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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]

2016-12-06T09:51:44-08:00

Maize from Tehuacan bears markers of isolated population A 4-cm-long ancient maize cob dating 5,300 years ago. Image courtesy of Jaime Padilla (Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico). The history of maize begins around 9,000 years ago, when humans in central Mexico first began...



Profile of Charles M. Rice, Ralf F. W. Bartenschlager, and Michael J. Sofia, 2016 Lasker-DeBakey Clinical Medical Research Awardees [Profile]

2016-12-06T09:51:44-08:00

Hepatitis C: From chronic to curable Three researchers, Ralf F. W. Bartenschlager (University of Heidelberg), Charles M. Rice (The Rockefeller University), and Michael J. Sofia (Arbutus Biopharma, Inc.) (Fig. 1) share the 2016 Lasker–DeBakey Clinical Medical Research Award for their work, which has allowed for the development of a therapeutic...



Profile of William Kaelin, Peter Ratcliffe, and Greg Semenza, 2016 Albert Lasker Basic Medical Research Awardees [Profile]

2016-12-06T09:51:44-08:00

Fire in the air, fire in the cell Toward the end of the 18th century, the Swedish apothecary, Carl Scheele, determined that approximately one-fourth of the volume of air was “feuer luft,” or “fire air”: that is, the component of the atmosphere that allows substances to burn. At almost the...



Eruptible magma [Earth, Atmospheric, and Planetary Sciences]

2016-12-06T09:51:44-08:00

For those who remember the classic disaster-docudrama Supervolcano (BBC-Discovery Channel 2005), the adjective “eruptible” is likely to ring a bell. Set in the near future and generally quite scientifically literate, the movie envisions volcanologists trying desperately to evaluate the near-term threat posed by the giant Yellowstone magmatic system. At the...



The sluggish speed of making abiotic methane [Earth, Atmospheric, and Planetary Sciences]

2016-12-06T09:51:44-08:00

In searching for life beyond Earth, scientists have focused considerable attention on terrestrial bodies containing liquid water. These bodies are considered to be among the most promising locations for hosting the conditions and chemistry required for life (1). To understand how to detect the presence of habitable or inhabited environments,...



Genomic and brain expansion provide ants with refined sense of smell [Evolution]

2016-12-06T09:51:44-08:00

Chemical communication is the most ancient way of information transfer among organisms, and chemical senses, although universal, are particularly developed in social species. Many animals use odors in circumstances that are critical for survival and reproduction: to detect suitable food sources and nest sites, to avoid predators, and to find...



Linguistic positivity in historical texts reflects dynamic environmental and psychological factors [Psychological and Cognitive Sciences]

2016-12-06T09:51:45-08:00

People use more positive words than negative words. Referred to as “linguistic positivity bias” (LPB), this effect has been found across cultures and languages, prompting the conclusion that it is a panhuman tendency. However, although multiple competing explanations of LPB have been proposed, there is still no consensus on what...



Discovery of cofactor-specific, bactericidal Mycobacterium tuberculosis InhA inhibitors using DNA-encoded library technology [Applied Biological Sciences]

2016-12-06T09:51:45-08:00

Millions of individuals are infected with and die from tuberculosis (TB) each year, and multidrug-resistant (MDR) strains of TB are increasingly prevalent. As such, there is an urgent need to identify novel drugs to treat TB infections. Current frontline therapies include the drug isoniazid, which inhibits the essential NADH-dependent enoyl–acyl-carrier...



Substrate recognition and catalysis by GH47 {alpha}-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway [Biochemistry]

2016-12-06T09:51:45-08:00

Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) α-mannosidases, including endoplasmic reticulum (ER) α-mannosidase I (ERManI)...



Molecular evidence of keratin and melanosomes in feathers of the Early Cretaceous bird Eoconfuciusornis [Evolution]

2016-12-06T09:51:45-08:00

Microbodies associated with feathers of both nonavian dinosaurs and early birds were first identified as bacteria but have been reinterpreted as melanosomes. Whereas melanosomes in modern feathers are always surrounded by and embedded in keratin, melanosomes embedded in keratin in fossils has not been demonstrated. Here we provide multiple independent...



Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA [Immunology and Inflammation]

2016-12-06T09:51:45-08:00

HIV-1–infected individuals harbor a latent reservoir of infected CD4+ T cells that is not eradicated by antiretroviral therapy (ART). This reservoir presents the greatest barrier to an HIV-1 cure and has remained difficult to characterize, in part, because the vast majority of integrated sequences are defective and incapable of reactivation....



MIF allele-dependent regulation of the MIF coreceptor CD44 and role in rheumatoid arthritis [Medical Sciences]

2016-12-06T09:51:45-08:00

Fibroblast-like synoviocytes mediate joint destruction in rheumatoid arthritis and exhibit sustained proinflammatory and invasive properties. CD44 is a polymorphic transmembrane protein with defined roles in matrix interaction and tumor invasion that is also a signaling coreceptor for macrophage migration inhibitory factor (MIF), which engages cell surface CD74. High-expression MIF alleles...



An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers [Microbiology]

2016-12-06T09:51:45-08:00

Subsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H2. Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa,...



Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers [Microbiology]

2016-12-06T09:51:45-08:00

Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome...



Reconstitution of a Mycobacterium tuberculosis proteostasis network highlights essential cofactor interactions with chaperone DnaK [Microbiology]

2016-12-06T09:51:45-08:00

During host infection, Mycobacterium tuberculosis (Mtb) encounters several types of stress that impair protein integrity, including reactive oxygen and nitrogen species and chemotherapy. The resulting protein aggregates can be resolved or degraded by molecular machinery conserved from bacteria to eukaryotes. Eukaryotic Hsp104/Hsp70 and their bacterial homologs ClpB/DnaK are ATP-powered chaperones...



Context-dependent memory traces in the crab’s mushroom bodies: Functional support for a common origin of high-order memory centers [Neuroscience]

2016-12-06T09:51:45-08:00

The hypothesis of a common origin for the high-order memory centers in bilateral animals is based on the evidence that several key features, including gene expression and neuronal network patterns, are shared across several phyla. Central to this hypothesis is the assumption that the arthropods’ higher order neuropils of the...



Emergence of an abstract categorical code enabling the discrimination of temporally structured tactile stimuli [Neuroscience]

2016-12-06T09:51:45-08:00

The problem of neural coding in perceptual decision making revolves around two fundamental questions: (i) How are the neural representations of sensory stimuli related to perception, and (ii) what attributes of these neural responses are relevant for downstream networks, and how do they influence decision making? We studied these two...



Loss of {beta}-adrenergic-stimulated phosphorylation of CaV1.2 channels on Ser1700 leads to heart failure [Pharmacology]

2016-12-06T09:51:45-08:00

L-type Ca2+ currents conducted by voltage-gated calcium channel 1.2 (CaV1.2) initiate excitation–contraction coupling in the heart, and altered expression of CaV1.2 causes heart failure in mice. Here we show unexpectedly that reducing β-adrenergic regulation of CaV1.2 channels by mutation of a single PKA site, Ser1700, in the proximal C-terminal domain...



Mechanism of gating by calcium in connexin hemichannels [Physiology]

2016-12-06T09:51:45-08:00

Aberrant opening of nonjunctional connexin hemichannels at the plasma membrane is associated with many diseases, including ischemia and muscular dystrophy. Proper control of hemichannel opening is essential to maintain cell viability and is achieved by physiological levels of extracellular Ca2+, which drastically reduce hemichannel activity. Here we examined the role...



Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities [Plant Biology]

2016-12-06T09:51:45-08:00

Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established...



Regional diversity on the timing for the initial appearance of cereal cultivation and domestication in southwest Asia [Anthropology]

2016-12-06T09:51:44-08:00

Recent studies have broadened our knowledge regarding the origins of agriculture in southwest Asia by highlighting the multiregional and protracted nature of plant domestication. However, there have been few archaeobotanical data to examine whether the early adoption of wild cereal cultivation and the subsequent appearance of domesticated-type cereals occurred in...



Methyltransferase-like protein 16 binds the 3'-terminal triple helix of MALAT1 long noncoding RNA [Biochemistry]

2016-12-06T09:51:44-08:00

Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a cancer-promoting long noncoding RNA, accumulates in cells by using a 3′-triple-helical RNA stability element for nuclear expression (ENE). The ENE, a stem-loop structure containing a U-rich internal loop, interacts with a downstream A-rich tract (ENE+A) to form a blunt-ended triple helix composed of...



Characterization of the heterooligomeric red-type rubisco activase from red algae [Biochemistry]

2016-12-06T09:51:44-08:00

The photosynthetic CO2-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) is inhibited by nonproductive binding of its substrate ribulose-1,5-bisphosphate (RuBP) and other sugar phosphates. Reactivation requires ATP-hydrolysis–powered remodeling of the inhibited complexes by diverse molecular chaperones known as rubisco activases (Rcas). Eukaryotic phytoplankton of the red plastid lineage contain so-called red-type rubiscos,...



Efficient replacement of plasma membrane outer leaflet phospholipids and sphingolipids in cells with exogenous lipids [Biochemistry]

2016-12-06T09:51:44-08:00

Our understanding of membranes and membrane lipid function has lagged far behind that of nucleic acids and proteins, largely because it is difficult to manipulate cellular membrane lipid composition. To help solve this problem, we show that methyl-α-cyclodextrin (MαCD)-catalyzed lipid exchange can be used to maximally replace the sphingolipids and...



Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production [Biochemistry]

2016-12-06T09:51:44-08:00

The enzyme Dicer produces small silencing RNAs such as micro-RNAs (miRNAs) and small interfering RNAs (siRNAs). In Drosophila, Dicer-1 produces ∼22–24-nt miRNAs from pre-miRNAs, whereas Dicer-2 makes 21-nt siRNAs from long double-stranded RNAs (dsRNAs). How Dicer-2 precisely makes 21-nt siRNAs with a remarkably high fidelity is unknown. Here we report...



Molecular basis for the broad substrate selectivity of a peptide prenyltransferase [Biochemistry]

2016-12-06T09:51:44-08:00

The cyanobactin prenyltransferases catalyze a series of known or unprecedented reactions on millions of different substrates, with no easily observable recognition motif and exquisite regioselectivity. Here we define the basis of broad substrate tolerance for the otherwise uncharacterized TruF family. We determined the structures of the Tyr-prenylating enzyme PagF, in...



Fibrous nonlinear elasticity enables positive mechanical feedback between cells and ECMs [Biophysics and Computational Biology]

2016-12-06T09:51:44-08:00

In native states, animal cells of many types are supported by a fibrous network that forms the main structural component of the ECM. Mechanical interactions between cells and the 3D ECM critically regulate cell function, including growth and migration. However, the physical mechanism that governs the cell interaction with fibrous...



Atomistic insight into lipid translocation by a TMEM16 scramblase [Biophysics and Computational Biology]

2016-12-06T09:51:45-08:00

The transmembrane protein 16 (TMEM16) family of membrane proteins includes both lipid scramblases and ion channels involved in olfaction, nociception, and blood coagulation. The crystal structure of the fungal Nectria haematococca TMEM16 (nhTMEM16) scramblase suggested a putative mechanism of lipid transport, whereby polar and charged lipid headgroups move through the...



Interactions of divalent cations with calcium binding sites of BK channels reveal independent motions within the gating ring [Biophysics and Computational Biology]

2016-12-06T09:51:45-08:00

Large-conductance voltage- and calcium-activated K+ (BK) channels are key physiological players in muscle, nerve, and endocrine function by integrating intracellular Ca2+ and membrane voltage signals. The open probability of BK channels is regulated by the intracellular concentration of divalent cations sensed by a large structure in the BK channel called...



Graphene oxide-based efficient and scalable solar desalination under one sun with a confined 2D water path [Chemistry]

2016-12-06T09:51:44-08:00

Because it is able to produce desalinated water directly using solar energy with minimum carbon footprint, solar steam generation and desalination is considered one of the most important technologies to address the increasingly pressing global water scarcity. Despite tremendous progress in the past few years, efficient solar steam generation and...



Warm storage for arc magmas [Earth, Atmospheric, and Planetary Sciences]

2016-12-06T09:51:44-08:00

Felsic magmatic systems represent the vast majority of volcanic activity that poses a threat to human life. The tempo and magnitude of these eruptions depends on the physical conditions under which magmas are retained within the crust. Recently the case has been made that volcanic reservoirs are rarely molten and...



Abiotic methane formation during experimental serpentinization of olivine [Earth, Atmospheric, and Planetary Sciences]

2016-12-06T09:51:44-08:00

Fluids circulating through actively serpentinizing systems are often highly enriched in methane (CH4). In many cases, the CH4 in these fluids is thought to derive from abiotic reduction of inorganic carbon, but the conditions under which this process can occur in natural systems remain unclear. In recent years, several studies...



High-pressure phase of brucite stable at Earth’s mantle transition zone and lower mantle conditions [Earth, Atmospheric, and Planetary Sciences]

2016-12-06T09:51:44-08:00

We investigate the high-pressure phase diagram of the hydrous mineral brucite, Mg(OH)2, using structure search algorithms and ab initio simulations. We predict a high-pressure phase stable at pressure and temperature conditions found in cold subducting slabs in Earth’s mantle transition zone and lower mantle. This prediction implies that brucite can...



Evidence of isotopic fractionation of natural uranium in cultured human cells [Earth, Atmospheric, and Planetary Sciences]

2016-12-06T09:51:44-08:00

The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U,...



Sex and the shifting biodiversity dynamics of marine animals in deep time [Earth, Atmospheric, and Planetary Sciences]

2016-12-06T09:51:45-08:00

The fossil record of marine animals suggests that diversity-dependent processes exerted strong control on biodiversification: after the Ordovician Radiation, genus richness did not trend for hundreds of millions of years. However, diversity subsequently rose dramatically in the Cretaceous and Cenozoic (145 million years ago–present), indicating that limits on diversification can...



Disturbance is the key to plant invasions in cold environments [Ecology]

2016-12-06T09:51:45-08:00

Until now, nonnative plant species were rarely found at high elevations and latitudes. However, partly because of climate warming, biological invasions are now on the rise in these extremely cold environments. These plant invasions make it timely to undertake a thorough experimental assessment of what has previously been holding them...



Long-term aggregation of larval fish siblings during dispersal along an open coast [Ecology]

2016-12-06T09:51:45-08:00

Pelagic dispersal of most benthic marine organisms is a fundamental driver of population distribution and persistence and is thought to lead to highly mixed populations. However, the mechanisms driving dispersal pathways of larvae along open coastlines are largely unknown. To examine the degree to which early stages can remain spatially...



US daily temperature records past, present, and future [Environmental Sciences]

2016-12-06T09:51:44-08:00

Observed temperature extremes over the continental United States can be represented by the ratio of daily record high temperatures to daily record low minimum temperatures, and this ratio has increased to a value of about 2 to 1, averaged over the first decade of the 21st century, albeit with large...



Large numbers of vertebrates began rapid population decline in the late 19th century [Evolution]

2016-12-06T09:51:45-08:00

Accelerated losses of biodiversity are a hallmark of the current era. Large declines of population size have been widely observed and currently 22,176 species are threatened by extinction. The time at which a threatened species began rapid population decline (RPD) and the rate of RPD provide important clues about the...



On the (un)predictability of a large intragenic fitness landscape [Evolution]

2016-12-06T09:51:45-08:00

The study of fitness landscapes, which aims at mapping genotypes to fitness, is receiving ever-increasing attention. Novel experimental approaches combined with next-generation sequencing (NGS) methods enable accurate and extensive studies of the fitness effects of mutations, allowing us to test theoretical predictions and improve our understanding of the shape of...



Transcriptomics and neuroanatomy of the clonal raider ant implicate an expanded clade of odorant receptors in chemical communication [Evolution]

2016-12-06T09:51:45-08:00

A major aim of sociogenomic research is to uncover common principles in the molecular evolution of sociality. This endeavor has been hampered by the small number of specific genes currently known to function in social behavior. Here we provide several lines of evidence suggesting that ants have evolved a large...



The innate immune receptor Dectin-2 mediates the phagocytosis of cancer cells by Kupffer cells for the suppression of liver metastasis [Immunology and Inflammation]

2016-12-06T09:51:45-08:00

Tumor metastasis is the cause of most cancer deaths. Although metastases can form in multiple end organs, the liver is recognized as a highly permissive organ. Nevertheless, there is evidence for immune cell-mediated mechanisms that function to suppress liver metastasis by certain tumors, although the underlying mechanisms for the suppression...



Singular role for T-BET+CXCR3+ regulatory T cells in protection from autoimmune diabetes [Immunology and Inflammation]

2016-12-06T09:51:45-08:00

Foxp3+ regulatory T (Treg) cells are crucial for restraining inflammation in a variety of autoimmune diseases, including type 1 diabetes (T1D). However, the transcriptional and functional phenotypes of Treg cells within the pancreatic lesion remain poorly understood. Here we characterized pancreas-infiltrating Treg cells in the NOD mouse model of T1D...



Role of the receptor Mas in macrophage-mediated inflammation in vivo [Immunology and Inflammation]

2016-12-06T09:51:45-08:00

Recently, an alternative renin–angiotensin system pathway has been described, which involves binding of angiotensin-(1–7) to its receptor Mas. The Mas axis may counterbalance angiotensin-II–mediated proinflammatory effects, likely by affecting macrophage function. Here we investigate the role of Mas in murine models of autoimmune neuroinflammation and atherosclerosis, which both involve macrophage-driven...



Exon skipping of FcϵRI{beta} eliminates expression of the high-affinity IgE receptor in mast cells with therapeutic potential for allergy [Immunology and Inflammation]

2016-12-06T09:51:45-08:00

Allergic diseases are driven by activation of mast cells and release of mediators in response to IgE-directed antigens. However, there are no drugs currently available that can specifically down-regulate mast cell function in vivo when chronically administered. Here, we describe an innovative approach for targeting mast cells in vitro and...



Epstein-Barr virus super-enhancer eRNAs are essential for MYC oncogene expression and lymphoblast proliferation [Microbiology]

2016-12-06T09:51:45-08:00

Epstein–Barr virus (EBV) super-enhancers (ESEs) are essential for lymphoblastoid cell (LCL) growth and survival. Reanalyses of LCL global run-on sequencing (Gro-seq) data found abundant enhancer RNAs (eRNAs) being transcribed at ESEs. Inactivation of ESE components, EBV nuclear antigen 2 (EBNA2) and bromodomain-containing protein 4 (BRD4), significantly decreased eRNAs at ESEs...



Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe [Microbiology]

2016-12-06T09:51:45-08:00

A major roadblock to understanding how microbes in the gastrointestinal tract colonize and influence the physiology of their hosts is our inability to genetically manipulate new bacterial species and experimentally assess the function of their genes. We describe the application of population-based genomic sequencing after chemical mutagenesis to map bacterial...



Inner Workings: Uncovering the neuron’s internal skeleton [Neuroscience]

2016-12-06T09:51:44-08:00

Stain a neuron for actin and you see a colored tangle of threads. As an essential component of the neuron’s skeleton, actin shows up as filaments in the main cell body and a crowded knot at the tips of axons: the long, skinny projections that transmit electrical impulses to other...



Rapid recovery from the effects of early monocular deprivation is enabled by temporary inactivation of the retinas [Neuroscience]

2016-12-06T09:51:45-08:00

A half-century of research on the consequences of monocular deprivation (MD) in animals has revealed a great deal about the pathophysiology of amblyopia. MD initiates synaptic changes in the visual cortex that reduce acuity and binocular vision by causing neurons to lose responsiveness to the deprived eye. However, much less...



Direct bulk-sensitive probe of 5f symmetry in URu2Si2 [Physics]

2016-12-06T09:51:44-08:00

The second-order phase transition into a hidden order phase in URu2Si2 goes along with an order parameter that is still a mystery, despite 30 years of research. However, it is understood that the symmetry of the order parameter must be related to the symmetry of the low-lying local electronic f-states....



Optical magnetic detection of single-neuron action potentials using quantum defects in diamond [Physics]

2016-12-06T09:51:45-08:00

Magnetic fields from neuronal action potentials (APs) pass largely unperturbed through biological tissue, allowing magnetic measurements of AP dynamics to be performed extracellularly or even outside intact organisms. To date, however, magnetic techniques for sensing neuronal activity have either operated at the macroscale with coarse spatial and/or temporal resolution—e.g., magnetic...



Construction of a male sterility system for hybrid rice breeding and seed production using a nuclear male sterility gene [Plant Biology]

2016-12-06T09:51:45-08:00

The breeding and large-scale adoption of hybrid seeds is an important achievement in agriculture. Rice hybrid seed production uses cytoplasmic male sterile lines or photoperiod/thermo-sensitive genic male sterile lines (PTGMS) as female parent. Cytoplasmic male sterile lines are propagated via cross-pollination by corresponding maintainer lines, whereas PTGMS lines are propagated...



The earliest maize from San Marcos Tehuacan is a partial domesticate with genomic evidence of inbreeding [Plant Biology]

2016-12-06T09:51:45-08:00

Pioneering archaeological expeditions lead by Richard MacNeish in the 1960s identified the valley of Tehuacán as an important center of early Mesoamerican agriculture, providing by far the widest collection of ancient crop remains, including maize. In 2012, a new exploration of San Marcos cave (Tehuacán, Mexico) yielded nonmanipulated maize specimens...



Cytoskeleton dynamics control the first asymmetric cell division in Arabidopsis zygote [Plant Biology]

2016-12-06T09:51:45-08:00

The asymmetric cell division of the zygote is the initial and crucial developmental step in most multicellular organisms. In flowering plants, whether zygote polarity is inherited from the preexisting organization in the egg cell or reestablished after fertilization has remained elusive. How dynamically the intracellular organization is generated during zygote...



Preferential interactions promote blind cooperation and informed defection [Psychological and Cognitive Sciences]

2016-12-06T09:51:44-08:00

It is common sense that costs and benefits should be carefully weighed before deciding on a course of action. However, we often disapprove of people who do so, even when their actual decision benefits us. For example, we prefer people who directly agree to do us a favor over those...



Mechanical bounds to transcriptional noise [Systems Biology]

2016-12-06T09:51:44-08:00

Over the past several decades it has been increasingly recognized that stochastic processes play a central role in transcription. Although many stochastic effects have been explained, the source of transcriptional bursting (one of the most well-known sources of stochasticity) has continued to evade understanding. Recent results have pointed to mechanical...



Correction for Adel et al., Evolutionary alteration of ALOX15 specificity optimizes the biosynthesis of antiinflammatory and proresolving lipoxins [Correction]

2016-12-06T09:51:45-08:00

BIOCHEMISTRY Correction for “Evolutionary alteration of ALOX15 specificity optimizes the biosynthesis of antiinflammatory and proresolving lipoxins,” by Susan Adel, Felix Karst, Àngels González-Lafont, Mária Pekárová, Patricia Saura, Laura Masgrau, José M. Lluch, Sabine Stehling, Thomas Horn, Hartmut Kuhn, and Dagmar Heydeck, which appeared in issue 30, July 26, 2016, of...



Correction for Zhang et al., Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation [Correction]

2016-12-06T09:51:45-08:00

PLANT BIOLOGY Correction for “Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation,” by Bo Zhang, Denise M. Tieman, Chen Jiao, Yimin Xu, Kunsong Chen, Zhangjun Fe, James J. Giovannoni, and Harry J. Klee, which appeared in issue 44, November 1, 2016, of...



Correction to Supporting Information for Adel et al., Evolutionary alteration of ALOX15 specificity optimizes the biosynthesis of antiinflammatory and proresolving lipoxins [SI Correction]

2016-12-06T09:51:45-08:00

BIOCHEMISTRY Correction to Supporting Information for “Evolutionary alteration of ALOX15 specificity optimizes the biosynthesis of antiinflammatory and proresolving lipoxins,” by Susan Adel, Felix Karst, Àngels González-Lafont, Mária Pekárová, Patricia Saura, Laura Masgrau, José M. Lluch, Sabine Stehling, Thomas Horn, Hartmut Kuhn, and Dagmar Heydeck, which appeared in issue 30, July...



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...