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Proceedings of the National Academy of Sciences of the United States of America
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- 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
- http://dx.doi.org/10.1073/pnas.1312125110
- 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
- http://dx.doi.org/10.1073/pnas.1312009110
- 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:
- Inuit; solar radiation; calcium; magnesium; marine sediments; hunters; time series analysis; summer; mammals; ice; temperature; habitats; satellites; 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
- http://dx.doi.org/10.1073/pnas.1313775110
- 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
- http://dx.doi.org/10.1073/pnas.1315278110
- 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
- http://dx.doi.org/10.1073/pnas.1320145110
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
- http://dx.doi.org/10.1073/pnas.1311772110
- 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
- http://dx.doi.org/10.1073/pnas.1320074110
- 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
- http://dx.doi.org/10.1073/pnas.1311535110
- 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
- http://dx.doi.org/10.1073/pnas.1320124110
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
- http://dx.doi.org/10.1073/pnas.1302840110
- 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
- http://dx.doi.org/10.1073/pnas.1314529110
- 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
- http://dx.doi.org/10.1073/pnas.1309195110
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:
- primary productivity; benthic organisms; climate change; global carbon budget; food availability; particulate organic carbon; time series analysis; surface water; surpluses; 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
- http://dx.doi.org/10.1073/pnas.1315447110
- 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
- http://dx.doi.org/10.1073/pnas.1311120110
- 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
- http://dx.doi.org/10.1073/pnas.1319943110
- 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
- http://dx.doi.org/10.1073/pnas.1310838110
- 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
- http://dx.doi.org/10.1073/pnas.1300236110
- 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
- http://dx.doi.org/10.1073/pnas.1313677110
- 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
- http://dx.doi.org/10.1073/pnas.1319473110
- 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
- http://dx.doi.org/10.1073/pnas.1313825110
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