136,021 results match your criteria Proceedings of the National Academy of Sciences of the United States of America[Journal]


Transcription factors IRF8 and PU.1 are required for follicular B cell development and BCL6-driven germinal center responses.

Proc Natl Acad Sci U S A 2019 Apr 18. Epub 2019 Apr 18.

Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852;

The IRF and Ets families of transcription factors regulate the expression of a range of genes involved in immune cell development and function. However, the understanding of the molecular mechanisms of each family member has been limited due to their redundancy and broad effects on multiple lineages of cells. Here, we report that double deletion of floxed and (encoding PU. Read More

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http://dx.doi.org/10.1073/pnas.1901258116DOI Listing

RNAi expression tuning, microfluidic screening, and genome recombineering for improved protein production in .

Proc Natl Acad Sci U S A 2019 Apr 18. Epub 2019 Apr 18.

Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden;

The cellular machinery that supports protein synthesis and secretion lies at the foundation of cell factory-centered protein production. Due to the complexity of such cellular machinery, the challenge in generating a superior cell factory is to fully exploit the production potential by finding beneficial targets for optimized strains, which ideally could be used for improved secretion of other proteins. We focused on an approach in the yeast that allows for attenuation of gene expression, using RNAi combined with high-throughput microfluidic single-cell screening for cells with improved protein secretion. Read More

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http://dx.doi.org/10.1073/pnas.1820561116DOI Listing

DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.

Proc Natl Acad Sci U S A 2019 Apr 18. Epub 2019 Apr 18.

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;

Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In , active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. Read More

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http://dx.doi.org/10.1073/pnas.1821435116DOI Listing

Hippo signaling is intrinsically regulated during cell cycle progression by APC/C.

Proc Natl Acad Sci U S A 2019 Apr 18. Epub 2019 Apr 18.

Department of Developmental Biology, Harvard Stem Cell Institute, Harvard School of Dental Medicine, Boston, MA 02215;

The Hippo-YAP/TAZ signaling pathway plays a pivotal role in growth control during development and regeneration and its dysregulation is widely implicated in various cancers. To further understand the cellular and molecular mechanisms underlying Hippo signaling regulation, we have found that activities of core Hippo signaling components, large tumor suppressor (LATS) kinases and YAP/TAZ transcription factors, oscillate during mitotic cell cycle. We further identified that the anaphase-promoting complex/cyclosome (APC/C) E3 ubiquitin ligase complex, which plays a key role governing eukaryotic cell cycle progression, intrinsically regulates Hippo signaling activities. Read More

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http://dx.doi.org/10.1073/pnas.1821370116DOI Listing
April 2019
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Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase.

Proc Natl Acad Sci U S A 2019 Apr 18. Epub 2019 Apr 18.

Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921;

Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) exhibits the protease and RNA helicase activities that are required for viral RNA replication and transcription. Unlike for the C-terminal protease, the structure of the N-terminal RNA helicase (nsP2h) has not been determined. Read More

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http://dx.doi.org/10.1073/pnas.1900656116DOI Listing
April 2019
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Cystine/glutamate antiporter xCT (SLC7A11) facilitates oncogenic RAS transformation by preserving intracellular redox balance.

Proc Natl Acad Sci U S A 2019 Apr 18. Epub 2019 Apr 18.

Department of Molecular Oncology, BC Cancer, Vancouver V5Z 1L3, Canada;

The family of proto-oncogenes are among the most commonly mutated genes in human cancers and predict poor clinical outcome. Several mechanisms underlying oncogenic RAS transformation are well documented, including constitutive signaling through the RAF-MEK-ERK proproliferative pathway as well as the PI3K-AKT prosurvival pathway. Notably, control of redox balance has also been proposed to contribute to RAS transformation. Read More

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http://dx.doi.org/10.1073/pnas.1821323116DOI Listing

Electrically induced bacterial membrane-potential dynamics correspond to cellular proliferation capacity.

Proc Natl Acad Sci U S A 2019 Apr 18. Epub 2019 Apr 18.

School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom;

Membrane-potential dynamics mediate bacterial electrical signaling at both intra- and intercellular levels. Membrane potential is also central to cellular proliferation. It is unclear whether the cellular response to external electrical stimuli is influenced by the cellular proliferative capacity. Read More

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http://dx.doi.org/10.1073/pnas.1901788116DOI Listing

Forging tools for refining predicted protein structures.

Proc Natl Acad Sci U S A 2019 Apr 18. Epub 2019 Apr 18.

Center for Theoretical Biological Physics, Rice University, Houston, TX 77030;

Refining predicted protein structures with all-atom molecular dynamics simulations is one route to producing, entirely by computational means, structural models of proteins that rival in quality those that are determined by X-ray diffraction experiments. Slow rearrangements within the compact folded state, however, make routine refinement of predicted structures by unrestrained simulations infeasible. In this work, we draw inspiration from the fields of metallurgy and blacksmithing, where practitioners have worked out practical means of controlling equilibration by mechanically deforming their samples. Read More

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http://www.pnas.org/lookup/doi/10.1073/pnas.1900778116
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http://dx.doi.org/10.1073/pnas.1900778116DOI Listing
April 2019
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Competitive binding predicts nonlinear responses of olfactory receptors to complex mixtures.

Proc Natl Acad Sci U S A 2019 Apr 18. Epub 2019 Apr 18.

Monell Chemical Senses Center, Philadelphia, PA 19104.

In color vision, the quantitative rules for mixing lights to make a target color are well understood. By contrast, the rules for mixing odorants to make a target odor remain elusive. A solution to this problem in vision relied on characterizing receptor responses to different wavelengths of light and subsequently relating these responses to perception. Read More

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http://dx.doi.org/10.1073/pnas.1813230116DOI Listing
April 2019
2 Reads

Topological descriptions of protein folding.

Proc Natl Acad Sci U S A 2019 Apr 18. Epub 2019 Apr 18.

Department of Mathematical Sciences, Claremont McKenna College, Claremont, CA 91711

How knotted proteins fold has remained controversial since the identification of deeply knotted proteins nearly two decades ago. Both computational and experimental approaches have been used to investigate protein knot formation. Motivated by the computer simulations of Bölinger et al. Read More

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http://dx.doi.org/10.1073/pnas.1808312116DOI Listing

Cancer stemness, intratumoral heterogeneity, and immune response across cancers.

Proc Natl Acad Sci U S A 2019 Apr 17. Epub 2019 Apr 17.

Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada;

Regulatory programs that control the function of stem cells are active in cancer and confer properties that promote progression and therapy resistance. However, the impact of a stem cell-like tumor phenotype ("stemness") on the immunological properties of cancer has not been systematically explored. Using gene-expression-based metrics, we evaluated the association of stemness with immune cell infiltration and genomic, transcriptomic, and clinical parameters across 21 solid cancers. Read More

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http://www.pnas.org/lookup/doi/10.1073/pnas.1818210116
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http://dx.doi.org/10.1073/pnas.1818210116DOI Listing
April 2019
1 Read

Causal inference accounts for heading perception in the presence of object motion.

Proc Natl Acad Sci U S A 2019 Apr 17. Epub 2019 Apr 17.

Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030;

The brain infers our spatial orientation and properties of the world from ambiguous and noisy sensory cues. Judging self-motion (heading) in the presence of independently moving objects poses a challenging inference problem because the image motion of an object could be attributed to movement of the object, self-motion, or some combination of the two. We test whether perception of heading and object motion follows predictions of a normative causal inference framework. Read More

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http://dx.doi.org/10.1073/pnas.1820373116DOI Listing
April 2019
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Modular, stereocontrolled C-H/C-C activation of alkyl carboxylic acids.

Proc Natl Acad Sci U S A 2019 Apr 17. Epub 2019 Apr 17.

Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037;

The union of two powerful transformations, directed C-H activation and decarboxylative cross-coupling, for the enantioselective synthesis of vicinally functionalized alkyl, carbocyclic, and heterocyclic compounds is described. Starting from simple carboxylic acid building blocks, this modular sequence exploits the residual directing group to access more than 50 scaffolds that would be otherwise extremely difficult to prepare. The tactical use of these two transformations accomplishes a formal vicinal difunctionalization of carbon centers in a way that is modular and thus, amenable to rapid diversity incorporation. Read More

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http://dx.doi.org/10.1073/pnas.1903048116DOI Listing
April 2019
1 Read

Tiling and somatotopic alignment of mammalian low-threshold mechanoreceptors.

Proc Natl Acad Sci U S A 2019 Apr 17. Epub 2019 Apr 17.

Department of Neurobiology, Harvard Medical School, Boston, MA 02115;

Innocuous mechanical stimuli acting on the skin are detected by sensory neurons, known as low-threshold mechanoreceptors (LTMRs). LTMRs are classified based on their response properties, action potential conduction velocity, rate of adaptation to static indentation of the skin, and terminal anatomy. Here, we report organizational properties of the cutaneous and central axonal projections of the five principal hairy skin LTMR subtypes. Read More

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http://dx.doi.org/10.1073/pnas.1901378116DOI Listing
April 2019
2 Reads

Rapid screening of engineered microbial therapies in a 3D multicellular model.

Proc Natl Acad Sci U S A 2019 Apr 17. Epub 2019 Apr 17.

Department of Biomedical Engineering, Columbia University, New York, NY 10027;

Synthetic biology is transforming therapeutic paradigms by engineering living cells and microbes to intelligently sense and respond to diseases including inflammation, infections, metabolic disorders, and cancer. However, the ability to rapidly engineer new therapies far outpaces the throughput of animal-based testing regimes, creating a major bottleneck for clinical translation. In vitro approaches to address this challenge have been limited in scalability and broad applicability. Read More

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http://dx.doi.org/10.1073/pnas.1820824116DOI Listing
April 2019
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Dating glacier ice of the last millennium by quantum technology.

Proc Natl Acad Sci U S A 2019 Apr 17. Epub 2019 Apr 17.

Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.

Radiometric dating with Ar covers a unique time span and offers key advances in interpreting environmental archives of the last millennium. Although this tracer has been acknowledged for decades, studies so far have been limited by the low abundance and radioactivity, thus requiring huge sample sizes. Atom trap trace analysis, an application of techniques from quantum physics such as laser cooling and trapping, allows us to reduce the sample volume by several orders of magnitude compared with conventional techniques. Read More

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http://dx.doi.org/10.1073/pnas.1816468116DOI Listing
April 2019
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Phase-conjugate mirror for water waves driven by the Faraday instability.

Proc Natl Acad Sci U S A 2019 Apr 17. Epub 2019 Apr 17.

Institut Langevin, ESPCI Paris, PSL University, CNRS, 75005 Paris, France;

The Faraday instability appears on liquid baths submitted to vertical oscillations above a critical value. The pattern of standing ripples at half the vibrating frequency that results from this parametric forcing is usually shaped by the boundary conditions imposed by the enclosing receptacle. Here, we show that the time modulation of the medium involved in the Faraday instability can act as a phase-conjugate mirror--a fact which is hidden in the extensively studied case of the boundary-driven regime. Read More

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http://dx.doi.org/10.1073/pnas.1818742116DOI Listing
April 2019
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Protease-independent action of tissue plasminogen activator in brain plasticity and neurological recovery after ischemic stroke.

Proc Natl Acad Sci U S A 2019 Apr 17. Epub 2019 Apr 17.

Pittsburgh Institute of Brain Disorders and Recovery, University of Pittsburgh, Pittsburgh, PA 15213;

Emerging evidence suggests that tissue plasminogen activator (tPA), currently the only FDA-approved medication for ischemic stroke, exerts important biological actions on the CNS besides its well-known thrombolytic effect. In this study, we investigated the role of tPA on primary neurons in culture and on brain recovery and plasticity after ischemic stroke in mice. Treatment with recombinant tPA stimulated axonal growth in culture, an effect independent of its protease activity and achieved through epidermal growth factor receptor (EGFR) signaling. Read More

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http://dx.doi.org/10.1073/pnas.1821979116DOI Listing

Science and Culture: Can climate change games boost public understanding?

Authors:
Roberta Kwok

Proc Natl Acad Sci U S A 2019 Apr;116(16):7602-7604

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http://dx.doi.org/10.1073/pnas.1903508116DOI Listing
April 2019
1 Read

Radiocarbon dating the end of urban services in a late Roman town.

Proc Natl Acad Sci U S A 2019 Apr 16. Epub 2019 Apr 16.

Initiative for the Science of the Human Past at Harvard, Department of History, Harvard University, Cambridge, MA 02138;

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http://dx.doi.org/10.1073/pnas.1904037116DOI Listing

Inequality brokered.

Authors:
Peter Hegarty

Proc Natl Acad Sci U S A 2019 Apr 16. Epub 2019 Apr 16.

Department of Psychological Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom

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http://dx.doi.org/10.1073/pnas.1904267116DOI Listing
April 2019
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Testing the role of trait reversal in evolutionary diversification using song loss in wild crickets.

Proc Natl Acad Sci U S A 2019 Apr 16. Epub 2019 Apr 16.

School of Life Sciences, University of Lincoln, Lincoln LN6 7DL, United Kingdom

The mechanisms underlying rapid macroevolution are controversial. One largely untested hypothesis that could inform this debate is that evolutionary reversals might release variation in vestigial traits, which then facilitates subsequent diversification. We evaluated this idea by testing key predictions about vestigial traits arising from sexual trait reversal in wild field crickets. Read More

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http://dx.doi.org/10.1073/pnas.1818998116DOI Listing

Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.

Proc Natl Acad Sci U S A 2019 Apr 16. Epub 2019 Apr 16.

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637;

The dimensions that unfolded proteins, including intrinsically disordered proteins (IDPs), adopt in the absence of denaturant remain controversial. We developed an analysis procedure for small-angle X-ray scattering (SAXS) profiles and used it to demonstrate that even relatively hydrophobic IDPs remain nearly as expanded in water as they are in high denaturant concentrations. In contrast, as demonstrated here, most fluorescence resonance energy transfer (FRET) measurements have indicated that relatively hydrophobic IDPs contract significantly in the absence of denaturant. Read More

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http://dx.doi.org/10.1073/pnas.1813038116DOI Listing
April 2019
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Select sequencing of clonally expanded CD8 T cells reveals limits to clonal expansion.

Proc Natl Acad Sci U S A 2019 Apr 16. Epub 2019 Apr 16.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305;

To permit the recognition of antigens, T cells generate a vast diversity of T cell receptor (TCR) sequences. Upon binding of the TCR to an antigen-MHC complex, T cells clonally expand to establish an immune response. To study antigen-specific T cell clonality, we have developed a method that allows selection of rare cells, based on RNA expression, before in-depth scRNA-seq (named SELECT-seq). Read More

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http://dx.doi.org/10.1073/pnas.1902649116DOI Listing
April 2019
1 Read

Lending practices to same-sex borrowers.

Authors:
Hua Sun Lei Gao

Proc Natl Acad Sci U S A 2019 Apr 16. Epub 2019 Apr 16.

Department of Finance, Ivy College of Business, Iowa State University, Ames, IA 50011

Using massive US mortgage lending data, we propose a method to infer a borrower's sexual orientation indirectly without a self-identification requirement and demonstrate the method's potential to approximately measure the sexual orientation of the US population at the local level annually over decades. We continue to examine the lending practices to same-sex borrowers and its spillover effects. The persistent results since 1990 reveal that, in contrast with otherwise comparable different-sex loan applicants, the approval rate for same-sex applicants is ∼3-8% lower. Read More

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http://dx.doi.org/10.1073/pnas.1903592116DOI Listing

Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan.

Proc Natl Acad Sci U S A 2019 Apr 16. Epub 2019 Apr 16.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461;

Accumulation of mutations in somatic cells has been implicated as a cause of aging since the 1950s. However, attempts to establish a causal relationship between somatic mutations and aging have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan using a highly accurate single-cell whole-genome sequencing method. Read More

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http://dx.doi.org/10.1073/pnas.1902510116DOI Listing
April 2019
9.809 Impact Factor

Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions.

Proc Natl Acad Sci U S A 2019 Apr 16. Epub 2019 Apr 16.

Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043.

While studying spontaneous mutations at the maize () locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate new mutations from several stocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stable mutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneous mutations [Wessler S (1997) , pp 385-386]. Read More

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http://dx.doi.org/10.1073/pnas.1903809116DOI Listing

Science, health, and cultural literacy in a rapidly changing communications landscape.

Proc Natl Acad Sci U S A 2019 Apr 15;116(16):7650-7655. Epub 2019 Apr 15.

The Nevin Scrimshaw International Nutrition Foundation, Boston, MA 02111

There is a gap between how many scientists communicate and how most people understand and interpret messages. This article argues that the extensive science communications literature needs to be joined by the health literacy literature and anthropological work on cultural variations in hearing and understanding messages. Rapid changes and differences in how people in the United States get information are also discussed. Read More

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http://dx.doi.org/10.1073/pnas.1807218116DOI Listing

Conflict across representational gaps: Threats to and opportunities for improved communication.

Proc Natl Acad Sci U S A 2019 Apr 15;116(16):7642-7649. Epub 2019 Apr 15.

Tepper School of Business, Carnegie Mellon University, Pittsburgh, PA 15213.

Often, the senders and receivers of scientific communication have different knowledge bases. While such communication is essential for solving the complex social and technological problems that affect multiple stakeholders, a diversity of knowledge among communicators can create representational gaps (rGaps). rGaps occur when senders make assumptions that receivers do not, creating conflict over the meaning and value of the information communicated. Read More

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http://dx.doi.org/10.1073/pnas.1805866116DOI Listing

The Science of Science Communication III.

Proc Natl Acad Sci U S A 2019 Apr 15;116(16):7632-7633. Epub 2019 Apr 15.

Department of Life Sciences Communication, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI 53706.

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http://dx.doi.org/10.1073/pnas.1902256116DOI Listing

Correlated interfacial water transport and proton conductivity in perfluorosulfonic acid membranes.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, D-55128 Mainz, Germany;

Water must be effectively transported and is also essential for maximizing proton conductivity within fuel-cell proton-exchange membranes (PEMs). Therefore, identifying relationships between PEM properties, water transport, and proton conductivity is essential for designing optimal PEMs. Here, we use coherent Raman spectroscopy to quantify real-time, in situ diffusivities of water subspecies, bulk-like and nonbulk-like (interfacial) water, in five different perfluorosulfonic acid (PFSA) PEMs. Read More

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http://dx.doi.org/10.1073/pnas.1817470116DOI Listing

Functional characterization of 3D protein structures informed by human genetic diversity.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

The Scripps Research Institute, La Jolla, CA 92037;

Sequence variation data of the human proteome can be used to analyze 3D protein structures to derive functional insights. We used genetic variant data from nearly 140,000 individuals to analyze 3D positional conservation in 4,715 proteins and 3,951 homology models using 860,292 missense and 465,886 synonymous variants. Sixty percent of protein structures harbor at least one intolerant 3D site as defined by significant depletion of observed over expected missense variation. Read More

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http://www.pnas.org/lookup/doi/10.1073/pnas.1820813116
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http://dx.doi.org/10.1073/pnas.1820813116DOI Listing
April 2019
1 Read

Interaction between p53 N terminus and core domain regulates specific and nonspecific DNA binding.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Molecular Oncology Department, Moffitt Cancer Center, Tampa, FL 33612;

The p53 tumor suppressor is a sequence-specific DNA binding protein that activates gene transcription to regulate cell survival and proliferation. Dynamic control of p53 degradation and DNA binding in response to stress signals are critical for tumor suppression. The p53 N terminus (NT) contains two transactivation domains (TAD1 and TAD2), a proline-rich region (PRR), and multiple phosphorylation sites. Read More

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http://dx.doi.org/10.1073/pnas.1903077116DOI Listing

Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Department of Physics, University of Missouri, Columbia, MO 65211;

While CRISPR/Cas9 is a powerful tool in genome engineering, the on-target activity and off-target effects of the system widely vary because of the differences in guide RNA (gRNA) sequences and genomic environments. Traditional approaches rely on separate models and parameters to treat on- and off-target cleavage activities. Here, we demonstrate that a free-energy scheme dominates the Cas9 editing efficacy and delineate a method that simultaneously considers on-target activities and off-target effects. Read More

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http://dx.doi.org/10.1073/pnas.1820523116DOI Listing
April 2019
1 Read

How a well-adapting immune system remembers.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Laboratoire de Physique de l'École Normale Supérieure, PSL University, Centre National de la Recherche Scientifique, Sorbonne University, University Paris-Diderot, 75005 Paris, France;

An adaptive agent predicting the future state of an environment must weigh trust in new observations against prior experiences. In this light, we propose a view of the adaptive immune system as a dynamic Bayesian machinery that updates its memory repertoire by balancing evidence from new pathogen encounters against past experience of infection to predict and prepare for future threats. This framework links the observed initial rapid increase of the memory pool early in life followed by a midlife plateau to the ease of learning salient features of sparse environments. Read More

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http://dx.doi.org/10.1073/pnas.1812810116DOI Listing

Strain-induced spontaneous Hall effect in an epitaxial thin film of a Luttinger semimetal.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan;

Pyrochlore iridates have provided a plethora of novel phenomena owing to the combination of topology and correlation. Among them, much attention has been paid to [Formula: see text], as it is known as a Luttinger semimetal characterized by quadratic band touching at the Brillouin zone center, suggesting that the topology of its electronic states can be tuned by a moderate lattice strain and external magnetic field. Here, we report that our epitaxial [Formula: see text] thin films grown by solid-state epitaxy exhibit a spontaneous Hall effect that persists up to 50 K without having spontaneous magnetization within our experimental accuracy. Read More

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http://dx.doi.org/10.1073/pnas.1819489116DOI Listing

Functional connectomics of affective and psychotic pathology.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Center for Depression, Anxiety and Stress Research, McLean Hospital, Belmont, MA 02478;

Converging evidence indicates that groups of patients with nominally distinct psychiatric diagnoses are not separated by sharp or discontinuous neurobiological boundaries. In healthy populations, individual differences in behavior are reflected in variability across the collective set of functional brain connections (functional connectome). These data suggest that the spectra of transdiagnostic symptom profiles observed in psychiatric patients may map onto detectable patterns of network function. Read More

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http://dx.doi.org/10.1073/pnas.1820780116DOI Listing

Anthropogenic strath terrace formation caused by reduced sediment retention.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195.

Across North America, human activities have been shown to cause river incision into unconsolidated alluvium. Human-caused erosion through bedrock, however, has only been observed in local and isolated outcrops. Here, we test whether splash-dam logging, which decreased in-stream alluvial cover by removing much of the alluvium-trapping wood, caused basin-wide bedrock river incision in a forested mountain catchment in Washington State. Read More

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http://dx.doi.org/10.1073/pnas.1814627116DOI Listing

Systematic assessment of the sex ratio at birth for all countries and estimation of national imbalances and regional reference levels.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003-9304.

The sex ratio at birth (SRB; ratio of male to female live births) imbalance in parts of the world over the past few decades is a direct consequence of sex-selective abortion, driven by the coexistence of son preference, readily available technology of prenatal sex determination, and fertility decline. Estimation of the degree of SRB imbalance is complicated because of unknown SRB reference levels and because of the uncertainty associated with SRB observations. There are needs for reproducible methods to construct SRB estimates with uncertainty, and to assess SRB inflation due to sex-selective abortion. Read More

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http://dx.doi.org/10.1073/pnas.1812593116DOI Listing

Compulsive drug use is associated with imbalance of orbitofrontal- and prelimbic-striatal circuits in punishment-resistant individuals.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Neuroimaging Research Branch, National Institute on Drug Abuse, Intramural Research Programs, National Institutes of Health, Baltimore, MD 21224;

Substance use disorders (SUDs) impose severe negative impacts upon individuals, their families, and society. Clinical studies demonstrate that some chronic stimulant users are able to curtail their drug use when faced with adverse consequences while others continue to compulsively use drugs. The mechanisms underlying this dichotomy are poorly understood, which hampers the development of effective individualized treatments of a disorder that currently has no Food and Drug Administration-approved pharmacological treatments. Read More

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http://dx.doi.org/10.1073/pnas.1819978116DOI Listing
April 2019
1 Read

GUN1 interacts with MORF2 to regulate plastid RNA editing during retrograde signaling.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037;

During development or under stress, chloroplasts generate signals that regulate the expression of a large number of nuclear genes, a process called retrograde signaling. GENOMES UNCOUPLED 1 (GUN1) is an important regulator of this pathway. In this study, we have discovered an unexpected role for GUN1 in plastid RNA editing, as mutations affect RNA-editing efficiency at multiple sites in plastids during retrograde signaling. Read More

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http://dx.doi.org/10.1073/pnas.1820426116DOI Listing

Deep learning in turbulent convection networks.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Department of Physics, New York University, New York, NY 10012;

We explore heat transport properties of turbulent Rayleigh-Bénard convection in horizontally extended systems by using deep-learning algorithms that greatly reduce the number of degrees of freedom. Particular attention is paid to the slowly evolving turbulent superstructures-so called because they are larger in extent than the height of the convection layer-which appear as temporal patterns of ridges of hot upwelling and cold downwelling fluid, including defects where the ridges merge or end. The machine-learning algorithm trains a deep convolutional neural network (CNN) with U-shaped architecture, consisting of a contraction and a subsequent expansion branch, to reduce the complex 3D turbulent superstructure to a temporal planar network in the midplane of the layer. Read More

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http://dx.doi.org/10.1073/pnas.1900358116DOI Listing

DNA threads released by activated CD4 T lymphocytes provide autocrine costimulation.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Department of Research, Molecular Immunology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.

The extrusion of DNA traps contributes to a key mechanism in which innate immune cells clear pathogens or induce sterile inflammation. Here we provide evidence that CD4 T cells, a critical regulator of adaptive immunity, release extracellular threads of DNA on activation. These DNA extrusions convey autocrine costimulatory signals to T lymphocytes and can be detected in lymph nodes isolated during the priming phase of experimental autoimmune encephalomyelitis (EAE), a CD4 T cell-driven mouse model of multiple sclerosis. Read More

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http://dx.doi.org/10.1073/pnas.1822013116DOI Listing
April 2019
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Predators attacking virtual prey reveal the costs and benefits of leadership.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Edward Grey Institute, Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom.

A long-standing assumption in social behavior is that leadership incurs costs as well as benefits, and this tradeoff can result in diversified social roles in groups. The major cost of leadership in moving animal groups is assumed to be predation, with individuals leading from the front of groups being targeted more often by predators. Nevertheless, empirical evidence for this is limited, and experimental tests are entirely lacking. Read More

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http://dx.doi.org/10.1073/pnas.1816323116DOI Listing

Correction for Anreiter et al., Epigenetic mechanisms modulate differences in foraging behavior.

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Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

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http://dx.doi.org/10.1073/pnas.1905223116DOI Listing

Same-sex marriage legalization associated with reduced implicit and explicit antigay bias.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Department of Psychology, McGill University, Montréal, QC H3A 0G4, Canada.

The current research tested whether the passing of government legislation, signaling the prevailing attitudes of the local majority, was associated with changes in citizens' attitudes. Specifically, with ∼1 million responses over a 12-y window, we tested whether state-by-state same-sex marriage legislation was associated with decreases in antigay implicit and explicit bias. Results across five operationalizations consistently provide support for this possibility. Read More

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http://dx.doi.org/10.1073/pnas.1806000116DOI Listing

Indian annual ambient air quality standard is achievable by completely mitigating emissions from household sources.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Department of Atmospheric Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801.

Exposures to ambient and household fine-particulate matter (PM) together are among the largest single causes of premature mortality in India according to the Global Burden of Disease Studies (GBD). Several recent investigations have estimated that household emissions are the largest contributor to ambient PM exposure in the country. Using satellite-derived district-level PM exposure and an Eulerian photochemical dispersion model CAMx (Comprehensive Air Quality Model with Extensions), we estimate the benefit in terms of population exposure of mitigating household sources--biomass for cooking, space- and water-heating, and kerosene for lighting. Read More

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http://dx.doi.org/10.1073/pnas.1900888116DOI Listing
April 2019
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Characterizing the cultural niches of North American birds.

Proc Natl Acad Sci U S A 2019 Apr 15. Epub 2019 Apr 15.

Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850;

Efforts to mitigate the current biodiversity crisis require a better understanding of how and why humans value other species. We use Internet query data and citizen science data to characterize public interest in 621 bird species across the United States. We estimate the relative popularity of different birds by quantifying how frequently people use Google to search for species, relative to the rates at which they are encountered in the environment. Read More

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http://dx.doi.org/10.1073/pnas.1820670116DOI Listing
April 2019
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