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Preview: Proceedings of the National Academy of Sciences recent issues

Proceedings of the National Academy of Sciences recent issues



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



 



In This Issue [This Week in PNAS]

2017-11-14T10:46:37-08:00

Amnesic mice retain silent memory engrams Hippocampal dentate gyrus engram cells (red) store fear memories. Memory engrams refer to long-lasting, learning-induced physical or chemical changes that occur in brain networks. Researchers have shown that the reactivation of these engram cells, which are located in the dentate gyrus of the hippocampus,...



Better choices than optical angular momentum multiplexing for communications [Physical Sciences]

2017-11-14T10:46:38-08:00

Using optical angular momentum (OAM) beams, Shi et al. (1) demonstrate multiple acoustic channels between arrays of sources and detection points. Even better channels with fewer resources are, however, possible. OAM is not an additional degree of freedom beyond normal spatial multiplexing; using only the OAM “topological charge,” l particularly...



Reply to Miller: Misunderstanding and mix-up of acoustic and optical communications [Physical Sciences]

2017-11-14T10:46:38-08:00

In a Letter in PNAS, Miller (1) comments on our work on high-speed acoustic communication (2) by stating “using optical angular momentum (OAM) beams.” This clearly is a misunderstanding by the author: we did not use optical angular momentum; rather, we use the acoustic wave modulation. The author also misunderstands...



Theory, simulations, and experiments show that proteins fold by multiple pathways [Biological Sciences]

2017-11-14T10:46:38-08:00

In PNAS (1), Englander and Mayne repeat an assertion, already made by them along with Bai and Sosnick in 1995 (2), that the modern energy landscape theory of protein folding, by emphasizing the parallelism of potential folding pathways, is incompatible with evidence that in some cases a single particular sequence...



Reply to Eaton and Wolynes: How do proteins fold? [Biological Sciences]

2017-11-14T10:46:38-08:00

Eaton and Wolynes (1) take issue with our recent paper on protein folding (2) in which we compare the defined-pathway model (3, 4) and the many-pathway funneled-energy landscape model (5, 6) with informative experimental results. Eaton and Wolynes (1) do not dispute our main points. Over a dozen proteins have...



Harmful algal blooms in the Eastern North Atlantic Ocean [Biological Sciences]

2017-11-14T10:46:38-08:00

Applying a mathematical model to the period 1982–2016, in PNAS Gobler et al. (1) propose that ocean warming has expanded the niche for harmful algal blooms (HABs) of the species Dinophysis acuminata and Alexandrium fundyense, which can generate shellfish toxicity and pose risks to human health. The authors’ model predicts...



Reply to Dees et al.: Ocean warming promotes species-specific increases in the cellular growth rates of harmful algal blooms [Biological Sciences]

2017-11-14T10:46:38-08:00

Recently, we (1) reported that, since 1982, several regions across the North Atlantic and North Pacific Oceans have experienced warming in specific seasons and locations that have significantly increased the potential cellular growth rates and bloom seasons of two harmful algae, Alexandrium fundyense and Dinophysis acuminata, and that new blooms...



Reverse chemical ecology at the service of conservation biology [Biochemistry]

2017-11-14T10:46:37-08:00

Chemical ecology is the study of the chemical languages, cues, and mechanisms controlling interactions among living beings, including communication among individuals of the same species and between organisms and their environment. Organisms use chemicals to lure their mates, associate with symbionts, deter enemies, and fend off pathogens (1). Since the...



Reducing gun violence in America [Economic Sciences]

2017-11-14T10:46:37-08:00

The rate of gun violence in the United States substantially exceeds that of most other developed nations (1). Within the United States, gun deaths—particularly homicides—contribute to disparities in life expectancy between whites and minority groups, particularly African-Americans (2). Scientific progress in understanding how to address this problem has been limited...



Climate warming drives large-scale changes in ecosystem function [Ecology]

2017-11-14T10:46:37-08:00

The Barents Sea is the continental shelf sea to the north of Scandinavia and Northwest Russia, and it supports some of the richest fisheries in Europe. Until recently, the northern Barents Sea was dominated by small-sized, slow-growing fish species with specialized diets, mostly living in close association with the sea...



How population growth relates to climate change [Sustainability Science]

2017-11-14T10:46:37-08:00

Currently, around 7.5 billion people live on our planet and scenarios for the future show a plausible range from 8.5 to over 12 billion before the population will level off or start to decline, depending on the future course of fertility and mortality (1, 2). These people will also have...



Continuum limit of the vibrational properties of amorphous solids [Applied Physical Sciences]

2017-11-14T10:46:38-08:00

The low-frequency vibrational and low-temperature thermal properties of amorphous solids are markedly different from those of crystalline solids. This situation is counterintuitive because all solid materials are expected to behave as a homogeneous elastic body in the continuum limit, in which vibrational modes are phonons that follow the Debye law....



Interplay of hemilability and redox activity in models of hydrogenase active sites [Chemistry]

2017-11-14T10:46:38-08:00

The hydrogen evolution reaction, as catalyzed by two electrocatalysts [M(N2S2)·Fe(NO)2]+, [Fe-Fe]+ (M = Fe(NO)) and [Ni-Fe]+ (M = Ni) was investigated by computational chemistry. As nominal models of hydrogenase active sites, these bimetallics feature two kinds of actor ligands: Hemilabile, MN2S2 ligands and redox-active, nitrosyl ligands, whose interplay guides the...



Combining disparate data sources for improved poverty prediction and mapping [Computer Sciences]

2017-11-14T10:46:38-08:00

More than 330 million people are still living in extreme poverty in Africa. Timely, accurate, and spatially fine-grained baseline data are essential to determining policy in favor of reducing poverty. The potential of “Big Data” to estimate socioeconomic factors in Africa has been proven. However, most current studies are limited...



Enhanced antibacterial activity through the controlled alignment of graphene oxide nanosheets [Environmental Sciences]

2017-11-14T10:46:38-08:00

The cytotoxicity of 2D graphene-based nanomaterials (GBNs) is highly important for engineered applications and environmental health. However, the isotropic orientation of GBNs, most notably graphene oxide (GO), in previous experimental studies obscured the interpretation of cytotoxic contributions of nanosheet edges. Here, we investigate the orientation-dependent interaction of GBNs with bacteria...



Reverse chemical ecology: Olfactory proteins from the giant panda and their interactions with putative pheromones and bamboo volatiles [Biochemistry]

2017-11-14T10:46:38-08:00

The giant panda Ailuropoda melanoleuca belongs to the family of Ursidae; however, it is not carnivorous, feeding almost exclusively on bamboo. Being equipped with a typical carnivorous digestive apparatus, the giant panda cannot get enough energy for an active life and spends most of its time digesting food or sleeping....



Molecular basis of the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1 [Biochemistry]

2017-11-14T10:46:38-08:00

The 14-3-3 proteins, a family of highly conserved scaffolding proteins ubiquitously expressed in all eukaryotic cells, interact with and regulate the function of several hundreds of partner proteins. Yeast neutral trehalases (Nth), enzymes responsible for the hydrolysis of trehalose to glucose, compared with trehalases from other organisms, possess distinct structure...



Role of the nucleotidyl cyclase helical domain in catalytically active dimer formation [Biochemistry]

2017-11-14T10:46:38-08:00

Nucleotidyl cyclases, including membrane-integral and soluble adenylyl and guanylyl cyclases, are central components in a wide range of signaling pathways. These proteins are architecturally diverse, yet many of them share a conserved feature, a helical region that precedes the catalytic cyclase domain. The role of this region in cyclase dimerization...



Protocadherin cis-dimer architecture and recognition unit diversity [Biochemistry]

2017-11-14T10:46:38-08:00

Clustered protocadherins (Pcdhs) mediate numerous neural patterning functions, including neuronal self-recognition and non–self-discrimination to direct self-avoidance among vertebrate neurons. Individual neurons stochastically express a subset of Pcdh isoforms, which assemble to form a stochastic repertoire of cis-dimers. We describe the structure of a PcdhγB7 cis-homodimer, which includes the membrane-proximal extracellular...



Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin [Biophysics and Computational Biology]

2017-11-14T10:46:38-08:00

Kinesin walks processively on microtubules (MTs) in an asymmetric hand-over-hand manner consuming one ATP molecule per 16-nm step. The individual contributions due to docking of the approximately 13-residue neck linker to the leading head (deemed to be the power stroke) and diffusion of the trailing head (TH) that contributes in...



Probing the cooperativity of Thermoplasma acidophilum proteasome core particle gating by NMR spectroscopy [Biophysics and Computational Biology]

2017-11-14T10:46:38-08:00

The 20S proteasome core particle (20S CP) plays an integral role in cellular homeostasis by degrading proteins no longer required for function. The process is, in part, controlled via gating residues localized to the ends of the heptameric barrel-like CP structure that occlude substrate entry pores, preventing unregulated degradation of...



Binding kinetics and substrate selectivity in HIV-1 protease-Gag interactions probed at atomic resolution by chemical exchange NMR [Biophysics and Computational Biology]

2017-11-14T10:46:38-08:00

The conversion of immature noninfectious HIV-1 particles to infectious virions is dependent upon the sequential cleavage of the precursor group-specific antigen (Gag) polyprotein by HIV-1 protease. The precise mechanism whereby protease recognizes distinct Gag cleavage sites, located in the intrinsically disordered linkers connecting the globular domains of Gag, remains unclear....



Sequences flanking the transmembrane segments facilitate mitochondrial localization and membrane fusion by mitofusin [Cell Biology]

2017-11-14T10:46:38-08:00

Mitochondria constantly divide and fuse. Homotypic fusion of the outer mitochondrial membranes requires the mitofusin (MFN) proteins, a family of dynamin-like GTPases. MFNs are anchored in the membrane by transmembrane (TM) segments, exposing both the N-terminal GTPase domain and the C-terminal tail (CT) to the cytosol. This arrangement is very...



Intercellular mRNA trafficking via membrane nanotube-like extensions in mammalian cells [Cell Biology]

2017-11-14T10:46:38-08:00

RNAs have been shown to undergo transfer between mammalian cells, although the mechanism behind this phenomenon and its overall importance to cell physiology is not well understood. Numerous publications have suggested that RNAs (microRNAs and incomplete mRNAs) undergo transfer via extracellular vesicles (e.g., exosomes). However, in contrast to a diffusion-based...



Probing and manipulating intracellular membrane traffic by microinjection of artificial vesicles [Cell Biology]

2017-11-14T10:46:38-08:00

There is still a large gap in our understanding between the functional complexity of cells and the reconstruction of partial cellular functions in vitro from purified or engineered parts. Here we have introduced artificial vesicles of defined composition into living cells to probe the capacity of the cellular cytoplasm in...



Patterns of conserved gp120 epitope presentation on attached HIV-1 virions [Cell Biology]

2017-11-14T10:46:38-08:00

A complete picture of HIV antigenicity during early replication is needed to elucidate the full range of options for controlling infection. Such information is frequently gained through analyses of isolated viral envelope antigens, host CD4 receptors, and cognate antibodies. However, direct examination of viral particles and virus–cell interactions is now...



A vimentin binding small molecule leads to mitotic disruption in mesenchymal cancers [Cell Biology]

2017-11-14T10:46:38-08:00

Expression of the transcription factor FOXC2 is induced and necessary for successful epithelial–mesenchymal transition, a developmental program that when activated in cancer endows cells with metastatic potential and the properties of stem cells. As such, identifying agents that inhibit the growth of FOXC2-transformed cells represents an attractive approach to inhibit...



Relevance of iPSC-derived human PGC-like cells at the surface of embryoid bodies to prechemotaxis migrating PGCs [Developmental Biology]

2017-11-14T10:46:38-08:00

Pluripotent stem cell-derived human primordial germ cell-like cells (hPGCLCs) provide important opportunities to study primordial germ cells (PGCs). We robustly produced CD38+ hPGCLCs [∼43% of FACS-sorted embryoid body (EB) cells] from primed-state induced pluripotent stem cells (iPSCs) after a 72-hour transient incubation in the four chemical inhibitors (4i)-naïve reprogramming medium...



Contaminants of emerging concern affect Trichoplusia ni growth and development on artificial diets and a key host plant [Environmental Sciences]

2017-11-14T10:46:38-08:00

Many countries are utilizing reclaimed wastewater for agriculture because drought, rising temperatures, and expanding human populations are increasing water demands. Unfortunately, wastewater often contains biologically active, pseudopersistent pharmaceuticals, even after treatment. Runoff from farms and output from wastewater treatment plants also contribute high concentrations of pharmaceuticals to the environment. This...



Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift [Evolution]

2017-11-14T10:46:38-08:00

Most natural populations are affected by seasonal changes in temperature, rainfall, or resource availability. Seasonally fluctuating selection could potentially make a large contribution to maintaining genetic polymorphism in populations. However, previous theory suggests that the conditions for multilocus polymorphism are restrictive. Here, we explore a more general class of models...



The immunopeptidomic landscape of ovarian carcinomas [Immunology and Inflammation]

2017-11-14T10:46:38-08:00

Immunotherapies, particularly checkpoint inhibitors, have set off a revolution in cancer therapy by releasing the power of the immune system. However, only little is known about the antigens that are essentially presented on cancer cells, capable of exposing them to immune cells. Large-scale HLA ligandome analysis has enabled us to...



Visual experience sculpts whole-cortex spontaneous infraslow activity patterns through an Arc-dependent mechanism [Neuroscience]

2017-11-14T10:46:38-08:00

Decades of work in experimental animals has established the importance of visual experience during critical periods for the development of normal sensory-evoked responses in the visual cortex. However, much less is known concerning the impact of early visual experience on the systems-level organization of spontaneous activity. Human resting-state fMRI has...



Electrical synapses mediate synergism between pheromone and food odors in Drosophila melanogaster [Neuroscience]

2017-11-14T10:46:38-08:00

In Drosophila melanogaster, the sex pheromone produced by males, cis-vaccenyl acetate (cVA), evokes a stereotypic gender-specific behavior in both males and females. As Drosophila adults feed, mate, and oviposit on food, they perceive the pheromone as a blend against a background of food odors. Previous studies have reported that food...



Silent memory engrams as the basis for retrograde amnesia [Neuroscience]

2017-11-14T10:46:38-08:00

Recent studies identified neuronal ensembles and circuits that hold specific memory information (memory engrams). Memory engrams are retained under protein synthesis inhibition-induced retrograde amnesia. These engram cells can be activated by optogenetic stimulation for full-fledged recall, but not by stimulation using natural recall cues (thus, amnesia). We call this state...



Active site voltage clamp fluorometry of the sodium glucose cotransporter hSGLT1 [Physiology]

2017-11-14T10:46:38-08:00

In the human sodium glucose cotransporter (hSGLT1) cycle, the protein undergoes conformational changes where the sugar-binding site alternatively faces the external and internal surfaces. Functional site-directed fluorometry was used to probe the conformational changes at the sugar-binding site. Residues (Y290, T287, H83, and N78) were mutated to cysteines. The mutants...



Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq [Physiology]

2017-11-14T10:46:38-08:00

Prior RNA sequencing (RNA-seq) studies have identified complete transcriptomes for most renal epithelial cell types. The exceptions are the cell types that make up the renal collecting duct, namely intercalated cells (ICs) and principal cells (PCs), which account for only a small fraction of the kidney mass, but play critical...



Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato [Plant Biology]

2017-11-14T10:46:38-08:00

Cultivated potatoes (Solanum tuberosum L.), domesticated from wild Solanum species native to the Andes of southern Peru, possess a diverse gene pool representing more than 100 tuber-bearing relatives (Solanum section Petota). A diversity panel of wild species, landraces, and cultivars was sequenced to assess genetic variation within tuber-bearing Solanum and...



MPSR1 is a cytoplasmic PQC E3 ligase for eliminating emergent misfolded proteins in Arabidopsis thaliana [Plant Biology]

2017-11-14T10:46:38-08:00

Ubiquitin E3 ligases are crucial for eliminating misfolded proteins before they form cytotoxic aggregates that threaten cell fitness and survival. However, it remains unclear how emerging misfolded proteins in the cytoplasm can be selectively recognized and eliminated by E3 ligases in plants. We found that Misfolded Protein Sensing RING E3...



Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation [Plant Biology]

2017-11-14T10:46:38-08:00

Eukaryotic transcriptomes contain a major non–protein-coding component that includes precursors of small RNAs as well as long noncoding RNA (lncRNAs). Here, we utilized the mapping of ribosome footprints on RNAs to explore translational regulation of coding and noncoding RNAs in roots of Arabidopsis thaliana shifted from replete to deficient phosphorous...



High-throughput characterization of protein-protein interactions by reprogramming yeast mating [Applied Biological Sciences]

2017-11-14T10:46:38-08:00

High-throughput methods for screening protein–protein interactions enable the rapid characterization of engineered binding proteins and interaction networks. While existing approaches are powerful, none allow quantitative library-on-library characterization of protein interactions in a modifiable extracellular environment. Here, we show that sexual agglutination of Saccharomyces cerevisiae can be reprogrammed to link interaction...



White blood cell population dynamics for risk stratification of acute coronary syndrome [Applied Mathematics]

2017-11-14T10:46:38-08:00

The complete blood count (CBC) provides a high-level assessment of a patient’s immunologic state and guides the diagnosis and treatment of almost all diseases. Hematology analyzers evaluate CBCs by making high-dimensional single-cell measurements of size and cytoplasmic and nuclear morphology in high throughput, but only the final cell counts are...



Sensing fluctuating airflow with spider silk [Applied Physical Sciences]

2017-11-14T10:46:37-08:00

The ultimate aim of flow sensing is to represent the perturbations of the medium perfectly. Hundreds of millions of years of evolution resulted in hair-based flow sensors in terrestrial arthropods that stand out among the most sensitive biological sensors known, even better than photoreceptors which can detect a single photon...



Mechanism of RNA polymerase II stalling by DNA alkylation [Biochemistry]

2017-11-14T10:46:38-08:00

Several anticancer agents that form DNA adducts in the minor groove interfere with DNA replication and transcription to induce apoptosis. Therapeutic resistance can occur, however, when cells are proficient in the removal of drug-induced damage. Acylfulvenes are a class of experimental anticancer agents with a unique repair profile suggesting their...



Large domain movements upon UvrD dimerization and helicase activation [Biochemistry]

2017-11-14T10:46:38-08:00

Escherichia coli UvrD DNA helicase functions in several DNA repair processes. As a monomer, UvrD can translocate rapidly and processively along ssDNA; however, the monomer is a poor helicase. To unwind duplex DNA in vitro, UvrD needs to be activated either by self-assembly to form a dimer or by interaction...



Inhibition of curli assembly and Escherichia coli biofilm formation by the human systemic amyloid precursor transthyretin [Biochemistry]

2017-11-14T10:46:38-08:00

During biofilm formation, Escherichia coli and other Enterobacteriaceae produce an extracellular matrix consisting of curli amyloid fibers and cellulose. The precursor of curli fibers is the amyloidogenic protein CsgA. The human systemic amyloid precursor protein transthyretin (TTR) is known to inhibit amyloid-β (Aβ) aggregation in vitro and suppress the Alzheimer’s-like...



De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture [Biophysics and Computational Biology]

2017-11-14T10:46:37-08:00

Inside the cell nucleus, genomes fold into organized structures that are characteristic of cell type. Here, we show that this chromatin architecture can be predicted de novo using epigenetic data derived from chromatin immunoprecipitation-sequencing (ChIP-Seq). We exploit the idea that chromosomes encode a 1D sequence of chromatin structural types. Interactions...



DsbA-L prevents obesity-induced inflammation and insulin resistance by suppressing the mtDNA release-activated cGAS-cGAMP-STING pathway [Cell Biology]

2017-11-14T10:46:38-08:00

Chronic inflammation in adipose tissue plays a key role in obesity-induced insulin resistance. However, the mechanisms underlying obesity-induced inflammation remain elusive. Here we show that obesity promotes mtDNA release into the cytosol, where it triggers inflammatory responses by activating the DNA-sensing cGAS-cGAMP-STING pathway. Fat-specific knockout of disulfide-bond A oxidoreductase-like protein...



Assembly of silver Trigons into a buckyball-like Ag180 nanocage [Chemistry]

2017-11-14T10:46:37-08:00

Buckminsterfullerene (C60) represents a perfect combination of geometry and molecular structural chemistry. It has inspired many creative ideas for building fullerene-like nanopolyhedra. These include other fullerenes, virus capsids, polyhedra based on DNA, and synthetic polynuclear metal clusters and cages. Indeed, the regular organization of large numbers of metal atoms into...



Strong texturing of lithium metal in batteries [Chemistry]

2017-11-14T10:46:37-08:00

Lithium, with its high theoretical specific capacity and lowest electrochemical potential, has been recognized as the ultimate negative electrode material for next-generation lithium-based high-energy-density batteries. However, a key challenge that has yet to be overcome is the inferior reversibility of Li plating and stripping, typically thought to be related to...



Early T cell receptor signals globally modulate ligand:receptor affinities during antigen discrimination [Chemistry]

2017-11-14T10:46:38-08:00

Antigen discrimination by T cells occurs at the junction between a T cell and an antigen-presenting cell. Juxtacrine binding between numerous adhesion, signaling, and costimulatory molecules defines both the topographical and lateral geometry of this cell–cell interface, within which T cell receptor (TCR) and peptide major histocompatibility complex (pMHC) interact....



Inner Workings: Special relationship between fungi and plants may have spurred changes to ancient climate [Earth, Atmospheric, and Planetary Sciences]

2017-11-14T10:46:37-08:00

Look at a plant, and you’re probably also looking at a fungus. More than 80% of land plants partner with fungi to help those plants extract nutrients—nitrogen and phosphorus—from the ground (1, 2). The plants return the favor with carbon from their photosynthesis. Biologists suspect that this partnership was a...



Giant boulders and Last Interglacial storm intensity in the North Atlantic [Earth, Atmospheric, and Planetary Sciences]

2017-11-14T10:46:37-08:00

As global climate warms and sea level rises, coastal areas will be subject to more frequent extreme flooding and hurricanes. Geologic evidence for extreme coastal storms during past warm periods has the potential to provide fundamental insights into their future intensity. Recent studies argue that during the Last Interglacial (MIS...



Climate-driven changes in functional biogeography of Arctic marine fish communities [Ecology]

2017-11-14T10:46:38-08:00

Climate change triggers poleward shifts in species distribution leading to changes in biogeography. In the marine environment, fish respond quickly to warming, causing community-wide reorganizations, which result in profound changes in ecosystem functioning. Functional biogeography provides a framework to address how ecosystem functioning may be affected by climate change over...



Pathogen-mediated selection in free-ranging elk populations infected by chronic wasting disease [Ecology]

2017-11-14T10:46:38-08:00

Pathogens can exert a large influence on the evolution of hosts via selection for alleles or genotypes that moderate pathogen virulence. Inconsistent interactions between parasites and the host genome, such as those resulting from genetic linkages and environmental stochasticity, have largely prevented observation of this process in wildlife species. We...



Handgun waiting periods reduce gun deaths [Economic Sciences]

2017-11-14T10:46:38-08:00

Handgun waiting periods are laws that impose a delay between the initiation of a purchase and final acquisition of a firearm. We show that waiting periods, which create a “cooling off” period among buyers, significantly reduce the incidence of gun violence. We estimate the impact of waiting periods on gun...



Impact of population growth and population ethics on climate change mitigation policy [Economic Sciences]

2017-11-14T10:46:38-08:00

Future population growth is uncertain and matters for climate policy: higher growth entails more emissions and means more people will be vulnerable to climate-related impacts. We show that how future population is valued importantly determines mitigation decisions. Using the Dynamic Integrated Climate-Economy model, we explore two approaches to valuing population:...



Direct observation of impact propagation and absorption in dense colloidal monolayers [Engineering]

2017-11-14T10:46:37-08:00

Dense colloidal suspensions can propagate and absorb large mechanical stresses, including impacts and shocks. The wave transport stems from the delicate interplay between the spatial arrangement of the structural units and solvent-mediated effects. For dynamic microscopic systems, elastic deformations of the colloids are usually disregarded due to the damping imposed...



Estimating mobility using sparse data: Application to human genetic variation [Evolution]

2017-11-14T10:46:38-08:00

Mobility is one of the most important processes shaping spatiotemporal patterns of variation in genetic, morphological, and cultural traits. However, current approaches for inferring past migration episodes in the fields of archaeology and population genetics lack either temporal resolution or formal quantification of the underlying mobility, are poorly suited to...



Testing the neutral hypothesis of phenotypic evolution [Evolution]

2017-11-14T10:46:38-08:00

Although evolution by natural selection is widely regarded as the most important principle of biology, it is unknown whether phenotypic variations within and between species are mostly adaptive or neutral due to the lack of relevant studies of large, unbiased samples of phenotypic traits. Here, we examine 210 yeast morphological...



DNA-RNA interactions are critical for chromosome condensation in Escherichia coli [Genetics]

2017-11-14T10:46:38-08:00

Bacterial chromosome (nucleoid) conformation dictates faithful regulation of gene transcription. The conformation is condition-dependent and is guided by several nucleoid-associated proteins (NAPs) and at least one nucleoid-associated noncoding RNA, naRNA4. Here we investigated the molecular mechanism of how naRNA4 and the major NAP, HU, acting together organize the chromosome structure...



Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize [Genetics]

2017-11-14T10:46:38-08:00

Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers (COs) and noncrossovers (NCOs). Recombination events are not distributed evenly along chromosomes but...



Core Concept: Tissue resident memory cells emerging as key player in health and disease [Immunology and Inflammation]

2017-11-14T10:46:37-08:00

Much of our understanding of the immune system has come from studying immune cells drawn from blood. Such samples are minimally invasive and relatively easy to collect, but they provide an incomplete and often misleading picture. Put simply, the biology of the immune system in blood doesn’t match the biology...



STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus [Immunology and Inflammation]

2017-11-14T10:46:37-08:00

Cytokines critically control immune responses, but how regulatory programs are altered to allow T cells to differentially respond to distinct cytokine stimuli remains poorly understood. Here, we have globally analyzed enhancer elements bound by IL-2–activated STAT5 and IL-21–activated STAT3 in T cells and identified Il2ra as the top-ranked gene regulated...



Dynamics of cell transformation in culture and its significance for tumor development in animals [Medical Sciences]

2017-11-14T10:46:38-08:00

NIH 3T3 cells grown in conventional Dulbecco’s modification of Eagle’s basal medium (DME) produce no transformed foci when grown to confluence in 10% calf serum (CS). A few cultures were transformed by ras oncogenes when transfected with DNA from neoplastic cells, but they failed to do so in 80 to...



Requirement of zinc transporter ZIP10 for epidermal development: Implication of the ZIP10-p63 axis in epithelial homeostasis [Medical Sciences]

2017-11-14T10:46:38-08:00

Skin tissues, in particular the epidermis, are severely affected by zinc deficiency. However, the zinc-mediated mechanisms that maintain the cells that form the epidermis have not been established. Here, we report that the zinc transporter ZIP10 is highly expressed in the outer root sheath of hair follicles and plays critical...



PRC2-mediated repression of SMARCA2 predicts EZH2 inhibitor activity in SWI/SNF mutant tumors [Medical Sciences]

2017-11-14T10:46:38-08:00

Subunits of the SWI/SNF chromatin remodeling complex are frequently mutated in human cancers leading to epigenetic dependencies that are therapeutically targetable. The dependency on the polycomb repressive complex (PRC2) and EZH2 represents one such vulnerability in tumors with mutations in the SWI/SNF complex subunit, SNF5; however, whether this vulnerability extends...



Rewriting nature’s assembly manual for a ssRNA virus [Microbiology]

2017-11-14T10:46:38-08:00

Satellite tobacco necrosis virus (STNV) is one of the smallest viruses known. Its genome encodes only its coat protein (CP) subunit, relying on the polymerase of its helper virus TNV for replication. The genome has been shown to contain a cryptic set of dispersed assembly signals in the form of...



O2 availability impacts iron homeostasis in Escherichia coli [Microbiology]

2017-11-14T10:46:38-08:00

The ferric-uptake regulator (Fur) is an Fe2+-responsive transcription factor that coordinates iron homeostasis in many bacteria. Recently, we reported that expression of the Escherichia coli Fur regulon is also impacted by O2 tension. Here, we show that for most of the Fur regulon, Fur binding and transcriptional repression increase under...



Phytopathogenic fungus hosts a plant virus: A naturally occurring cross-kingdom viral infection [Microbiology]

2017-11-14T10:46:38-08:00

The transmission of viral infections between plant and fungal hosts has been suspected to occur, based on phylogenetic and other findings, but has not been directly observed in nature. Here, we report the discovery of a natural infection of the phytopathogenic fungus Rhizoctonia solani by a plant virus, cucumber mosaic...



Replication of early and recent Zika virus isolates throughout mouse brain development [Microbiology]

2017-11-14T10:46:38-08:00

Fetal infection with Zika virus (ZIKV) can lead to congenital Zika virus syndrome (cZVS), which includes cortical malformations and microcephaly. The aspects of cortical development that are affected during virus infection are unknown. Using organotypic brain slice cultures generated from embryonic mice of various ages, sites of ZIKV replication including...



Facephenes and rainbows: Causal evidence for functional and anatomical specificity of face and color processing in the human brain [Neuroscience]

2017-11-14T10:46:38-08:00

Neuroscientists have long debated whether some regions of the human brain are exclusively engaged in a single specific mental process. Consistent with this view, fMRI has revealed cortical regions that respond selectively to certain stimulus classes such as faces. However, results from multivoxel pattern analyses (MVPA) challenge this view by...



The human visual cortex response to melanopsin-directed stimulation is accompanied by a distinct perceptual experience [Neuroscience]

2017-11-14T10:46:38-08:00

The photopigment melanopsin supports reflexive visual functions in people, such as pupil constriction and circadian photoentrainment. What contribution melanopsin makes to conscious visual perception is less studied. We devised a stimulus that targeted melanopsin separately from the cones using pulsed (3-s) spectral modulations around a photopic background. Pupillometry confirmed that...



Human hippocampal theta power indicates movement onset and distance travelled [Neuroscience]

2017-11-14T10:46:38-08:00

Theta frequency oscillations in the 6- to 10-Hz range dominate the rodent hippocampal local field potential during translational movement, suggesting that theta encodes self-motion. Increases in theta power have also been identified in the human hippocampus during both real and virtual movement but appear as transient bursts in distinct high-...



Cooperative cortical network for categorical processing of Chinese lexical tone [Neuroscience]

2017-11-14T10:46:38-08:00

In tonal languages such as Chinese, lexical tone with varying pitch contours serves as a key feature to provide contrast in word meaning. Similar to phoneme processing, behavioral studies have suggested that Chinese tone is categorically perceived. However, its underlying neural mechanism remains poorly understood. By conducting cortical surface recordings...



Endosomal signaling of the receptor for calcitonin gene-related peptide mediates pain transmission [Pharmacology]

2017-11-14T10:46:38-08:00

G protein-coupled receptors (GPCRs) are considered to function primarily at the plasma membrane, where they interact with extracellular ligands and couple to G proteins that transmit intracellular signals. Consequently, therapeutic drugs are designed to target GPCRs at the plasma membrane. Activated GPCRs undergo clathrin-dependent endocytosis. Whether GPCRs in endosomes control...



NOX4-dependent neuronal autotoxicity and BBB breakdown explain the superior sensitivity of the brain to ischemic damage [Pharmacology]

2017-11-14T10:46:38-08:00

Ischemic injury represents the most frequent cause of death and disability, and it remains unclear why, of all body organs, the brain is most sensitive to hypoxia. In many tissues, type 4 NADPH oxidase is induced upon ischemia or hypoxia, converting oxygen to reactive oxygen species. Here, we show in...



Catalysis of heat-to-work conversion in quantum machines [Physics]

2017-11-14T10:46:38-08:00

We propose a hitherto-unexplored concept in quantum thermodynamics: catalysis of heat-to-work conversion by quantum nonlinear pumping of the piston mode which extracts work from the machine. This concept is analogous to chemical reaction catalysis: Small energy investment by the catalyst (pump) may yield a large increase in heat-to-work conversion. Since...



COP1 mediates dark-specific degradation of microtubule-associated protein WDL3 in regulating Arabidopsis hypocotyl elongation [Plant Biology]

2017-11-14T10:46:38-08:00

CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a well-known E3 ubiquitin ligase, functions as a central regulator of plant growth and photomorphogenic development in plants, including hypocotyl elongation. It has been well-established that, in darkness, COP1 targets many photomorphogenesis-promoting factors for ubiquitination and degradation in the nucleus. However, increasing evidence has shown that...



Two rice receptor-like kinases maintain male fertility under changing temperatures [Plant Biology]

2017-11-14T10:46:38-08:00

Plants employ dynamic molecular networks to control development in response to environmental changes, yet the underlying mechanisms are largely unknown. Here we report the identification of two rice leucine-rich repeat receptor-like kinases, Thermo-Sensitive Genic Male Sterile 10 (TMS10) and its close homolog TMS10-Like (TMS10L), which redundantly function in the maintenance...



Using neurostimulation to understand the impact of pre-morbid individual differences on post-lesion outcomes [Psychological and Cognitive Sciences]

2017-11-14T10:46:38-08:00

Neuropsychological data have proven invaluable in advancing our understanding of higher cognition. The interpretation of such data is, however, complicated by the fact that post-lesion behavioral abnormalities could reflect pre-morbid individual differences in the cognitive domain of interest. Here we exploited the virtual lesion methodology offered by transcranial magnetic stimulation...



Supply and demand drive a critical transition to dysfunctional fisheries [Sustainability Science]

2017-11-14T10:46:38-08:00

There is growing awareness of the need for fishery management policies that are robust to changing environmental, social, and economic pressures. Here we use conventional bioeconomic theory to demonstrate that inherent biological constraints combined with nonlinear supply−demand relationships can generate threshold effects due to harvesting. As a result, increases in...



In This Issue [This Week in PNAS]

2017-11-07T09:07:26-08:00

Genomic history of Italian brown bears Apennine bear. Photo by Valentino Mastrella and image courtesy of Archive from the Abruzzo, Lazio e Molise National Park. Apennine bears are a critically endangered population of approximately 50 Italian brown bears that live in the central Apennine Mountains. Apennine bears (Ursus arctos marsicanus)...



Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals [Biological Sciences]

2017-11-07T09:07:26-08:00

Phylogenomic studies can settle long-standing debates but should be scrutinized when well-established clades are contradicted and divergence dates are highly incompatible with the fossil record. Liu et al. (1) construct a species tree for Mammalia based on 4,388 protein-coding genes from 90 taxa to derive a novel model for the...



Reply to Gatesy and Springer: Claims of homology errors and zombie lineages do not compromise the dating of placental diversification [Biological Sciences]

2017-11-07T09:07:26-08:00

Gatesy and Springer (1) consider 3 out of 89 nodes in our “preferred STAR tree” (2) unusual, raising suspicions that underlying alignment errors have generated these and other perceived misestimations in our analysis. As in their other critiques of our work, their claims are based on subjective and unrepeatable logic....



Cytokine signature in chronic fatigue syndrome [Biological Sciences]

2017-11-07T09:07:26-08:00

One of the major findings in the publication by Montoya et al. (1) on cytokine signatures in chronic fatigue syndrome is elevation of circulating TGF-β in patients with chronic fatigue syndrome (CFS). Unfortunately, the materials and methods of ref. 1 do not give much information on how the controls were...



Reply to Roerink et al: Methods for recruitment, serum separation, and storage were the same for patients and controls [Biological Sciences]

2017-11-07T09:07:26-08:00

Roerink et al. (1) raise important and potential methodological biases that could have accounted for our finding regarding elevated TGF-β levels in patients with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) (2). Here, we provide additional information as requested by Roerink et al. (1) that supports that the elevation of TGF-β in...



Artificial microtubules burst with energy [Chemistry]

2017-11-07T09:07:26-08:00

Among the multitude of biological machines that nature employs to keep the cell operational, molecular motor proteins are certainly among the most captivating. These proteins convert chemical energy into mechanical work and drive most forms of motion (1). Cytoplasmic motors, for example, are proteins that move along a track and...



Rising hazard of storm-surge flooding [Earth, Atmospheric, and Planetary Sciences]

2017-11-07T09:07:26-08:00

The 2017 Atlantic hurricane season is one for the history books. It has blown a number of records out of the water. Harvey dumped more rain on the United States than any previous hurricane. Irma maintained the highest category 5 longer than any storm anywhere in the world. September 2017...



Helicase SPRNTing through the nanopore [Biophysics and Computational Biology]

2017-11-07T09:07:26-08:00

Enzymes that move directionally on single-stranded nucleic acids are at the core of emerging nanopore sequencing technology. Of a particular use are DNA helicases, molecular motors that bind single-stranded DNA (ssDNA) independently of its sequence and use ATP to fuel their directional motion along the DNA (1). In nanopore-based sequencing,...



Controlling orientational order in block copolymers using low-intensity magnetic fields [Applied Physical Sciences]

2017-11-07T09:07:26-08:00

The interaction of fields with condensed matter during phase transitions produces a rich variety of physical phenomena. Self-assembly of liquid crystalline block copolymers (LC BCPs) in the presence of a magnetic field, for example, can result in highly oriented microstructures due to the LC BCP’s anisotropic magnetic susceptibility. We show...



Clinical validation of a nanodiamond-embedded thermoplastic biomaterial [Engineering]

2017-11-07T09:07:26-08:00

Detonation nanodiamonds (NDs) are promising drug delivery and imaging agents due to their uniquely faceted surfaces with diverse chemical groups, electrostatic properties, and biocompatibility. Based on the potential to harness ND properties to clinically address a broad range of disease indications, this work reports the in-human administration of NDs through...



Three-dimensional mesostructures as high-temperature growth templates, electronic cellular scaffolds, and self-propelled microrobots [Engineering]

2017-11-07T09:07:26-08:00

Recent work demonstrates that processes of stress release in prestrained elastomeric substrates can guide the assembly of sophisticated 3D micro/nanostructures in advanced materials. Reported application examples include soft electronic components, tunable electromagnetic and optical devices, vibrational metrology platforms, and other unusual technologies, each enabled by uniquely engineered 3D architectures. A...



Neurobiology of culturally common maternal responses to infant cry [Psychological and Cognitive Sciences]

2017-11-07T09:07:26-08:00

This report coordinates assessments of five types of behavioral responses in new mothers to their own infants’ cries with neurobiological responses in new mothers to their own infants’ cries and in experienced mothers and inexperienced nonmothers to infant cries and other emotional and control sounds. We found that 684 new...



Reconstitution of UCP1 using CRISPR/Cas9 in the white adipose tissue of pigs decreases fat deposition and improves thermogenic capacity [Agricultural Sciences]

2017-11-07T09:07:26-08:00

Uncoupling protein 1 (UCP1) is localized on the inner mitochondrial membrane and generates heat by uncoupling ATP synthesis from proton transit across the inner membrane. UCP1 is a key element of nonshivering thermogenesis and is most likely important in the regulation of body adiposity. Pigs (Artiodactyl family Suidae) lack a...



Identification and characterization of Sr13, a tetraploid wheat gene that confers resistance to the Ug99 stem rust race group [Agricultural Sciences]

2017-11-07T09:07:26-08:00

The Puccinia graminis f. sp. tritici (Pgt) Ug99 race group is virulent to most stem rust resistance genes currently deployed in wheat and poses a threat to global wheat production. The durum wheat (Triticum turgidum ssp. durum) gene Sr13 confers resistance to Ug99 and other virulent races, and is more...



A unique surface on Pat1 C-terminal domain directly interacts with Dcp2 decapping enzyme and Xrn1 5'-3' mRNA exonuclease in yeast [Biochemistry]

2017-11-07T09:07:26-08:00

The Pat1 protein is a central player of eukaryotic mRNA decay that has also been implicated in translational control. It is commonly considered a central platform responsible for the recruitment of several RNA decay factors. We demonstrate here that a yeast-specific C-terminal region from Pat1 interacts with several short motifs,...



Crystal structures of Mmm1 and Mdm12-Mmm1 reveal mechanistic insight into phospholipid trafficking at ER-mitochondria contact sites [Biochemistry]

2017-11-07T09:07:26-08:00

The endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) comprises mitochondrial distribution and morphology 12 (Mdm12), maintenance of mitochondrial morphology 1 (Mmm1), Mdm34, and Mdm10 and mediates physical membrane contact sites and nonvesicular lipid trafficking between the ER and mitochondria in yeast. Herein, we report two crystal structures of the synaptotagmin-like mitochondrial...



Bacteriorhodopsin-like channelrhodopsins: Alternative mechanism for control of cation conductance [Biochemistry]

2017-11-07T09:07:26-08:00

The recently discovered cation-conducting channelrhodopsins in cryptophyte algae are far more homologous to haloarchaeal rhodopsins, in particular the proton pump bacteriorhodopsin (BR), than to earlier known channelrhodopsins. They uniquely retain the two carboxylate residues that define the vectorial proton path in BR in which Asp-85 and Asp-96 serve as acceptor...



Structural insights into binding of STAC proteins to voltage-gated calcium channels [Biochemistry]

2017-11-07T09:07:26-08:00

Excitation–contraction (EC) coupling in skeletal muscle requires functional and mechanical coupling between L-type voltage-gated calcium channels (CaV1.1) and the ryanodine receptor (RyR1). Recently, STAC3 was identified as an essential protein for EC coupling and is part of a group of three proteins that can bind and modulate L-type voltage-gated calcium...



Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model [Biochemistry]

2017-11-07T09:07:26-08:00

During replication initiation, the core component of the helicase—the Mcm2-7 hexamer—is loaded on origin DNA as a double hexamer (DH). The two ring-shaped hexamers are staggered, leading to a kinked axial channel. How the origin DNA interacts with the axial channel is not understood, but the interaction could provide key...