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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]

2018-02-20T11:27:52-08:00

Ocean acidification and coral skeletal density Porites corals are dominant reef builders on most Indo-Pacific Reefs. Coral reefs are among the most diverse ecosystems on Earth, and ocean acidification is considered a major threat to their future survival. However, field and laboratory studies examining the effect of acidification on corals...



Causing confusion in the debate about the transition toward a more plant-based diet [Biological Sciences]

2018-02-20T11:27:52-08:00

White and Hall (1) recently assessed the contribution of animal-based agriculture to greenhouse gas emissions (GHGE) and nutrient provision of the United States society. Unfortunately, their study provides a misleading message. Reducing animal-based food is needed to meet climate goals and future global food demands (2). Hence, it is important...



Without animals, US farmers would reduce feed crop production [Biological Sciences]

2018-02-20T11:27:52-08:00

In “Nutritional and greenhouse gas impacts of removing animals from US agriculture,” White and Hall (1) imagine a future without animal agriculture but fail to address perhaps the single most influential aspect of livestock on US agriculture: land use for feed crops. The authors unrealistically assume that without livestock, Americans...



Feedlot diet for Americans that results from a misspecified optimization algorithm [Biological Sciences]

2018-02-20T11:27:52-08:00

White and Hall (1) suggest that removing animals from US agriculture would create a food supply incapable of supporting the United States population’s nutritional requirements and increase nutritional deficiencies compared with the current food system. However, their analysis suffers from an uncritical use of nutritional values and optimization algorithms, and...



Reply to Van Meerbeek and Svenning, Emery, and Springmann et al.: Clarifying assumptions and objectives in evaluating effects of food system shifts on human diets [Biological Sciences]

2018-02-20T11:27:53-08:00

Letters by Van Meerbeek and Svenning (1), Emery (2), and Springmann et al. (3), regarding the study by White and Hall (4), express concerns regarding assumptions of land allocation and proposed dietary characteristics. The authors (1–3) also present individual, diverse concerns. We attempt to address each concern below. Land Allocation...



Effective games and the confusion over spatial structure [Biological Sciences]

2018-02-20T11:27:53-08:00

A typical study of space in evolutionary game theory starts with a specification of how local interactions impact fitness, and then simulates that interaction over a model of space to show a surprising difference in dynamics between the spatial model and its nonspatial counterpart. Usually, this difference is revealed at...



QnAs with Martin Head-Gordon [QnAs]

2018-02-20T11:27:52-08:00

Introductory chemistry courses characterize chemical bonds as one of several types, such as ionic and covalent bonds. Bonds differ in their strength and mechanism of joining atoms together. However, bonds form through multiple mechanisms, each contributing to the bond’s strength and character. Martin Head-Gordon is a theoretical chemist at the...



Profile of Natasha V. Raikhel [Profile]

2018-02-20T11:27:52-08:00

A plane crash galvanized Natasha Raikhel and her family into leaving the Soviet Union for the United States. At the time, Raikhel was studying invertebrates while living in Leningrad. Raikhel’s husband and son had joined her on a field expedition to gather samples in Baku, Azerbaijan, and on the return...



Profile of Nancy Ip [Profile]

2018-02-20T11:27:52-08:00

Elected in 2015 as a foreign associate of the National Academy of Sciences, neuroscientist Nancy Ip has made seminal discoveries concerning neurotrophic factors and the molecular mechanisms underlying brain development and synaptic plasticity, as well as their dysregulation in neurodegenerative disorders. Bridging traditional Chinese and modern medicine, Ip, the Morningside...



Throwing back the big ones saves a fishery from hot water [Sustainability Science]

2018-02-20T11:27:52-08:00

In Lewis Carroll’s Alice in Wonderland, the Mock Turtle and the Gryphon teach Alice a dance in which everyone partners with a lobster and then throws it “as far out to sea as you can” (1). While the “porpoise” (as the Mock Turtle pronounces “purpose”) of throwing lobsters never becomes...



Biodiversity may wax or wane depending on metrics or taxa [Ecology]

2018-02-20T11:27:52-08:00

Biodiversity changes have proven surprisingly complex to estimate and understand. While there are negative trends at a global scale such as the substantial losses of vertebrate species (1), changes at local scales may show large variation, with no clear overall trend (2, 3). Because assessing and improving the status of...



Cooperative breeding and the evolutionary coexistence of helper and nonhelper strategies [Evolution]

2018-02-20T11:27:52-08:00

In some species individuals altruistically delay their chance of reproducing to help others raise their young. This is commonly referred to as cooperative breeding and is widespread across the animal kingdom, occurring in insects, crustaceans, fish, birds, and mammals, including humans (1, 2). This behavior has puzzled biologists for decades...



Stepping into the genetics of biological motion processing [Psychological and Cognitive Sciences]

2018-02-20T11:27:52-08:00

Person perception (1) and action understanding (2) are complex, interrelated skills at the very heart of our social world. The ability to process biological motion (BM)—to extract information by observing the movement of others (3)—provides one crucial link between these skills, and research into how we perceive moving bodies has...



Classification and interaction in random forests [Systems Biology]

2018-02-20T11:27:52-08:00

Suppose you are a physician with a patient whose complaint could arise from multiple diseases. To attain a specific diagnosis, you might ask yourself a series of yes/no questions depending on observed features describing the patient, such as clinical test results and reported symptoms. As some questions rule out certain...



15N detection harnesses the slow relaxation property of nitrogen: Delivering enhanced resolution for intrinsically disordered proteins [Biophysics and Computational Biology]

2018-02-20T11:27:53-08:00

Studies over the past decade have highlighted the functional significance of intrinsically disordered proteins (IDPs). Due to conformational heterogeneity and inherent dynamics, structural studies of IDPs have relied mostly on NMR spectroscopy, despite IDPs having characteristics that make them challenging to study using traditional 1H-detected biomolecular NMR techniques. Here, we...



Maturity of nearby faults influences seismic hazard from hydraulic fracturing [Earth, Atmospheric, and Planetary Sciences]

2018-02-20T11:27:53-08:00

Understanding the causes of human-induced earthquakes is paramount to reducing societal risk. We investigated five cases of seismicity associated with hydraulic fracturing (HF) in Ohio since 2013 that, because of their isolation from other injection activities, provide an ideal setting for studying the relations between high-pressure injection and earthquakes. Our...



Assessment of the Legionnaires’ disease outbreak in Flint, Michigan [Environmental Sciences]

2018-02-20T11:27:53-08:00

The 2014–2015 Legionnaires’ disease (LD) outbreak in Genesee County, MI, and the outbreak resolution in 2016 coincided with changes in the source of drinking water to Flint’s municipal water system. Following the switch in water supply from Detroit to Flint River water, the odds of a Flint resident presenting with...



A big data analysis of the relationship between future thinking and decision-making [Psychological and Cognitive Sciences]

2018-02-20T11:27:53-08:00

We use big data methods to investigate how decision-making might depend on future sightedness (that is, on how far into the future people’s thoughts about the future extend). In study 1, we establish a link between future thinking and decision-making at the population level in showing that US states with...



Uterine influences on conceptus development in fertility-classified animals [Agricultural Sciences]

2018-02-20T11:27:53-08:00

A major unresolved issue is how the uterus influences infertility and subfertility in cattle. Serial embryo transfer was previously used to classify heifers as high-fertile (HF), subfertile (SF), or infertile (IF). To assess pregnancy loss, two in vivo-produced embryos were transferred into HF, SF, and IF heifers on day 7,...



PARP-1-dependent recruitment of cold-inducible RNA-binding protein promotes double-strand break repair and genome stability [Biochemistry]

2018-02-20T11:27:53-08:00

Maintenance of genome integrity is critical for both faithful propagation of genetic information and prevention of mutagenesis induced by various DNA damage events. Here we report cold-inducible RNA-binding protein (CIRBP) as a newly identified key regulator in DNA double-strand break (DSB) repair. On DNA damage, CIRBP temporarily accumulates at the...



SLC39A14 deficiency alters manganese homeostasis and excretion resulting in brain manganese accumulation and motor deficits in mice [Biochemistry]

2018-02-20T11:27:53-08:00

Solute carrier family 39, member 14 (SLC39A14) is a transmembrane transporter that can mediate the cellular uptake of zinc, iron, and manganese (Mn). Studies of Slc39a14 knockout (Slc39a14−/−) mice have documented that SLC39A14 is required for systemic growth, hepatic zinc uptake during inflammation, and iron loading of the liver in...



A posttranslational modification of the mitotic kinesin Eg5 that enhances its mechanochemical coupling and alters its mitotic function [Biophysics and Computational Biology]

2018-02-20T11:27:53-08:00

Numerous posttranslational modifications have been described in kinesins, but their consequences on motor mechanics are largely unknown. We investigated one of these—acetylation of lysine 146 in Eg5—by creating an acetylation mimetic lysine to glutamine substitution (K146Q). Lysine 146 is located in the α2 helix of the motor domain, where it...



Single-channel recordings of RyR1 at microsecond resolution in CMOS-suspended membranes [Biophysics and Computational Biology]

2018-02-20T11:27:53-08:00

Single-channel recordings are widely used to explore functional properties of ion channels. Typically, such recordings are performed at bandwidths of less than 10 kHz because of signal-to-noise considerations, limiting the temporal resolution available for studying fast gating dynamics to greater than 100 µs. Here we present experimental methods that directly...



Lipid bilayer composition modulates the unfolding free energy of a knotted {alpha}-helical membrane protein [Biophysics and Computational Biology]

2018-02-20T11:27:53-08:00

α-Helical membrane proteins have eluded investigation of their thermodynamic stability in lipid bilayers. Reversible denaturation curves have enabled some headway in determining unfolding free energies. However, these parameters have been limited to detergent micelles or lipid bicelles, which do not possess the same mechanical properties as lipid bilayers that comprise...



Molecular model of the mitochondrial genome segregation machinery in Trypanosoma brucei [Cell Biology]

2018-02-20T11:27:53-08:00

In almost all eukaryotes, mitochondria maintain their own genome. Despite the discovery more than 50 y ago, still very little is known about how the genome is correctly segregated during cell division. The protozoan parasite Trypanosoma brucei contains a single mitochondrion with a singular genome, the kinetoplast DNA (kDNA). Electron...



Bacteriocyte cell death in the pea aphid/Buchnera symbiotic system [Evolution]

2018-02-20T11:27:53-08:00

Symbiotic associations play a pivotal role in multicellular life by facilitating acquisition of new traits and expanding the ecological capabilities of organisms. In insects that are obligatorily dependent on intracellular bacterial symbionts, novel host cells (bacteriocytes) or organs (bacteriomes) have evolved for harboring beneficial microbial partners. The processes regulating the...



General amino acid control in fission yeast is regulated by a nonconserved transcription factor, with functions analogous to Gcn4/Atf4 [Genetics]

2018-02-20T11:27:53-08:00

Eukaryotes respond to amino acid starvation by enhancing the translation of mRNAs encoding b-ZIP family transcription factors (GCN4 in Saccharomyces cerevisiae and ATF4 in mammals), which launch transcriptional programs to counter this stress. This pathway involves phosphorylation of the eIF2 translation factor by Gcn2-protein kinases and is regulated by upstream...



Global changes of H3K27me3 domains and Polycomb group protein distribution in the absence of recruiters Spps or Pho [Genetics]

2018-02-20T11:27:53-08:00

Polycomb group (PcG) proteins maintain the silenced state of key developmental genes in animals, but how these proteins are recruited to specific regions of the genome is still poorly understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) that include combinations of sites for sequence specific DNA...



16p11.2 transcription factor MAZ is a dosage-sensitive regulator of genitourinary development [Genetics]

2018-02-20T11:27:53-08:00

Genitourinary (GU) birth defects are among the most common yet least studied congenital malformations. Congenital anomalies of the kidney and urinary tract (CAKUTs) have high morbidity and mortality rates and account for ∼30% of structural birth defects. Copy number variation (CNV) mapping revealed that 16p11.2 is a hotspot for GU...



Damaging de novo mutations diminish motor skills in children on the autism spectrum [Genetics]

2018-02-20T11:27:53-08:00

In individuals with autism spectrum disorder (ASD), de novo mutations have previously been shown to be significantly correlated with lower IQ but not with the core characteristics of ASD: deficits in social communication and interaction and restricted interests and repetitive patterns of behavior. We extend these findings by demonstrating in...



5-Azacytidine prevents relapse and produces long-term complete remissions in leukemia xenografts treated with Moxetumomab pasudotox [Medical Sciences]

2018-02-20T11:27:53-08:00

Moxetumomab pasudotox (Moxe) is a chimeric protein composed of an anti-CD22 Fv fused to a portion of Pseudomonas exotoxin A and kills CD22-expressing leukemia cells. It is very active in hairy-cell leukemia, but many children with relapsed/refractory acute lymphoblastic leukemia (ALL) either respond transiently or are initially resistant. Resistance to...



NAD+ supplementation normalizes key Alzheimer’s features and DNA damage responses in a new AD mouse model with introduced DNA repair deficiency [Neuroscience]

2018-02-20T11:27:53-08:00

Emerging findings suggest that compromised cellular bioenergetics and DNA repair contribute to the pathogenesis of Alzheimer’s disease (AD), but their role in disease-defining pathology is unclear. We developed a DNA repair-deficient 3xTgAD/Polβ+/− mouse that exacerbates major features of human AD including phosphorylated Tau (pTau) pathologies, synaptic dysfunction, neuronal death, and...



Septal cholinergic neurons gate hippocampal output to entorhinal cortex via oriens lacunosum moleculare interneurons [Neuroscience]

2018-02-20T11:27:53-08:00

Neuromodulation of neural networks, whereby a selected circuit is regulated by a particular modulator, plays a critical role in learning and memory. Among neuromodulators, acetylcholine (ACh) plays a critical role in hippocampus-dependent memory and has been shown to modulate neuronal circuits in the hippocampus. However, it has remained unknown how...



Normal aging induces A1-like astrocyte reactivity [Neuroscience]

2018-02-20T11:27:53-08:00

The decline of cognitive function occurs with aging, but the mechanisms responsible are unknown. Astrocytes instruct the formation, maturation, and elimination of synapses, and impairment of these functions has been implicated in many diseases. These findings raise the question of whether astrocyte dysfunction could contribute to cognitive decline in aging....



Regulation of Arabidopsis brassinosteroid receptor BRI1 endocytosis and degradation by plant U-box PUB12/PUB13-mediated ubiquitination [Plant Biology]

2018-02-20T11:27:53-08:00

Plants largely rely on plasma membrane (PM)-resident receptor-like kinases (RLKs) to sense extracellular and intracellular stimuli and coordinate cell differentiation, growth, and immunity. Several RLKs have been shown to undergo internalization through the endocytic pathway with a poorly understood mechanism. Here, we show that endocytosis and protein abundance of the...



Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver [Systems Biology]

2018-02-20T11:27:53-08:00

The mammalian circadian clock coordinates physiology with environmental cycles through the regulation of daily oscillations of gene expression. Thousands of transcripts exhibit rhythmic accumulations across mouse tissues, as determined by the balance of their synthesis and degradation. While diurnally rhythmic transcription regulation is well studied and often thought to be...



Endocytosis as a stabilizing mechanism for tissue homeostasis [Systems Biology]

2018-02-20T11:27:53-08:00

Cells in tissues communicate by secreted growth factors (GF) and other signals. An important function of cell circuits is tissue homeostasis: maintaining proper balance between the amounts of different cell types. Homeostasis requires negative feedback on the GFs, to avoid a runaway situation in which cells stimulate each other and...



Science and Culture: Quantum games aim to demystify heady science [Applied Physical Sciences]

2018-02-20T11:27:52-08:00

In a video game called Quantum Moves, the players’ goal is straightforward: Move an atom from one place to another as quickly and efficiently as possible while a timer counts down the seconds. Atoms in the game aren’t represented as mini solar systems with electron “planets” moving around them, like...



Diamond anvil cell behavior up to 4 Mbar [Applied Physical Sciences]

2018-02-20T11:27:52-08:00

The diamond anvil cell (DAC) is considered one of the dominant devices to generate ultrahigh static pressure. The development of the DAC technique has enabled researchers to explore rich high-pressure science in the multimegabar pressure range. Here, we investigated the behavior of the DAC up to 400 GPa, which is...



Role of ubiquitylation of components of mitotic checkpoint complex in their dissociation from anaphase-promoting complex/cyclosome [Biochemistry]

2018-02-20T11:27:52-08:00

The mitotic checkpoint system ensures the fidelity of chromosome segregation in mitosis by preventing premature initiation of anaphase until correct bipolar attachment of chromosomes to the mitotic spindle is reached. It promotes the assembly of a mitotic checkpoint complex (MCC), composed of BubR1, Bub3, Cdc20, and Mad2, which inhibits the...



Mechanism of ubiquitin transfer promoted by TRAF6 [Biochemistry]

2018-02-20T11:27:52-08:00

Tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) plays a vital role in immune signal transduction pathways by acting as a ubiquitin ligase (E3) for Lys63-linked polyubiquitin chain synthesis. However, the detailed mechanism by which the TRAF6 RING dimer promotes ubiquitin transfer was unknown. Through structural modeling and biochemical analysis,...



Poldip2 is an oxygen-sensitive protein that controls PDH and {alpha}KGDH lipoylation and activation to support metabolic adaptation in hypoxia and cancer [Biochemistry]

2018-02-20T11:27:52-08:00

Although the addition of the prosthetic group lipoate is essential to the activity of critical mitochondrial catabolic enzymes, its regulation is unknown. Here, we show that lipoylation of the pyruvate dehydrogenase and α-ketoglutarate dehydrogenase (αKDH) complexes is a dynamically regulated process that is inhibited under hypoxia and in cancer cells...



Elucidating the structural basis for differing enzyme inhibitor potency by cryo-EM [Biochemistry]

2018-02-20T11:27:52-08:00

Histidine biosynthesis is an essential process in plants and microorganisms, making it an attractive target for the development of herbicides and antibacterial agents. Imidazoleglycerol-phosphate dehydratase (IGPD), a key enzyme within this pathway, has been biochemically characterized in both Saccharomyces cerevisiae (Sc_IGPD) and Arabidopsis thaliana (At_IGPD). The plant enzyme, having been...



Changes in the flagellar bundling time account for variations in swimming behavior of flagellated bacteria in viscous media [Biophysics and Computational Biology]

2018-02-20T11:27:52-08:00

Although the motility of the flagellated bacteria, Escherichia coli, has been widely studied, the effect of viscosity on swimming speed remains controversial. The swimming mode of wild-type E. coli is often idealized as a run-and-tumble sequence in which periods of swimming at a constant speed are randomly interrupted by a...



Naked mole rats can undergo developmental, oncogene-induced and DNA damage-induced cellular senescence [Cell Biology]

2018-02-20T11:27:52-08:00

Cellular senescence is an important anticancer mechanism that restricts proliferation of damaged or premalignant cells. Cellular senescence also plays an important role in tissue remodeling during development. However, there is a trade-off associated with cellular senescence as senescent cells contribute to aging pathologies. The naked mole rat (NMR) (Heterocephalus glaber)...



Fast and accurate quantum Monte Carlo for molecular crystals [Chemistry]

2018-02-20T11:27:52-08:00

Computer simulation plays a central role in modern-day materials science. The utility of a given computational approach depends largely on the balance it provides between accuracy and computational cost. Molecular crystals are a class of materials of great technological importance which are challenging for even the most sophisticated ab initio...



Control of chemoselectivity in asymmetric tandem reactions: Direct synthesis of chiral amines bearing nonadjacent stereocenters [Chemistry]

2018-02-20T11:27:52-08:00

This paper describes the mechanistic insight-guided development of a catalyst system, employing a phenolic proton donor catalyst in addition to a cinchonium-derived phase-transfer catalyst, to control the chemoselectivity of two distinct intermediates, thereby enabling the desired asymmetric tandem conjugate addition–protonation pathway to dominate over a number of side-reaction pathways to...



Capicua controls Toll/IL-1 signaling targets independently of RTK regulation [Developmental Biology]

2018-02-20T11:27:52-08:00

The HMG-box protein Capicua (Cic) is a conserved transcriptional repressor that functions downstream of receptor tyrosine kinase (RTK) signaling pathways in a relatively simple switch: In the absence of signaling, Cic represses RTK-responsive genes by binding to nearly invariant sites in DNA, whereas activation of RTK signaling down-regulates Cic activity,...



Germ-layer commitment and axis formation in sea anemone embryonic cell aggregates [Developmental Biology]

2018-02-20T11:27:52-08:00

Robust morphogenetic events are pivotal for animal embryogenesis. However, comparison of the modes of development of different members of a phylum suggests that the spectrum of developmental trajectories accessible for a species might be far broader than can be concluded from the observation of normal development. Here, by using a...



Double abdomen in a short-germ insect: Zygotic control of axis formation revealed in the beetle Tribolium castaneum [Developmental Biology]

2018-02-20T11:27:52-08:00

The distinction of anterior versus posterior is a crucial first step in animal embryogenesis. In the fly Drosophila, this axis is established by morphogenetic gradients contributed by the mother that regulate zygotic target genes. This principle has been considered to hold true for insects in general but is fundamentally different...



Identification and paleoclimatic significance of magnetite nanoparticles in soils [Earth, Atmospheric, and Planetary Sciences]

2018-02-20T11:27:52-08:00

In the world-famous sediments of the Chinese Loess Plateau, fossil soils alternate with windblown dust layers to record monsoonal variations over the last ∼3 My. The less-weathered, weakly magnetic dust layers reflect drier, colder glaciations. The fossil soils (paleosols) contain variable concentrations of nanoscale, strongly magnetic iron oxides, formed in...



Pressure-induced structural change in MgSiO3 glass at pressures near the Earth’s core-mantle boundary [Earth, Atmospheric, and Planetary Sciences]

2018-02-20T11:27:52-08:00

Knowledge of the structure and properties of silicate magma under extreme pressure plays an important role in understanding the nature and evolution of Earth’s deep interior. Here we report the structure of MgSiO3 glass, considered an analog of silicate melts, up to 111 GPa. The first (r1) and second (r2)...



Ocean acidification affects coral growth by reducing skeletal density [Ecology]

2018-02-20T11:27:52-08:00

Ocean acidification (OA) is considered an important threat to coral reef ecosystems, because it reduces the availability of carbonate ions that reef-building corals need to produce their skeletons. However, while theory predicts that coral calcification rates decline as carbonate ion concentrations decrease, this prediction is not consistently borne out in...



Phylogenetic classification of the world’s tropical forests [Ecology]

2018-02-20T11:27:52-08:00

Knowledge about the biogeographic affinities of the world’s tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global...



Divergent biodiversity change within ecosystems [Ecology]

2018-02-20T11:27:52-08:00

The Earth’s ecosystems are under unprecedented pressure, yet the nature of contemporary biodiversity change is not well understood. Growing evidence that community size is regulated highlights the need for improved understanding of community dynamics. As stability in community size could be underpinned by marked temporal turnover, a key question is...



Range dynamics of mountain plants decrease with elevation [Ecology]

2018-02-20T11:27:52-08:00

Many studies report that mountain plant species are shifting upward in elevation. However, the majority of these reports focus on shifts of upper limits. Here, we expand the focus and simultaneously analyze changes of both range limits, optima, and abundances of 183 mountain plant species. We therefore resurveyed 1,576 vegetation...



Field study of charitable giving reveals that reciprocity decays over time [Economic Sciences]

2018-02-20T11:27:52-08:00

We examine how reciprocity changes over time by studying a large quasiexperiment in the field. Specifically, we analyze administrative data from a university hospital system. The data include information about over 18,000 donation requests made by the hospital system via mail to a set of its former patients in the...



Geometrical control of dissipation during the spreading of liquids on soft solids [Engineering]

2018-02-20T11:27:52-08:00

Gel layers bound to a rigid substrate are used in cell culture to control differentiation and migration and to lower the friction and tailor the wetting of solids. Their thickness, often considered a negligible parameter, affects cell mechanosensing or the shape of sessile droplets. Here, we show that the adjustment...



Hamilton's inclusive fitness maintains heritable altruism polymorphism through rb = c [Evolution]

2018-02-20T11:27:52-08:00

How can altruism evolve or be maintained in a selfish world? Hamilton’s rule shows that the former process will occur when rb > c—the benefits to the recipients of an altruistic act b, weighted by the relatedness between the social partners r, exceed the costs to the altruists c—drives altruistic...



Divergent and parallel routes of biochemical adaptation in high-altitude passerine birds from the Qinghai-Tibet Plateau [Evolution]

2018-02-20T11:27:52-08:00

When different species experience similar selection pressures, the probability of evolving similar adaptive solutions may be influenced by legacies of evolutionary history, such as lineage-specific changes in genetic background. Here we test for adaptive convergence in hemoglobin (Hb) function among high-altitude passerine birds that are native to the Qinghai-Tibet Plateau,...



Detection of aneuploidy in patients with cancer through amplification of long interspersed nucleotide elements (LINEs) [Genetics]

2018-02-20T11:27:52-08:00

Aneuploidy is a feature of most cancer cells, and a myriad of approaches have been developed to detect it in clinical samples. We previously described primers that could be used to amplify ∼38,000 unique long interspersed nucleotide elements (LINEs) from throughout the genome. Here we have developed an approach to...



T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable [Immunology and Inflammation]

2018-02-20T11:27:52-08:00

HIV controllers (HCs) are individuals who can naturally control HIV infection, partially due to potent HIV-specific CD8+ T cell responses. Here, we examined the hypothesis that superior function of CD8+ T cells from HCs is encoded by their T cell receptors (TCRs). We compared the functional properties of immunodominant HIV-specific...



Thymic involution and rising disease incidence with age [Immunology and Inflammation]

2018-02-20T11:27:52-08:00

For many cancer types, incidence rises rapidly with age as an apparent power law, supporting the idea that cancer is caused by a gradual accumulation of genetic mutations. Similarly, the incidence of many infectious diseases strongly increases with age. Here, combining data from immunology and epidemiology, we show that many...



Role of a selecting ligand in shaping the murine {gamma}{delta}-TCR repertoire [Immunology and Inflammation]

2018-02-20T11:27:52-08:00

Unlike αβ-T lineage cells, where the role of ligand in intrathymic selection is well established, the role of ligand in the development of γδ-T cells remains controversial. Here we provide evidence for the role of a bona fide selecting ligand in shaping the γδ-T cell-receptor (TCR) repertoire. Reactivity of the...



Accelerated wound healing in mice by on-site production and delivery of CXCL12 by transformed lactic acid bacteria [Immunology and Inflammation]

2018-02-20T11:27:52-08:00

Impaired wound closure is a growing medical problem associated with metabolic diseases and aging. Immune cells play important roles in wound healing by following instructions from the microenvironment. Here, we developed a technology to bioengineer the wound microenvironment and enhance healing abilities of the immune cells. This resulted in strongly...



Adaptive antibody diversification through N-linked glycosylation of the immunoglobulin variable region [Immunology and Inflammation]

2018-02-20T11:27:52-08:00

A hallmark of B-cell immunity is the generation of a diverse repertoire of antibodies from a limited set of germline V(D)J genes. This repertoire is usually defined in terms of amino acid composition. However, variable domains may also acquire N-linked glycans, a process conditional on the introduction of consensus amino...



Cysteinyl leukotriene receptor 1 antagonism prevents experimental abdominal aortic aneurysm [Medical Sciences]

2018-02-20T11:27:52-08:00

Cysteinyl-leukotrienes (cys-LTs) are 5-lipoxygenase-derived lipid mediators involved in the pathogenesis and progression of inflammatory disorders, in particular asthma. We have previously found evidence linking these mediators to increased levels of proteolytic enzymes in tissue specimens of human abdominal aortic aneurysm (AAA). Here we show that antagonism of the CysLT1 receptor...



Polo-like kinase 4 inhibition produces polyploidy and apoptotic death of lung cancers [Medical Sciences]

2018-02-20T11:27:52-08:00

Polo-like kinase 4 (PLK4) is a serine/threonine kinase regulating centriole duplication. CFI-400945 is a highly selective PLK4 inhibitor that deregulates centriole duplication, causing mitotic defects and death of aneuploid cancers. Prior work was substantially extended by showing CFI-400945 causes polyploidy, growth inhibition, and apoptotic death of murine and human lung...



Single-bacterial genomics validates rich and varied specialized metabolism of uncultivated Entotheonella sponge symbionts [Microbiology]

2018-02-20T11:27:52-08:00

Marine sponges are prolific sources of unique bioactive natural products. The sponge Theonella swinhoei is represented by several distinct variants with largely nonoverlapping chemistry. For the Japanese chemotype Y harboring diverse complex polyketides and peptides, we previously provided genomic and functional evidence that a single symbiont, the filamentous, multicellular organism...



Identification of genetic risk factors in the Chinese population implicates a role of immune system in Alzheimer’s disease pathogenesis [Neuroscience]

2018-02-20T11:27:52-08:00

Alzheimer’s disease (AD) is a leading cause of mortality among the elderly. We performed a whole-genome sequencing study of AD in the Chinese population. In addition to the variants identified in or around the APOE locus (sentinel variant rs73052335, P = 1.44 × 10−14), two common variants, GCH1 (rs72713460, P...



Three classes of recurrent DNA break clusters in brain progenitors identified by 3D proximity-based break joining assay [Neuroscience]

2018-02-20T11:27:52-08:00

We recently discovered 27 recurrent DNA double-strand break (DSB) clusters (RDCs) in mouse neural stem/progenitor cells (NSPCs). Most RDCs occurred across long, late-replicating RDC genes and were found only after mild inhibition of DNA replication. RDC genes share intriguing characteristics, including encoding surface proteins that organize brain architecture and neuronal...



Maximizing the information learned from finite data selects a simple model [Physics]

2018-02-20T11:27:52-08:00

We use the language of uninformative Bayesian prior choice to study the selection of appropriately simple effective models. We advocate for the prior which maximizes the mutual information between parameters and predictions, learning as much as possible from limited data. When many parameters are poorly constrained by the available data,...



Spatial patterns of tree yield explained by endogenous forces through a correspondence between the Ising model and ecology [Physics]

2018-02-20T11:27:52-08:00

Spatial patterning of periodic dynamics is a dramatic and ubiquitous ecological phenomenon arising in systems ranging from diseases to plants to mammals. The degree to which spatial correlations in cyclic dynamics are the result of endogenous factors related to local dynamics vs. exogenous forcing has been one of the central...



Piezo2 channel regulates RhoA and actin cytoskeleton to promote cell mechanobiological responses [Physiology]

2018-02-20T11:27:52-08:00

Actin polymerization and assembly into stress fibers (SFs) is central to many cellular processes. However, how SFs form in response to the mechanical interaction of cells with their environment is not fully understood. Here we have identified Piezo2 mechanosensitive cationic channel as a transducer of environmental physical cues into mechanobiological...



Ancient duons may underpin spatial patterning of gene expression in C4 leaves [Plant Biology]

2018-02-20T11:27:52-08:00

If the highly efficient C4 photosynthesis pathway could be transferred to crops with the C3 pathway there could be yield gains of up to 50%. It has been proposed that the multiple metabolic and developmental modifications associated with C4 photosynthesis are underpinned by relatively few master regulators that have allowed...



Personal bests as reference points [Psychological and Cognitive Sciences]

2018-02-20T11:27:52-08:00

Personal bests act as reference points. Examining 133 million chess games, we find that players exert effort to set new personal best ratings and quit once they have done so. Although specific and difficult goals have been shown to inspire greater motivation than vague pronouncements to “do your best,” doing...



Heritable aspects of biological motion perception and its covariation with autistic traits [Psychological and Cognitive Sciences]

2018-02-20T11:27:52-08:00

The ability to detect biological motion (BM) and decipher the meaning therein is essential to human survival and social interaction. However, at the individual level, we are not equally equipped with this ability. In particular, impaired BM perception and abnormal neural responses to BM have been observed in autism spectrum...



Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees [Statistics]

2018-02-20T11:27:52-08:00

The Bayesian method is noted to produce spuriously high posterior probabilities for phylogenetic trees in analysis of large datasets, but the precise reasons for this overconfidence are unknown. In general, the performance of Bayesian selection of misspecified models is poorly understood, even though this is of great scientific interest since...



Iterative random forests to discover predictive and stable high-order interactions [Statistics]

2018-02-20T11:27:52-08:00

Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo as components of larger molecular machines. Understanding how these high-order interactions drive gene expression presents a substantial statistical challenge. Building...



Climate vulnerability and resilience in the most valuable North American fishery [Sustainability Science]

2018-02-20T11:27:52-08:00

Managing natural resources in an era of increasing climate impacts requires accounting for the synergistic effects of climate, ecosystem changes, and harvesting on resource productivity. Coincident with recent exceptional warming of the northwest Atlantic Ocean and removal of large predatory fish, the American lobster has become the most valuable fishery...



Correction for Mano et al., Optimal run-and-tumble-based transportation of a Janus particle with active steering [Corrections]

2018-02-20T11:27:53-08:00

PHYSICS Correction for “Optimal run-and-tumble–based transportation of a Janus particle with active steering,” by Tomoyuki Mano, Jean-Baptiste Delfau, Junichiro Iwasawa, and Masaki Sano, which was first published March 14, 2017; 10.1073/pnas.1616013114 (Proc Natl Acad Sci USA 114:E2580–E2589). The authors wish to note the following: “We wish to acknowledge that during...



In This Issue [This Week in PNAS]

2018-02-13T09:51:54-08:00

How centipedes slay giant prey Golden head centipede attacks a mouse. Centipedes are known to subdue large prey by using potent, broad-acting venom. However, venom synthesis requires substantial metabolic investment, and the mechanisms of action of centipede venoms remain unclear. Lei Luo et al. (pp. 1646–1651) report that a golden...



An evolutionary perspective on nutrition and social decision making [Social Sciences]

2018-02-13T09:51:55-08:00

We were intrigued by findings reported by Strang et al. (1) that the balance of carbohydrate to protein in a breakfast preparation influenced subsequent human social decision making. Specifically, compared with a low-carbohydrate/high-protein breakfast, consumption of a high-carbohydrate/low-protein breakfast increased participants’ tendency to punish violations of social norms, assessed as...



Reply to Raison and Raichlen: Why does nutrition impact social decision making? [Social Sciences]

2018-02-13T09:51:55-08:00

In our PNAS article (1), we show how the macronutrient composition of a meal can impact social decision making. Specifically, with a greater protein intake, participants' plasma tyrosine levels were elevated, which resulted in a more tolerant participants’ response toward unfair offers. In other words, with a greater carbohydrate intake,...



Weighing the evidence for a body mass-regulating gravitostat [Biological Sciences]

2018-02-13T09:51:55-08:00

The intriguing paper by Jansson et al. (1) reports the identification of a body mass-regulating homeostat that operates in rodents independently of leptin. In response to implantation of capsules weighing 15% of body weight the authors observed that ∼80% of this load was offset by a reduction in biological body...



Reply to Lund: Where does the gravitostat fit in? [Biological Sciences]

2018-02-13T09:51:55-08:00

We appreciate the thoughtful reflection by Jens Lund (1) on different aspects of our recent article in PNAS (2). Lund is right to point out that results from studies of the effects of hypergravity on body mass and body fat in rodents support the gravitostat hypothesis (2). Hypergravity and increased...



Profile of Steve Granick [Profiles]

2018-02-13T09:51:54-08:00

Steve Granick says a simple underlying principle—the desire for an interesting life with meaningful human relations—has guided his career. During undergraduate study at Princeton University, Granick majored in sociology, mainly because he was interested in literature, humanities, and social sciences. He took just one obligatory science class—introductory physics—and found it...



Resolving single-actin filaments within the contractile ring of fission yeast [Cell Biology]

2018-02-13T09:51:54-08:00

Cell division is an essential step in the life of all cells. Fungi, amoeboid, and mammalian cells divide by the assembly and constriction of a contractile ring of actin, myosin, and other highly conserved proteins (1). The mechanism of cytokinesis is best understood in the fission yeast Schizosaccharomyces pombe. Combined...



Tobacco smoking, E-cigarettes, and nicotine harm [Medical Sciences]

2018-02-13T09:51:54-08:00

Tobacco smoking has caused more than 20 million premature American deaths in the 50 y after the first US Surgeon General Report of Smoking and Health (1). The recognition of this major health hazard has led to efforts to both prevent the initiation of smoking and aid smokers in quitting,...



Conceptualizing degrees of theory of mind [Psychological and Cognitive Sciences]

2018-02-13T09:51:54-08:00

Successful navigation of the social world requires making accurate inferences about the contents of other people’s minds, being able to represent in one’s own mind the thoughts, beliefs, and intentions of another. This “theory of mind” (ToM) ability allows us to explain and predict others’ behavior in terms of their...



Unique parasite aDNA in moa coprolites from New Zealand suggests mass parasite extinctions followed human-induced megafauna extinctions [Ecology]

2018-02-13T09:51:54-08:00

Having split early from Gondwana, Zealandia (now modern New Zealand) escaped discovery until the late 13th century, and therefore remains an important glimpse into a human-free world. Without humans or other land mammals, diverse and peculiar birds evolved in isolation, including several flightless moa species, the giant pouakai eagle (Harpagornis...



Adaptive value of novel MHC immune gene variants [Evolution]

2018-02-13T09:51:54-08:00

The major histocompatibility complex (MHC) is a core component of the vertebrate immune system and has puzzled immunologists, geneticists, and evolutionary biologists for more than half a century. The so-called classical MHC genes (in humans also called HLA) code for cell surface molecules that present antigens to immune effector cells...



On the complex dynamics of savanna landscapes [Applied Mathematics]

2018-02-13T09:51:55-08:00

Simple mathematical models can exhibit rich and complex behaviors. Prototypical examples of these drawn from biology and other disciplines have provided insights that extend well beyond the situations that inspired them. Here, we explore a set of simple, yet realistic, models for savanna–forest vegetation dynamics based on minimal ecological assumptions....



RNA force field with accuracy comparable to state-of-the-art protein force fields [Biophysics and Computational Biology]

2018-02-13T09:51:55-08:00

Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an atomic level of detail the conformational changes undergone by proteins. The application of such simulations to RNA structures, however, has proven more challenging, due in large part to the fact that the physical models (“force fields”) available...



Landau-Ginzburg theory of cortex dynamics: Scale-free avalanches emerge at the edge of synchronization [Biophysics and Computational Biology]

2018-02-13T09:51:55-08:00

Understanding the origin, nature, and functional significance of complex patterns of neural activity, as recorded by diverse electrophysiological and neuroimaging techniques, is a central challenge in neuroscience. Such patterns include collective oscillations emerging out of neural synchronization as well as highly heterogeneous outbursts of activity interspersed by periods of quiescence,...



Superresolution imaging of individual replication forks reveals unexpected prodrug resistance mechanism [Chemistry]

2018-02-13T09:51:55-08:00

Many drugs require extensive metabolism en route to their targets. High-resolution visualization of prodrug metabolism should therefore utilize analogs containing a small modification that does not interfere with its metabolism or mode of action. In addition to serving as mechanistic probes, such analogs provide candidates for theranostics when applied in...



Wireless optoelectronic photometers for monitoring neuronal dynamics in the deep brain [Engineering]

2018-02-13T09:51:55-08:00

Capabilities for recording neural activity in behaving mammals have greatly expanded our understanding of brain function. Some of the most sophisticated approaches use light delivered by an implanted fiber-optic cable to optically excite genetically encoded calcium indicators and to record the resulting changes in fluorescence. Physical constraints induced by the...



Auxetic metamaterials from disordered networks [Engineering]

2018-02-13T09:51:55-08:00

Recent theoretical work suggests that systematic pruning of disordered networks consisting of nodes connected by springs can lead to materials that exhibit a host of unusual mechanical properties. In particular, global properties such as Poisson’s ratio or local responses related to deformation can be precisely altered. Tunable mechanical responses would...



Light-enabled reversible self-assembly and tunable optical properties of stable hairy nanoparticles [Engineering]

2018-02-13T09:51:55-08:00

The ability to dynamically organize functional nanoparticles (NPs) via the use of environmental triggers (temperature, pH, light, or solvent polarity) opens up important perspectives for rapid and convenient construction of a rich variety of complex assemblies and materials with new structures and functionalities. Here, we report an unconventional strategy for...



K63 ubiquitylation triggers proteasomal degradation by seeding branched ubiquitin chains [Biochemistry]

2018-02-13T09:51:55-08:00

Different polyubiquitin chain linkages direct substrates toward distinct cellular pathways. K63-linked ubiquitylation is known to regulate proteasome-independent events such as signal transduction, but its function in the context of heterogeneous ubiquitin chains remains unclear. Here, we report that K63 ubiquitylation plays a critical role in proteasome-mediated substrate degradation by serving...