been shown to control...



Statistics of natural reverberation enable perceptual separation of sound and space [Psychological and Cognitive Sciences]

2016-11-29T08:48:08-08:00

In everyday listening, sound reaches our ears directly from a source as well as indirectly via reflections known as reverberation. Reverberation profoundly distorts the sound from a source, yet humans can both identify sound sources and distinguish environments from the resulting sound, via mechanisms that remain unclear. The core computational...



Phylogenetic approach to the evolution of color term systems [Anthropology]

2016-11-29T08:48:07-08:00

The naming of colors has long been a topic of interest in the study of human culture and cognition. Color term research has asked diverse questions about thought and communication, but no previous research has used an evolutionary framework. We show that there is broad support for the most influential...



Late Archaic-Early Formative period microbotanical evidence for potato at Jiskairumoko in the Titicaca Basin of southern Peru [Anthropology]

2016-11-29T08:48:07-08:00

The data presented in this paper provide direct microbotanical evidence concerning the early use of potato (Solanum tuberosum) within its botanical locus of origin in the high south-central Andes. The data derive from Jiskairumoko, an early village site in the western Titicaca Basin dating to the Late Archaic to Early...



Regional asynchronicity in dairy production and processing in early farming communities of the northern Mediterranean [Anthropology]

2016-11-29T08:48:07-08:00

In the absence of any direct evidence, the relative importance of meat and dairy productions to Neolithic prehistoric Mediterranean communities has been extensively debated. Here, we combine lipid residue analysis of ceramic vessels with osteo-archaeological age-at-death analysis from 82 northern Mediterranean and Near Eastern sites dating from the seventh to...



Achieving high power factor and output power density in p-type half-Heuslers Nb1-xTixFeSb [Applied Physical Sciences]

2016-11-29T08:48:07-08:00

Improvements in thermoelectric material performance over the past two decades have largely been based on decreasing the phonon thermal conductivity. Enhancing the power factor has been less successful in comparison. In this work, a peak power factor of ∼106 μW⋅cm−1⋅K−2 is achieved by increasing the hot pressing temperature up to...



Molecular mechanism for cavitation in water under tension [Applied Physical Sciences]

2016-11-29T08:48:07-08:00

Despite its relevance in biology and engineering, the molecular mechanism driving cavitation in water remains unknown. Using computer simulations, we investigate the structure and dynamics of vapor bubbles emerging from metastable water at negative pressures. We find that in the early stages of cavitation, bubbles are irregularly shaped and become...



Mapping membrane activity in undiscovered peptide sequence space using machine learning [Applied Physical Sciences]

2016-11-29T08:48:07-08:00

There are some ∼1,100 known antimicrobial peptides (AMPs), which permeabilize microbial membranes but have diverse sequences. Here, we develop a support vector machine (SVM)-based classifier to investigate ⍺-helical AMPs and the interrelated nature of their functional commonality and sequence homology. SVM is used to search the undiscovered peptide sequence space...



Ligand-induced and small-molecule control of substrate loading in a hexameric helicase [Biochemistry]

2016-11-29T08:48:07-08:00

Processive, ring-shaped protein and nucleic acid protein translocases control essential biochemical processes throughout biology and are considered high-prospect therapeutic targets. The Escherichia coli Rho factor is an exemplar hexameric RNA translocase that terminates transcription in bacteria. As with many ring-shaped motor proteins, Rho activity is modulated by a variety of...



Tetraphenylethene-based highly emissive metallacage as a component of theranostic supramolecular nanoparticles [Biochemistry]

2016-11-29T08:48:07-08:00

A theranostic agent combines diagnostic reporter with therapeutic activity in a single entity, an approach that seeks to increase the efficacy of cancer treatment. Herein, we describe the synthesis of a highly emissive tetraphenylethene-based metallacage using multicomponent coordination-driven self-assembly that exhibits a coordination-triggered aggregation-induced emission (AIE) enhancement. The formation of...



Structural basis of N-Myc binding by Aurora-A and its destabilization by kinase inhibitors [Biochemistry]

2016-11-29T08:48:07-08:00

Myc family proteins promote cancer by inducing widespread changes in gene expression. Their rapid turnover by the ubiquitin–proteasome pathway is regulated through phosphorylation of Myc Box I and ubiquitination by the E3 ubiquitin ligase SCFFbxW7. However, N-Myc protein (the product of the MYCN oncogene) is stabilized in neuroblastoma by the...



Global transformation of erythrocyte properties via engagement of an SH2-like sequence in band 3 [Biochemistry]

2016-11-29T08:48:07-08:00

Src homology 2 (SH2) domains are composed of weakly conserved sequences of ∼100 aa that bind phosphotyrosines in signaling proteins and thereby mediate intra- and intermolecular protein–protein interactions. In exploring the mechanism whereby tyrosine phosphorylation of the erythrocyte anion transporter, band 3, triggers membrane destabilization, vesiculation, and fragmentation, we discovered...



Topic modeling for untargeted substructure exploration in metabolomics [Biochemistry]

2016-11-29T08:48:07-08:00

The potential of untargeted metabolomics to answer important questions across the life sciences is hindered because of a paucity of computational tools that enable extraction of key biochemically relevant information. Available tools focus on using mass spectrometry fragmentation spectra to identify molecules whose behavior suggests they are relevant to the...



Two proofreading steps amplify the accuracy of genetic code translation [Biochemistry]

2016-11-29T08:48:07-08:00

Aminoacyl-tRNAs (aa-tRNAs) are selected by the messenger RNA programmed ribosome in ternary complex with elongation factor Tu (EF-Tu) and GTP and then, again, in a proofreading step after GTP hydrolysis on EF-Tu. We use tRNA mutants with different affinities for EF-Tu to demonstrate that proofreading of aa-tRNAs occurs in two...



An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis [Biochemistry]

2016-11-29T08:48:07-08:00

HD domain phosphohydrolase enzymes are characterized by a conserved set of histidine and aspartate residues that coordinate an active site metallocenter. Despite the important roles these enzymes play in nucleotide metabolism and signal transduction, few have been both biochemically and structurally characterized. Here, we present X-ray crystal structures and biochemical...



Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states [Biochemistry]

2016-11-29T08:48:07-08:00

MTAN (5′-methylthioadenosine nucleosidase) catalyzes the hydrolysis of the N-ribosidic bond of a variety of adenosine-containing metabolites. The Helicobacter pylori MTAN (HpMTAN) hydrolyzes 6-amino-6-deoxyfutalosine in the second step of the alternative menaquinone biosynthetic pathway. Substrate binding of the adenine moiety is mediated almost exclusively by hydrogen bonds, and the proposed catalytic...



Predicting protein-ligand affinity with a random matrix framework [Biophysics and Computational Biology]

2016-11-29T08:48:07-08:00

Rapid determination of whether a candidate compound will bind to a particular target receptor remains a stumbling block in drug discovery. We use an approach inspired by random matrix theory to decompose the known ligand set of a target in terms of orthogonal “signals” of salient chemical features, and distinguish...



Fluorine-19 NMR and computational quantification of isoflurane binding to the voltage-gated sodium channel NaChBac [Biophysics and Computational Biology]

2016-11-29T08:48:07-08:00

Voltage-gated sodium channels (NaV) play an important role in general anesthesia. Electrophysiology measurements suggest that volatile anesthetics such as isoflurane inhibit NaV by stabilizing the inactivated state or altering the inactivation kinetics. Recent computational studies suggested the existence of multiple isoflurane binding sites in NaV, but experimental binding data are...



Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers [Biophysics and Computational Biology]

2016-11-29T08:48:07-08:00

Tumor genomes are mosaics of somatic structural variants (SVs) that may contribute to the activation of oncogenes or inactivation of tumor suppressors, for example, by altering gene copy number amplitude. However, there are multiple other ways in which SVs can modulate transcription, but the general impact of such events on...



DNA polymerase {zeta} limits chromosomal damage and promotes cell survival following aflatoxin exposure [Cell Biology]

2016-11-29T08:48:07-08:00

Routine dietary consumption of foods that contain aflatoxins is the second leading cause of environmental carcinogenesis worldwide. Aflatoxin-driven mutagenesis is initiated through metabolic activation of aflatoxin B1 (AFB1) to its epoxide form that reacts with N7 guanine in DNA. The resulting AFB1-N7-dG adduct undergoes either spontaneous depurination or imidazole-ring opening...



Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice-Ramsperger-Kassel theory [Chemistry]

2016-11-29T08:48:07-08:00

Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate...



Synergistic reaction of silver nitrate, silver nanoparticles, and methylene blue against bacteria [Chemistry]

2016-11-29T08:48:07-08:00

In this paper we describe the antibacterial effect of methylene blue, MB, and silver nitrate reacting alone and in combination against five bacterial strains including Serratia marcescens and Escherichia coli bacteria. The data presented suggest that when the two components are combined and react together against bacteria, the effects can...



Multiple pathways of crystal nucleation in an extremely supersaturated aqueous potassium dihydrogen phosphate (KDP) solution droplet [Chemistry]

2016-11-29T08:48:07-08:00

Solution studies have proposed that crystal nucleation can take more complex pathways than previously expected in classical nucleation theory, such as formation of prenucleation clusters or densified amorphous/liquid phases. These findings show that it is possible to separate fluctuations in the different order parameters governing crystal nucleation, that is, density...



Diameter-dependent wetting of tungsten disulfide nanotubes [Chemistry]

2016-11-29T08:48:07-08:00

The simple process of a liquid wetting a solid surface is controlled by a plethora of factors—surface texture, liquid droplet size and shape, energetics of both liquid and solid surfaces, as well as their interface. Studying these events at the nanoscale provides insights into the molecular basis of wetting. Nanotube...



Persistent sulfate formation from London Fog to Chinese haze [Earth, Atmospheric, and Planetary Sciences]

2016-11-29T08:48:07-08:00

Sulfate aerosols exert profound impacts on human and ecosystem health, weather, and climate, but their formation mechanism remains uncertain. Atmospheric models consistently underpredict sulfate levels under diverse environmental conditions. From atmospheric measurements in two Chinese megacities and complementary laboratory experiments, we show that the aqueous oxidation of SO2 by NO2...



Predators catalyze an increase in chloroviruses by foraging on the symbiotic hosts of zoochlorellae [Ecology]

2016-11-29T08:48:07-08:00

Virus population growth depends on contacts between viruses and their hosts. It is often unclear how sufficient contacts are made between viruses and their specific hosts to generate spikes in viral abundance. Here, we show that copepods, acting as predators, can bring aquatic viruses and their algal hosts into contact....



Global patterns of kelp forest change over the past half-century [Ecology]

2016-11-29T08:48:07-08:00

Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change...



Long-term empirical evidence of ocean warming leading to tropicalization of fish communities, increased herbivory, and loss of kelp [Ecology]

2016-11-29T08:48:07-08:00

Some of the most profound effects of climate change on ecological communities are due to alterations in species interactions rather than direct physiological effects of changing environmental conditions. Empirical evidence of historical changes in species interactions within climate-impacted communities is, however, rare and difficult to obtain. Here, we demonstrate the...



Universal screening increases the representation of low-income and minority students in gifted education [Economic Sciences]

2016-11-29T08:48:07-08:00

Low-income and minority students are substantially underrepresented in gifted education programs. The disparities persist despite efforts by many states and school districts to broaden participation through changes in their eligibility criteria. One explanation for the persistent gap is that standard processes for identifying gifted students, which are based largely on...



Opinion: The dangers of faulty, biased, or malicious algorithms requires independent oversight [Engineering]

2016-11-29T08:48:07-08:00

The recent crash of a driverless car sends a clear warning about how algorithms can be deadly (1). Similarly, there are clear dangers in vital national services, such as communications, financial trading, healthcare, and transportation. These services depend on sophisticated algorithms, some relying on unpredictable artificial intelligence techniques, such as...



Temperature response of soil respiration largely unaltered with experimental warming [Environmental Sciences]

2016-11-29T08:48:07-08:00

The respiratory release of carbon dioxide (CO2) from soil is a major yet poorly understood flux in the global carbon cycle. Climatic warming is hypothesized to increase rates of soil respiration, potentially fueling further increases in global temperatures. However, despite considerable scientific attention in recent decades, the overall response of...



Sibling conflict and dishonest signaling in birds [Evolution]

2016-11-29T08:48:07-08:00

Offspring survival can often depend on successful communication with parents about their state of need. Theory suggests that offspring will be less likely to honestly signal their need when they experience greater competition from either a greater number of nestmates or less-related nestmates. We found support for this hypothesis with...



Multiple mechanisms contribute to double-strand break repair at rereplication forks in Drosophila follicle cells [Genetics]

2016-11-29T08:48:07-08:00

Rereplication generates double-strand breaks (DSBs) at sites of fork collisions and causes genomic damage, including repeat instability and chromosomal aberrations. However, the primary mechanism used to repair rereplication DSBs varies across different experimental systems. In Drosophila follicle cells, developmentally regulated rereplication is used to amplify six genomic regions, two of...



Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination [Genetics]

2016-11-29T08:48:07-08:00

Defensins constitute an evolutionary conserved family of cationic antimicrobial peptides that play a key role in host innate immune responses to infection. Defensin genes generally reside in complex genomic regions that are prone to structural variation, and defensin genes exhibit extensive copy number variation in humans and in other species....



Mouse model for acute Epstein-Barr virus infection [Immunology and Inflammation]

2016-11-29T08:48:07-08:00

Epstein–Barr Virus (EBV) infects human B cells and drives them into continuous proliferation. Two key viral factors in this process are the latent membrane proteins LMP1 and LMP2A, which mimic constitutively activated CD40 receptor and B-cell receptor signaling, respectively. EBV-infected B cells elicit a powerful T-cell response that clears the...



Graft versus self (GvS) against T-cell autoantigens is a mechanism of graft-host interaction [Immunology and Inflammation]

2016-11-29T08:48:07-08:00

Graft-versus-host disease (GVHD) represents the major nonrelapse complication of allogeneic hematopoietic cell transplantation. Although rare, the CNS and the eye can be affected. In this study, manifestation in the retina as part of the CNS and T-cell epitopes recognized by the allogeneic T cells were evaluated. In 2 of 6...



Gram-positive bacteria are held at a distance in the colon mucus by the lectin-like protein ZG16 [Immunology and Inflammation]

2016-11-29T08:48:07-08:00

The distal colon functions as a bioreactor and harbors an enormous amount of bacteria in a mutualistic relationship with the host. The microbiota have to be kept at a safe distance to prevent inflammation, something that is achieved by a dense inner mucus layer that lines the epithelial cells. The...



Controlling DNA-nanoparticle serum interactions [Medical Sciences]

2016-11-29T08:48:07-08:00

Understanding the interaction of molecularly assembled nanoparticles with physiological fluids is critical to their use for in vivo delivery of drugs and contrast agents. Here, we systematically investigated the factors and mechanisms that govern the degradation of DNA on the nanoparticle surface in serum. We discovered that a higher DNA...



Disparities in influenza mortality and transmission related to sociodemographic factors within Chicago in the pandemic of 1918 [Medical Sciences]

2016-11-29T08:48:07-08:00

Social factors have been shown to create differential burden of influenza across different geographic areas. We explored the relationship between potential aggregate-level social determinants and mortality during the 1918 influenza pandemic in Chicago using a historical dataset of 7,971 influenza and pneumonia deaths. Census tract-level social factors, including rates of...



Epipolymorphisms associated with the clinical outcome of autoimmune arthritis affect CD4+ T cell activation pathways [Medical Sciences]

2016-11-29T08:48:07-08:00

Multifactorial diseases, including autoimmune juvenile idiopathic arthritis (JIA), result from a complex interplay between genetics and environment. Epigenetic mechanisms are believed to integrate such gene–environment interactions, fine-tuning gene expression, and possibly contributing to immune system dysregulation. Although anti-TNF therapy has strongly increased JIA remission rates, it is not curative and...



Amyloid fibrils from the N-terminal prion protein fragment are infectious [Medical Sciences]

2016-11-29T08:48:07-08:00

Recombinant C-terminally truncated prion protein PrP23-144 (which corresponds to the Y145Stop PrP variant associated with a Gerstmann–Sträussler–Scheinker-like prion disease) spontaneously forms amyloid fibrils with a parallel in-register β-sheet architecture and β-sheet core mapping to residues ∼112–139. Here we report that mice (both tga20 and wild type) inoculated with a murine...



Nanoparticle engineered TRAIL-overexpressing adipose-derived stem cells target and eradicate glioblastoma via intracranial delivery [Medical Sciences]

2016-11-29T08:48:07-08:00

Glioblastoma multiforme (GBM) is one of the most intractable of human cancers, principally because of the highly infiltrative nature of these neoplasms. Tracking and eradicating infiltrating GBM cells and tumor microsatellites is of utmost importance for the treatment of this devastating disease, yet effective strategies remain elusive. Here we report...



Yellow fever virus capsid protein is a potent suppressor of RNA silencing that binds double-stranded RNA [Microbiology]

2016-11-29T08:48:07-08:00

Mosquito-borne flaviviruses, including yellow fever virus (YFV), Zika virus (ZIKV), and West Nile virus (WNV), profoundly affect human health. The successful transmission of these viruses to a human host depends on the pathogen’s ability to overcome a potentially sterilizing immune response in the vector mosquito. Similar to other invertebrate animals...



Structural and functional analysis of an anchorless fibronectin-binding protein FBPS from Gram-positive bacterium Streptococcus suis [Microbiology]

2016-11-29T08:48:07-08:00

The anchorless fibronectin-binding proteins (FnBPs) are a group of important virulence factors for which the structures are not available and the functions are not well defined. In this study we performed comprehensive studies on a prototypic member of this group: the fibronectin-/fibrinogen-binding protein from Streptococcus suis (FBPS). The structures of...



Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island [Microbiology]

2016-11-29T08:48:08-08:00

Horizontal gene transfer (HGT) of genomic islands is a driving force of bacterial evolution. Many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. However, the role of the host in this process remains unclear. Here, we show...



Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis [Microbiology]

2016-11-29T08:48:08-08:00

The “Beijing” Mycobacterium tuberculosis (Mtb) lineage 2 (L2) is spreading globally and has been associated with accelerated disease progression and increased antibiotic resistance. Here we performed a phylodynamic reconstruction of one of the L2 sublineages, the central Asian clade (CAC), which has recently spread to western Europe. We find that...



Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont [Microbiology]

2016-11-29T08:48:08-08:00

Animal guts are often colonized by host-specialized bacterial species to the exclusion of other transient microorganisms, but the genetic basis of colonization ability is largely unknown. The bacterium Snodgrassella alvi is a dominant gut symbiont in honey bees, specialized in colonizing the hindgut epithelium. We developed methods for transposon-based mutagenesis...



Endogenous central amygdala mu-opioid receptor signaling promotes sodium appetite in mice [Neuroscience]

2016-11-29T08:48:08-08:00

Due to the importance of dietary sodium and its paucity within many inland environments, terrestrial animals have evolved an instinctive sodium appetite that is commensurate with sodium deficiency. Despite a well-established role for central opioid signaling in sodium appetite, the endogenous influence of specific opioid receptor subtypes within distinct brain...



Spontaneous default network activity reflects behavioral variability independent of mind-wandering [Neuroscience]

2016-11-29T08:48:08-08:00

The brain’s default mode network (DMN) is highly active during wakeful rest when people are not overtly engaged with a sensory stimulus or externally oriented task. In multiple contexts, increased spontaneous DMN activity has been associated with self-reported episodes of mind-wandering, or thoughts that are unrelated to the present sensory...



Quantum entanglement of angular momentum states with quantum numbers up to 10,010 [Physics]

2016-11-29T08:48:07-08:00

Photons with a twisted phase front carry a quantized amount of orbital angular momentum (OAM) and have become important in various fields of optics, such as quantum and classical information science or optical tweezers. Because no upper limit on the OAM content per photon is known, they are also interesting...



Twisted light transmission over 143 km [Physics]

2016-11-29T08:48:07-08:00

Spatial modes of light can potentially carry a vast amount of information, making them promising candidates for both classical and quantum communication. However, the distribution of such modes over large distances remains difficult. Intermodal coupling complicates their use with common fibers, whereas free-space transmission is thought to be strongly influenced...



Fermi liquid behavior of the in-plane resistivity in the pseudogap state of YBa2Cu4O8 [Physics]

2016-11-29T08:48:07-08:00

Our knowledge of the ground state of underdoped hole-doped cuprates has evolved considerably over the last few years. There is now compelling evidence that, inside the pseudogap phase, charge order breaks translational symmetry leading to a reconstructed Fermi surface made of small pockets. Quantum oscillations [Doiron-Leyraud N, et al. (2007)...



Anomalous dynamics of interstitial dopants in soft crystals [Physics]

2016-11-29T08:48:07-08:00

The dynamics of interstitial dopants govern the properties of a wide variety of doped crystalline materials. To describe the hopping dynamics of such interstitial impurities, classical approaches often assume that dopant particles do not interact and travel through a static potential energy landscape. Here we show, using computer simulations, how...



Atomic determinants of BK channel activation by polyunsaturated fatty acids [Physiology]

2016-11-29T08:48:08-08:00

Docosahexaenoic acid (DHA), a polyunsaturated ω-3 fatty acid enriched in oily fish, contributes to better health by affecting multiple targets. Large-conductance Ca2+- and voltage-gated Slo1 BK channels are directly activated by nanomolar levels of DHA. We investigated DHA–channel interaction by manipulating both the fatty acid structure and the channel composition...



Standing genetic variation in a tissue-specific enhancer underlies selfing-syndrome evolution in Capsella [Plant Biology]

2016-11-29T08:48:08-08:00

Mating system shifts recurrently drive specific changes in organ dimensions. The shift in mating system from out-breeding to selfing is one of the most frequent evolutionary transitions in flowering plants and is often associated with an organ-specific reduction in flower size. However, the evolutionary paths along which polygenic traits, such...



Arabidopsis thaliana GH3.5 acyl acid amido synthetase mediates metabolic crosstalk in auxin and salicylic acid homeostasis [Plant Biology]

2016-11-29T08:48:08-08:00

In Arabidopsis thaliana, the acyl acid amido synthetase Gretchen Hagen 3.5 (AtGH3.5) conjugates both indole-3-acetic acid (IAA) and salicylic acid (SA) to modulate auxin and pathogen response pathways. To understand the molecular basis for the activity of AtGH3.5, we determined the X-ray crystal structure of the enzyme in complex with...



Effect of holding office on the behavior of politicians [Political Sciences]

2016-11-29T08:48:07-08:00

Reciprocity is central to our understanding of politics. Most political exchanges—whether they involve legislative vote trading, interbranch bargaining, constituent service, or even the corrupt exchange of public resources for private wealth—require reciprocity. But how does reciprocity arise? Do government officials learn reciprocity while holding office, or do recruitment and selection...



Cortical networks involved in visual awareness independent of visual attention [Psychological and Cognitive Sciences]

2016-11-29T08:48:08-08:00

It is now well established that visual attention, as measured with standard spatial attention tasks, and visual awareness, as measured by report, can be dissociated. It is possible to attend to a stimulus with no reported awareness of the stimulus. We used a behavioral paradigm in which people were aware...



Adolescents growing up amidst intractable conflict attenuate brain response to pain of outgroup [Psychological and Cognitive Sciences]

2016-11-29T08:48:07-08:00

Adolescents’ participation in intergroup conflicts comprises an imminent global risk, and understanding its neural underpinnings may open new perspectives. We assessed Jewish-Israeli and Arab-Palestinian adolescents for brain response to the pain of ingroup/outgroup protagonists using magnetoencephalography (MEG), one-on-one positive and conflictual interactions with an outgroup member, attitudes toward the regional...



The double identity of linguistic doubling [Psychological and Cognitive Sciences]

2016-11-29T08:48:07-08:00

Does knowledge of language consist of abstract principles, or is it fully embodied in the sensorimotor system? To address this question, we investigate the double identity of doubling (e.g., slaflaf, or generally, XX; where X stands for a phonological constituent). Across languages, doubling is known to elicit conflicting preferences at...



Wind speed reductions by large-scale wind turbine deployments lower turbine efficiencies and set low generation limits [Sustainability Science]

2016-11-29T08:48:07-08:00

Wind turbines generate electricity by removing kinetic energy from the atmosphere. Large numbers of wind turbines are likely to reduce wind speeds, which lowers estimates of electricity generation from what would be presumed from unaffected conditions. Here, we test how well wind power limits that account for this effect can...



Identification and characterization of high methane-emitting abandoned oil and gas wells [Sustainability Science]

2016-11-29T08:48:07-08:00

Recent measurements of methane emissions from abandoned oil/gas wells show that these wells can be a substantial source of methane to the atmosphere, particularly from a small proportion of high-emitting wells. However, identifying high emitters remains a challenge. We couple 163 well measurements of methane flow rates; ethane, propane, and...



Socioecological transitions trigger fire regime shifts and modulate fire-climate interactions in the Sierra Nevada, USA, 1600-2015 CE [Sustainability Science]

2016-11-29T08:48:07-08:00

Large wildfires in California cause significant socioecological impacts, and half of the federal funds for fire suppression are spent each year in California. Future fire activity is projected to increase with climate change, but predictions are uncertain because humans can modulate or even override climatic effects on fire activity. Here...



Multiplex social ecological network analysis reveals how social changes affect community robustness more than resource depletion [Sustainability Science]

2016-11-29T08:48:07-08:00

Network analysis provides a powerful tool to analyze complex influences of social and ecological structures on community and household dynamics. Most network studies of social–ecological systems use simple, undirected, unweighted networks. We analyze multiplex, directed, and weighted networks of subsistence food flows collected in three small indigenous communities in Arctic...



Correction for Sakata et al., Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid [Correction]

2016-11-29T08:48:08-08:00

BIOPHYSICS AND COMPUTATIONAL BIOLOGY Correction for “Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid,” by Souhei Sakata, Yuka Jinno, Akira Kawanabe, and Yasushi Okamura, which appeared in issue 27, July 5, 2016, of Proc Natl Acad Sci USA (113:7521–7526; first published June 21,...



Correction for Delgehyr et al., Drosophila Mgr, a Prefoldin subunit cooperating with von Hippel Lindau to regulate tubulin stability [Correction]

2016-11-29T08:48:08-08:00

CELL BIOLOGY Correction for “Drosophila Mgr, a Prefoldin subunit cooperating with von Hippel Lindau to regulate tubulin stability,” by Nathalie Delgehyr, Uta Wieland, Hélène Rangone, Xavier Pinson, Guojie Mao, Nikola S. Dzhindzhev, Doris McLean, Maria G. Riparbelli, Salud Llamazares, Giuliano Callaini, Cayetano Gonzalez, and David M. Glover, which appeared in...



Correction for Coates et al., Wildfire, climate, and invasive grass interactions negatively impact an indicator species by reshaping sagebrush ecosystems [Correction]

2016-11-29T08:48:08-08:00

ECOLOGY Correction for “Wildfire, climate, and invasive grass interactions negatively impact an indicator species by reshaping sagebrush ecosystems,” by Peter S. Coates, Mark A. Ricca, Brian G. Prochazka, Matthew L. Brooks, Kevin E. Doherty, Travis Kroger, Erik J. Blomberg, Christian A. Hagen, and Michael L. Casazza, which appeared in issue...



Correction to Supporting Information for Biswas et al., E-cadherin junction formation involves an active kinetic nucleation process [SI Correction]

2016-11-29T08:48:08-08:00

BIOPHYSICS AND COMPUTATIONAL BIOLOGY Correction to Supporting Information for “E-cadherin junction formation involves an active kinetic nucleation process,” by Kabir H. Biswas, Kevin L. Hartman, Cheng-han Yu, Oliver J. Harrison, Hang Song, Adam W. Smith, William Y. C. Huang, Wan-Chen Lin, Zhenhuan Guo, Anup Padmanabhan, Sergey M. Troyanovsky, Michael L....