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You searched for: Journal Proceedings of the National Academy of Sciences of the United States of America Remove constraint Journal: Proceedings of the National Academy of Sciences of the United States of America Publication Year 2013 Remove constraint Publication Year: 2013 Source 2013 v.110 no.49 Remove constraint Source: 2013 v.110 no.49
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1. A multiplicative reinforcement learning model capturing learning dynamics and interindividual variability in mice

Author:
Bathellier, Brice; Tee, Sui Poh; Hrovat, Christina; Rumpel, Simon
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19950-19955
ISSN:
0027-8424
Subject:
brain; humans; learning; mice; models; neurons; operant conditioning; strength (mechanics)
Abstract:
... Both in humans and in animals, different individuals may learn the same task with strikingly different speeds; however, the sources of this variability remain elusive. In standard learning models, interindividual variability is often explained by variations of the learning rate, a parameter indicating how much synapses are updated on each learning event. Here, we theoretically show that the initia ...
DOI:
10.1073/pnas.1312125110
PubMed:
24255115
PubMed Central:
PMC3856837

2. Analysis of DNA methylation reveals a partial reprogramming of the Müller glia genome during retina regeneration

Author:
Powell, Curtis; Grant, Ana R.; Cornblath, Eli; Goldman, Daniel
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19814-19819
ISSN:
0027-8424
Subject:
DNA; DNA methylation; Danio rerio; gene expression; gene induction; genes; mice; protein synthesis; retina; somatic cells; stem cells
Abstract:
... Upon retinal injury, zebrafish Müller glia (MG) transition from a quiescent supportive cell to a progenitor cell (MGPC). This event is accompanied by the induction of key transcription and pluripotency factors. Because somatic cell reprogramming during induced pluripotent stem cell generation is accompanied by changes in DNA methylation, especially in pluripotency factor gene promoters, we were in ...
DOI:
10.1073/pnas.1312009110
PubMed:
24248357
PubMed Central:
PMC3856824

3. Arctic sea-ice decline archived by multicentury annual-resolution record from crustose coralline algal proxy

Author:
Halfar, Jochen; Adey, Walter H.; Kronz, Andreas; Hetzinger, Steffen; Edinger, Evan; Fitzhugh, William W.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19737-19741
ISSN:
0027-8424
Subject:
Algae; Inuit; calcium; habitats; hunters; ice; magnesium; mammals; marine sediments; satellites; solar radiation; summer; temperature; time series analysis; Arctic region
Abstract:
... Northern Hemisphere sea ice has been declining sharply over the past decades and 2012 exhibited the lowest Arctic summer sea-ice cover in historic times. Whereas ongoing changes are closely monitored through satellite observations, we have only limited data of past Arctic sea-ice cover derived from short historical records, indirect terrestrial proxies, and low-resolution marine sediment cores. A ...
DOI:
10.1073/pnas.1313775110
PubMed:
24248344
PubMed Central:
PMC3856805

4. Bacterial natural transformation by highly fragmented and damaged DNA

Author:
Overballe-Petersen, Søren; Harms, Klaus; Orlando, Ludovic A. A.; Mayar, J. Victor Moreno; Rasmussen, Simon; Dahl, Tais W.; Rosing, Minik T.; Poole, Anthony M.; Sicheritz-Ponten, Thomas; Brunak, Søren; Inselmann, Sabrina; de Vries, Johann; Wackernagel, Wilfried; Pybus, Oliver G.; Nielsen, Rasmus; Johnsen, Pål Jarle; Nielsen, Kaare Magne; Willerslev, Eske
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19860-19865
ISSN:
0027-8424
Subject:
Acinetobacter; DNA; DNA fragmentation; DNA repair; DNA replication; bacteria; base pair mismatch; crosslinking; environment; evolution; genetic recombination; genome; organic matter
Abstract:
... DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often <100 bp) and may persist in the environment for more than half a million years. Fragmented DNA is recognized as nutrient source for microbes, but not as potential substrate for bacterial evolution. Here, we show that fragmented DNA ...
DOI:
10.1073/pnas.1315278110
PubMed:
24248361
PubMed Central:
PMC3856829

5. Beneficial innate signaling interference for antibacterial responses by a Toll-like receptor–mediated enhancement of the MKP-IRF3 axis

Author:
Negishi, Hideo; Matsuki, Kosuke; Endo, Nobuyasu; Sarashina, Hana; Miki, Shoji; Matsuda, Atsushi; Fukazawa, Keiko; Taguchi-Atarashi, Naoko; Ikushima, Hiroaki; Yanai, Hideyuki; Nishio, Junko; Honda, Kenya; Fujioka, Yoichiro; Ohba, Yusuke; Noda, Tetsuo; Taniguchi, Shun’ichiro; Nishida, Eisuke; Zhang, Yongliang; Chi, Hongbo; Flavell, Richard A.; Taniguchi, Tadatsugu
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19884-19889
ISSN:
0027-8424
Subject:
Listeria monocytogenes; Toll-like receptors; antibacterial properties; bacterial infections; gene induction; immune response; macrophages; mitogen-activated protein kinase; pathogens; signal transduction; transcription factors
Abstract:
... A major function of innate immune receptors is to recognize pathogen-associated molecular patterns and then evoke immune responses appropriate to the nature of the invading pathogen(s). Because innate immune cells express various types of these receptors, distinct combinations of signaling pathways are activated in response to a given pathogen. Although the conventional wisdom is that these signal ...
DOI:
10.1073/pnas.1320145110
PubMed:
24248350
PubMed Central:
PMC3856811

6. Causal interactions between fronto-parietal central executive and default-mode networks in humans

Author:
Chen, Ashley C.; Oathes, Desmond J.; Chang, Catie; Bradley, Travis; Zhou, Zheng-Wei; Williams, Leanne M.; Glover, Gary H.; Deisseroth, Karl; Etkin, Amit
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19944-19949
ISSN:
0027-8424
Subject:
brain; cognition; humans; magnetic resonance imaging; neural networks
Abstract:
... Information processing during human cognitive and emotional operations is thought to involve the dynamic interplay of several large-scale neural networks, including the fronto-parietal central executive network (CEN), cingulo-opercular salience network (SN), and the medial prefrontal-medial parietal default mode networks (DMN). It has been theorized that there is a causal neural mechanism by which ...
DOI:
10.1073/pnas.1311772110
PubMed:
24248372
PubMed Central:
PMC3856839

7. Centromere proteins CENP-C and CAL1 functionally interact in meiosis for centromere clustering, pairing, and chromosome segregation

Author:
Unhavaithaya, Yingdee; Orr-Weaver, Terry L.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19878-19883
ISSN:
0027-8424
Subject:
Drosophila; cell nucleolus; chromatids; chromosome segregation; heterozygosity; kinetochores; mitosis; mutants; mutation; proteins; synaptonemal complex; yeasts
Abstract:
... Meiotic chromosome segregation involves pairing and segregation of homologous chromosomes in the first division and segregation of sister chromatids in the second division. Although it is known that the centromere and kinetochore are responsible for chromosome movement in meiosis as in mitosis, potential specialized meiotic functions are being uncovered. Centromere pairing early in meiosis I, even ...
DOI:
10.1073/pnas.1320074110
PubMed:
24248385
PubMed Central:
PMC3856785

8. Chronic exposure to arsenic in drinking water can lead to resistance to antimonial drugs in a mouse model of visceral leishmaniasis

Author:
Perry, Meghan R.; Wyllie, Susan; Raab, Andrea; Feldmann, Joerg; Fairlamb, Alan H.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19932-19937
ISSN:
0027-8424
Subject:
Leishmania donovani; animal models; antimony; arsenic; biopsy; chronic exposure; cross resistance; drinking water; drugs; humans; liver; macrophages; mice; parasites; patients; sodium; tissues; visceral leishmaniasis; India
Abstract:
... The Indian subcontinent is the only region where arsenic contamination of drinking water coexists with widespread resistance to antimonial drugs that are used to treat the parasitic disease visceral leishmaniasis. We have previously proposed that selection for parasite resistance within visceral leishmaniasis patients who have been exposed to trivalent arsenic results in cross-resistance to the re ...
DOI:
10.1073/pnas.1311535110
PubMed:
24167266
PubMed Central:
PMC3856816

9. Circular dichroism and site-directed spin labeling reveal structural and dynamical features of high-pressure states of myoglobin

Author:
Lerch, Michael T.; Horwitz, Joseph; McCoy, John; Hubbell, Wayne L.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. E4714
ISSN:
0027-8424
Subject:
circular dichroism spectroscopy; high pressure treatment; myoglobin; pH; topology
Abstract:
... Excited states of proteins may play important roles in function, yet are difficult to study spectroscopically because of their sparse population. High hydrostatic pressure increases the equilibrium population of excited states, enabling their characterization [Akasaka K (2003) Biochemistry 42:10875–85]. High-pressure site-directed spin-labeling EPR (SDSL-EPR) was developed recently to map the site ...
DOI:
10.1073/pnas.1320124110
PubMed:
24248390
PubMed Central:
PMC3856799

10. Control of creatine metabolism by HIF is an endogenous mechanism of barrier regulation in colitis

Author:
Glover, Louise E.; Bowers, Brittelle E.; Saeedi, Bejan; Ehrentraut, Stefan F.; Campbell, Eric L.; Bayless, Amanda J.; Dobrinskikh, Evgenia; Kendrick, Agnieszka A.; Kelly, Caleb J.; Burgess, Adrianne; Miller, Lauren; Kominsky, Douglas J.; Jedlicka, Paul; Colgan, Sean P.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19820-19825
ISSN:
0027-8424
Subject:
Crohn disease; adenosine triphosphate; adherens junctions; colitis; creatine; dietary supplements; disease severity; energy metabolism; epithelial cells; gastrointestinal system; genes; homeostasis; hypoxia; hypoxia-inducible factor 1; inflammation; models; mucosa; oxygen; patients; phosphotransferases (kinases); transcriptional activation
Abstract:
... Mucosal surfaces of the lower gastrointestinal tract are subject to frequent, pronounced fluctuations in oxygen tension, particularly during inflammation. Adaptive responses to hypoxia are orchestrated largely by the hypoxia-inducible transcription factors (HIFs). As HIF-1α and HIF-2α are coexpressed in mucosal epithelia that constitute the barrier between the lumen and the underlying immune milie ...
DOI:
10.1073/pnas.1302840110
PubMed:
24248342
PubMed Central:
PMC3856803

11. Copper control of bacterial nitrous oxide emission and its impact on vitamin B₁₂-dependent metabolism

Author:
Sullivan, Matthew J.; Gates, Andrew J.; Appia-Ayme, Corinne; Rowley, Gary; Richardson, David J.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19926-19931
ISSN:
0027-8424
Subject:
Paracoccus denitrificans; biochemical pathways; denitrifying bacteria; gene expression; genes; greenhouse gas emissions; metabolism; nitrates; nitrous oxide; nitrous-oxide reductase; soil; transcription (genetics); vitamin B12
Abstract:
... Global agricultural emissions of the greenhouse gas nitrous oxide (N ₂O) have increased by around 20% over the last 100 y, but regulation of these emissions and their impact on bacterial cellular metabolism are poorly understood. Denitrifying bacteria convert nitrate in soils to inert di-nitrogen gas (N ₂) via N ₂O and the biochemistry of this process has been studied extensively in Paracoccus den ...
DOI:
10.1073/pnas.1314529110
PubMed:
24248380
PubMed Central:
PMC3856849

12. Coxiella burnetii effector protein subverts clathrin-mediated vesicular trafficking for pathogen vacuole biogenesis

Author:
Larson, Charles L.; Beare, Paul A.; Howe, Dale; Heinzen, Robert A.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. E4770
ISSN:
0027-8424
Subject:
Coxiella burnetii; Q fever; biogenesis; clathrin; cytosol; endosomes; humans; macrophages; mutants; mutation; pathogens; peptides; physiological transport; secretion; small interfering RNA; transferrin; tyrosine; vacuoles
Abstract:
... Successful macrophage colonization by Coxiella burnetii , the cause of human Q fever, requires pathogen-directed biogenesis of a large, growth-permissive parasitophorous vacuole (PV) with phagolysosomal characteristics. The vesicular trafficking pathways co-opted by C. burnetii for PV development are poorly defined; however, it is predicted that effector proteins delivered to the cytosol by a defe ...
DOI:
10.1073/pnas.1309195110
PubMed:
24248335
PubMed Central:
PMC3856779

13. Deep ocean communities impacted by changing climate over 24 y in the abyssal northeast Pacific Ocean

Author:
Smith, Kenneth L.; Ruhl, Henry A.; Kahru, Mati; Huffard, Christine L.; Sherman, Alana D.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19838-19841
ISSN:
0027-8424
Subject:
benthic organisms; carbon; climate change; food availability; global carbon budget; particulate organic carbon; primary productivity; surface water; surpluses; time series analysis; Pacific Ocean
Abstract:
... The deep ocean, covering a vast expanse of the globe, relies almost exclusively on a food supply originating from primary production in surface waters. With well-documented warming of oceanic surface waters and conflicting reports of increasing and decreasing primary production trends, questions persist about how such changes impact deep ocean communities. A 24-y time-series study of sinking parti ...
DOI:
10.1073/pnas.1315447110
PubMed:
24218565
PubMed Central:
PMC3856801

14. Design and formulation of functional pluripotent stem cell-derived cardiac microtissues

Author:
Thavandiran, Nimalan; Dubois, Nicole; Mikryukov, Alexander; Massé, Stéphane; Beca, Bogdan; Simmons, Craig A.; Deshpande, Vikram S.; McGarry, J. Patrick; Chen, Christopher S.; Nanthakumar, Kumaraswamy; Keller, Gordon M.; Radisic, Milica; Zandstra, Peter W.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. E4698
ISSN:
0027-8424
Subject:
cardiomyocytes; collagen; drugs; electrodes; electrophysiology; functional properties; gene expression; heart diseases; humans; in vitro studies; mechanics; models; screening; stem cells
Abstract:
... Access to robust and information-rich human cardiac tissue models would accelerate drug-based strategies for treating heart disease. Despite significant effort, the generation of high-fidelity adult-like human cardiac tissue analogs remains challenging. We used computational modeling of tissue contraction and assembly mechanics in conjunction with microfabricated constraints to guide the design of ...
DOI:
10.1073/pnas.1311120110
PubMed:
24255110
PubMed Central:
PMC3856835

15. Diffusion modifies the connectivity of kinetic schemes for multisite binding and catalysis

Author:
Gopich, Irina V.; Szabo, Attila
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19784-19789
ISSN:
0027-8424
Subject:
active sites; catalytic activity; equations; models; phosphorylation; reaction kinetics
Abstract:
... The simplest way to describe the influence of the relative diffusion of the reactants on the time course of bimolecular reactions is to modify or renormalize the phenomenological rate constants that enter into the rate equations of conventional chemical kinetics. However, for macromolecules with multiple inequivalent reactive sites, this is no longer sufficient, even in the low concentration limit ...
DOI:
10.1073/pnas.1319943110
PubMed:
24248348
PubMed Central:
PMC3856809

16. Dimerization of LTβR by LTα₁β₂ is necessary and sufficient for signal transduction

Author:
Sudhamsu, Jawahar; Yin, JianPing; Chiang, Eugene Y.; Starovasnik, Melissa A.; Grogan, Jane L.; Hymowitz, Sarah G.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19896-19901
ISSN:
0027-8424
Subject:
antibodies; binding sites; crystal structure; dimerization; ligands; lymphotoxin; mutation; organogenesis; receptors; signal transduction; transcription factor NF-kappa B
Abstract:
... Homotrimeric TNF superfamily ligands signal by inducing trimers of their cognate receptors. As a biologically active heterotrimer, Lymphotoxin(LT)α ₁β ₂ is unique in the TNF superfamily. How the three unique potential receptor-binding interfaces in LTα ₁β ₂ trigger signaling via LTβ Receptor (LTβR) resulting in lymphoid organogenesis and propagation of inflammatory signals is poorly understood. He ...
DOI:
10.1073/pnas.1310838110
PubMed:
24248355
PubMed Central:
PMC3856818

17. Dislocation is a developmental mechanism in Dictyostelium and vertebrates

Author:
Durston, Antony J.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19826-19831
ISSN:
0027-8424
Subject:
Dictyostelium discoideum; morphogenesis; vertebrates
Abstract:
... The excitable cells of Dictyostelium discoideum show traveling waves of signaling and generate a variety of complex wave forms during their morphogenesis. Important among these wave forms is the 3D spiral or scroll wave, which has been proposed previously to have a twisted variant: the “turbine wave.” Herein we argue that a D. discoideum scroll or concentric wave territory containing prespore and ...
DOI:
10.1073/pnas.1300236110
PubMed:
24255112
PubMed Central:
PMC3856777

18. Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

Author:
Zanni, Vanessa; Eymery, Angéline; Coiffet, Michael; Zytnicki, Matthias; Luyten, Isabelle; Quesneville, Hadi; Vaury, Chantal; Jensen, Silke
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19842-19847
ISSN:
0027-8424
Subject:
Drosophila; RNA; biogenesis; evolution; genetic variation; heterochromatin; loci; retrotransposons; transposition (genetics); transposons
Abstract:
... Most of our understanding of Drosophila heterochromatin structure and evolution has come from the annotation of heterochromatin from the isogenic y; cn bw sp strain. However, almost nothing is known about the heterochromatin’s structural dynamics and evolution. Here, we focus on a 180-kb heterochromatic locus producing Piwi-interacting RNAs (piRNA cluster), the flamenco (flam) locus, known to be r ...
DOI:
10.1073/pnas.1313677110
PubMed:
24248389
PubMed Central:
PMC3856796

19. Distribution of directional change as a signature of complex dynamics

Author:
Burov, Stanislav; Tabei, S. M. Ali; Huynh, Toan; Murrell, Michael P.; Philipson, Louis H.; Rice, Stuart A.; Gardel, Margaret L.; Scherer, Norbert F.; Dinner, Aaron R.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19689-19694
ISSN:
0027-8424
Subject:
kinesin; models; stochastic processes
Abstract:
... Analyses of random walks traditionally use the mean square displacement (MSD) as an order parameter characterizing dynamics. We show that the distribution of relative angles of motion between successive time intervals of random walks in two or more dimensions provides information about stochastic processes beyond the MSD. We illustrate the behavior of this measure for common models and apply it to ...
DOI:
10.1073/pnas.1319473110
PubMed:
24248363
PubMed Central:
PMC3856831

20. Effect of the Fukushima nuclear accident on the risk perception of residents near a nuclear power plant in China

Author:
Huang, Lei; Zhou, Ying; Han, Yuting; Hammitt, James K.; Bi, Jun; Liu, Yang
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.49 pp. 19742-19747
ISSN:
0027-8424
Subject:
equations; females; income; models; nuclear power; power plants; regression analysis; risk perception; surveys; China
Abstract:
... We assessed the influence of the Fukushima nuclear accident (FNA) on the Chinese public’s attitude and acceptance of nuclear power plants in China. Two surveys (before and after the FNA) were administered to separate subsamples of residents near the Tianwan nuclear power plant in Lianyungang, China. A structural equation model was constructed to describe the public acceptance of nuclear power and ...
DOI:
10.1073/pnas.1313825110
PubMed:
24248341
PubMed Central:
PMC3856800