Mutation, specialization, and hypersensitivity in highly optimized tolerance.

Abstract:

:We introduce a model of evolution in which competing organisms are represented by percolation lattice models. Fitness is based on the number of occupied sites remaining after removing a cluster connected to a randomly selected site. High-fitness individuals arising through mutation and selection must trade off density versus robustness to loss, and are characterized by cellular barrier patterns that prevent large cascading losses to common disturbances. This model shows that Highly Optimized Tolerance (HOT), which links complexity to robustness in designed systems, arises naturally through Darwinian mechanisms. Although the model is a severe abstraction of biology, it produces a surprisingly wide variety of micro- and macroevolutionary features strikingly similar to real biological evolution.

authors

Zhou T,Carlson JM,Doyle J

doi

10.1073/pnas.261714399

keywords:

subject

Has Abstract

pub_date

2002-02-19 00:00:00

pages

2049-54

issue

4

eissn

0027-8424

issn

1091-6490

pii

261714399

journal_volume

99

pub_type

杂志文章
  • A long noncoding RNA regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation.

    abstract::Proper resolution of inflammation is vital for repair and restoration of homeostasis after tissue damage, and its dysregulation underlies various noncommunicable diseases, such as cardiovascular and metabolic diseases. Macrophages play diverse roles throughout initial inflammation, its resolution, and tissue repair. D...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2005924117

    authors: Nakayama Y,Fujiu K,Yuki R,Oishi Y,Morioka MS,Isagawa T,Matsuda J,Oshima T,Matsubara T,Sugita J,Kudo F,Kaneda A,Endo Y,Nakayama T,Nagai R,Komuro I,Manabe I

    更新日期:2020-06-23 00:00:00

  • The nucleocapsid protein specifically anneals tRNALys-3 onto a noncomplementary primer binding site within the HIV-1 RNA genome in vitro.

    abstract::HIV type 1 (HIV-1) specifically uses host cell tRNALys-3 as a primer for reverse transcription. The 3' 18 nucleotides of this tRNA are complementary to a region on the HIV RNA genome known as the primer binding site (PBS). HIV-1 has a strong preference for maintaining a lysine-specific PBS in vivo, and viral genomes w...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.25.13530

    authors: Chan B,Musier-Forsyth K

    更新日期:1997-12-09 00:00:00

  • Chemosensing in Escherichia coli: two regimes of two-state receptors.

    abstract::The chemotaxis network in Escherichia coli is remarkable for its sensitivity to small relative changes in the concentrations of multiple chemical signals. We present a model for signal integration by mixed clusters of interacting two-state chemoreceptors. Our model results compare favorably to the results obtained by ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0507438103

    authors: Keymer JE,Endres RG,Skoge M,Meir Y,Wingreen NS

    更新日期:2006-02-07 00:00:00

  • Solar thermal desalination as a nonlinear optical process.

    abstract::The ever-increasing global need for potable water requires practical, sustainable approaches for purifying abundant alternative sources such as seawater, high-salinity processed water, or underground reservoirs. Evaporation-based solutions are of particular interest for treating high salinity water, since conventional...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1905311116

    authors: Dongare PD,Alabastri A,Neumann O,Nordlander P,Halas NJ

    更新日期:2019-07-02 00:00:00

  • A language-familiarity effect for speaker discrimination without comprehension.

    abstract::The influence of language familiarity upon speaker identification is well established, to such an extent that it has been argued that "Human voice recognition depends on language ability" [Perrachione TK, Del Tufo SN, Gabrieli JDE (2011) Science 333(6042):595]. However, 7-mo-old infants discriminate speakers of their ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 临床试验,杂志文章

    doi:10.1073/pnas.1401383111

    authors: Fleming D,Giordano BL,Caldara R,Belin P

    更新日期:2014-09-23 00:00:00

  • Structure-based design of an osteoclast-selective, nonpeptide src homology 2 inhibitor with in vivo antiresorptive activity.

    abstract::Targeted disruption of the pp60(src) (Src) gene has implicated this tyrosine kinase in osteoclast-mediated bone resorption and as a therapeutic target for the treatment of osteoporosis and other bone-related diseases. Herein we describe the discovery of a nonpeptide inhibitor (AP22408) of Src that demonstrates in vivo...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.97.17.9373

    authors: Shakespeare W,Yang M,Bohacek R,Cerasoli F,Stebbins K,Sundaramoorthi R,Azimioara M,Vu C,Pradeepan S,Metcalf C 3rd,Haraldson C,Merry T,Dalgarno D,Narula S,Hatada M,Lu X,van Schravendijk MR,Adams S,Violette S,Smith J,

    更新日期:2000-08-15 00:00:00

  • Mortality traps and the dynamics of health transitions.

    abstract::An examination of life expectancy in 1963 reveals twin peaks in the empirical distribution across countries: one group of countries clustered around a life expectancy of 40 years and a second group clustered around a life expectancy of 65 years. By 2003, the mode of each cluster had moved up by approximately 10 years....

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0702012104

    authors: Bloom DE,Canning D

    更新日期:2007-10-09 00:00:00

  • A second exopolysaccharide of Rhizobium meliloti strain SU47 that can function in root nodule invasion.

    abstract::Rhizobium meliloti strain SU47 produces the calcofluor-binding exopolysaccharide, succinoglycan, that is required for alfalfa root nodule invasion. Strains derived from R. meliloti SU47 secreted an acidic exopolysaccharide, EPSb, that replaced succinoglycan in nodule invasion. EPSb, which has not formerly been identif...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.9.3055

    authors: Zhan HJ,Levery SB,Lee CC,Leigh JA

    更新日期:1989-05-01 00:00:00

  • Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex.

    abstract::Transcriptional regulation by nuclear hormone receptors is thought to involve interactions with putative cofactors that may potentiate receptor function. Here we show that human thyroid hormone receptor alpha purified from HeLa cells grown in the presence of thyroid hormone (T3) is associated with a group of distinct ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.16.8329

    authors: Fondell JD,Ge H,Roeder RG

    更新日期:1996-08-06 00:00:00

  • The affinity-labeling of partially purified acetylcholine receptor from electric tissue of Electrophorus.

    abstract::The receptor for acetylcholine was partially purified by affinity chromatography of an extract in Triton X-100 of membrane fragments from electric tissue. The receptor was assayed, after its reduction with dithiothreitol, by reaction with the affinity-alkylating agent, [methyl-(3)H]4-(N-maleimido)-benzyltrimethylammon...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.70.12.3636

    authors: Karlin A,Cowburn D

    更新日期:1973-12-01 00:00:00

  • Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria.

    abstract::Modern European genetic structure demonstrates strong correlations with geography, while genetic analysis of prehistoric humans has indicated at least two major waves of immigration from outside the continent during periods of cultural change. However, population-level genome data that could shed light on the demograp...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 历史文章,杂志文章

    doi:10.1073/pnas.1719880115

    authors: Veeramah KR,Rott A,Groß M,van Dorp L,López S,Kirsanow K,Sell C,Blöcher J,Wegmann D,Link V,Hofmanová Z,Peters J,Trautmann B,Gairhos A,Haberstroh J,Päffgen B,Hellenthal G,Haas-Gebhard B,Harbeck M,Burger J

    更新日期:2018-03-27 00:00:00

  • Endonuclease III (nth) mutants of Escherichia coli.

    abstract::Two strains that overproduce endonuclease III were found in a colony bank containing hybrid ColE1-Escherichia coli plasmids. The enzyme was identified in crude extracts by the degradation of partially depyrimidinated DNA in the presence of EDTA, by its sedimentation velocity, and by its associated thymine glycol-DNA g...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.82.2.474

    authors: Cunningham RP,Weiss B

    更新日期:1985-01-01 00:00:00

  • Size polymorphism of chicken major histocompatibility complex-encoded B-G molecules is due to length variation in the cytoplasmic heptad repeat region.

    abstract::B-G antigens are cell-surface molecules encoded by a highly polymorphic multigene family located in the chicken major histocompatibility complex (MHC). Rabbit antisera to B-G molecules immunoprecipitate 3-6 bands from iodinated erythrocytes by sodium dodecyl sulfate (SDS) gels under reducing conditions. These are all ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.21.8277

    authors: Kaufman J,Salomonsen J,Skjødt K,Thorpe D

    更新日期:1990-11-01 00:00:00

  • Structure-guided enzymology of the lipid A acyltransferase LpxM reveals a dual activity mechanism.

    abstract::Gram-negative bacteria possess a characteristic outer membrane, of which the lipid A constituent elicits a strong host immune response through the Toll-like receptor 4 complex, and acts as a component of the permeability barrier to prevent uptake of bactericidal compounds. Lipid A species comprise the bulk of the oute...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1610746113

    authors: Dovala D,Rath CM,Hu Q,Sawyer WS,Shia S,Elling RA,Knapp MS,Metzger LE 4th

    更新日期:2016-10-11 00:00:00

  • N-Nitroso-N-methylurea elicits mammary cancer in resistant and sensitive rat strains.

    abstract::A single intravenous (i.v.) injection of the water-soluble mammary carcinogen N-nitroso-N-methylurea (NMU; 35 mg/kg of body weight) elicited cancer of the breast in young female rats of two strains in the following incidence: Long-Evans strain, 4%; Sprague-Dawley strain, 70%. In sisters of these rats, a set of 5 i.v. ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.78.2.1185

    authors: Huggins CB,Ueda N,Wiessler M

    更新日期:1981-02-01 00:00:00

  • Deficient Smad7 expression: a putative molecular defect in scleroderma.

    abstract::Scleroderma is a chronic systemic disease that leads to fibrosis of affected organs. Transforming growth factor (TGF) beta has been implicated in the pathogenesis of scleroderma. Smad proteins are signaling transducers downstream from TGF-beta receptors. Three families of Smads have been identified: (i) receptor-regul...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章,收录出版

    doi:10.1073/pnas.062010399

    authors: Dong C,Zhu S,Wang T,Yoon W,Li Z,Alvarez RJ,ten Dijke P,White B,Wigley FM,Goldschmidt-Clermont PJ

    更新日期:2002-03-19 00:00:00

  • Electron spin resonance studies of spin-labeled mammalian cells by detection of surface-membrane signals.

    abstract::Lipid-soluble spin labels were incorporated into human lymphocytes and mouse L-cells and the resulting electron spin resonance spectra were compared with spectra obtained from similarly labeled human erythrocytes. Spin labels were found in all subcellular fractions of the nucleated cells that contained membranes. Spin...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.70.1.66

    authors: Kaplan J,Canonico PG,Caspary WJ

    更新日期:1973-01-01 00:00:00

  • Honey bees navigate according to a map-like spatial memory.

    abstract::By using harmonic radar, we report the complete flight paths of displaced bees. Test bees forage at a feeder or are recruited by a waggle dance indicating the feeder. The flights are recorded after the bees are captured when leaving the hive or the feeder and are released at an unexpected release site. A sequence of b...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0408550102

    authors: Menzel R,Greggers U,Smith A,Berger S,Brandt R,Brunke S,Bundrock G,Hülse S,Plümpe T,Schaupp F,Schüttler E,Stach S,Stindt J,Stollhoff N,Watzl S

    更新日期:2005-02-22 00:00:00

  • Probing the environment along the protein import pathways in yeast mitochondria by site-specific photocrosslinking.

    abstract::Artificially aminoacylated suppressor tRNAs were used to introduce photoreactive amino acids into model mitochondrial precursor proteins to probe the environment along the protein import pathway. Amino acids with benzophenone side chains of various lengths [DL-2-amino-3-(p-benzoylphenyl)propanoic acid (1) and DL-2-ami...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.2.485

    authors: Kanamori T,Nishikawa S,Shin I,Schultz PG,Endo T

    更新日期:1997-01-21 00:00:00

  • N-terminal domain of complexin independently activates calcium-triggered fusion.

    abstract::Complexin activates Ca(2+)-triggered neurotransmitter release and regulates spontaneous release in the presynaptic terminal by cooperating with the neuronal soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and the Ca(2+)-sensor synaptotagmin. The N-terminal domain of complexin is importa...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1604348113

    authors: Lai Y,Choi UB,Zhang Y,Zhao M,Pfuetzner RA,Wang AL,Diao J,Brunger AT

    更新日期:2016-08-09 00:00:00

  • Multipotent nestin-positive, keratin-negative hair-follicle bulge stem cells can form neurons.

    abstract::We have recently shown that the expression of nestin, the neural stem cell marker protein, is expressed in bulge-area stem cells of the hair follicle. We used transgenic mice with GFP expression driven by the nestin regulatory element [nestin-driven GFP (ND-GFP)]. The ND-GFP stem cells give rise to the outer-root shea...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0501263102

    authors: Amoh Y,Li L,Katsuoka K,Penman S,Hoffman RM

    更新日期:2005-04-12 00:00:00

  • Detecting larval export from marine reserves.

    abstract::Marine reserve theory suggests that where large, productive populations are protected within no-take marine reserves, fished areas outside reserves will benefit through the spillover of larvae produced in the reserves. However, empirical evidence for larval export has been sparse. Here we use a simple idealized coastl...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0907368107

    authors: Pelc RA,Warner RR,Gaines SD,Paris CB

    更新日期:2010-10-26 00:00:00

  • DNA replication origins in the Schizosaccharomyces pombe genome.

    abstract::Origins of DNA replication in Schizosaccharomyces pombe lack a specific consensus sequence analogous to the Saccharomyces cerevisiae autonomously replicating sequence (ARS) consensus, raising the question of how they are recognized by the replication machinery. Because all well characterized S. pombe origins are locat...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0408811102

    authors: Dai J,Chuang RY,Kelly TJ

    更新日期:2005-01-11 00:00:00

  • Computational design of orthogonal membrane receptor-effector switches for rewiring signaling pathways.

    abstract::Membrane receptors regulate numerous intracellular functions. However, the molecular underpinnings remain poorly understood because most receptors initiate multiple signaling pathways through distinct interaction interfaces that are structurally uncharacterized. We present an integrated computational and experimental ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1718489115

    authors: Young M,Dahoun T,Sokrat B,Arber C,Chen KM,Bouvier M,Barth P

    更新日期:2018-07-03 00:00:00

  • Ontogeny and phylogeny of language.

    abstract::How did language evolve? A popular approach points to the similarities between the ontogeny and phylogeny of language. Young children's language and nonhuman primates' signing both appear formulaic with limited syntactic combinations, thereby suggesting a degree of continuity in their cognitive abilities. To evaluate ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1216803110

    authors: Yang C

    更新日期:2013-04-16 00:00:00

  • HLA class II allelic variation and susceptibility to pemphigus vulgaris.

    abstract::The autoimmune dermatologic disease pemphigus vulgaris (PV) is associated with the HLA serotypes DR4 and DRw6. Susceptibility to PV could be conferred either by sequences shared between the DR4 and DRw6 haplotypes or by different sequences in these haplotypes. We have examined the distribution of DR and DQ beta-chain ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.10.3504

    authors: Scharf SJ,Friedmann A,Brautbar C,Szafer F,Steinman L,Horn G,Gyllensten U,Erlich HA

    更新日期:1988-05-01 00:00:00

  • The role of platelet adhesion receptor GPIbalpha far exceeds that of its main ligand, von Willebrand factor, in arterial thrombosis.

    abstract::GPIbalpha binding to von Willebrand factor (VWF) exposed at a site of vascular injury is thought to be the first step in the formation of a hemostatic plug. However, our previous studies in VWF-deficient mice demonstrated delayed but not absent arterial thrombus formation, suggesting that, under these conditions, GPIb...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0608207103

    authors: Bergmeier W,Piffath CL,Goerge T,Cifuni SM,Ruggeri ZM,Ware J,Wagner DD

    更新日期:2006-11-07 00:00:00

  • Molecular cloning and derived primary structure of cobra venom factor.

    abstract::Cobra venom factor (CVF) is the complement-activating protein in cobra venom. Like C3b, CVF forms with factor B and factor D in human and mammalian serum the bimolecular C3/C5 convertase. This functional similarity of CVF and C3 correlates with many structural similarities, which led to the suggestion that CVF is evol...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.26.12775

    authors: Fritzinger DC,Bredehorst R,Vogel CW

    更新日期:1994-12-20 00:00:00

  • The importance of the Montreal Protocol in protecting climate.

    abstract::The 1987 Montreal Protocol on Substances that Deplete the Ozone Layer is a landmark agreement that has successfully reduced the global production, consumption, and emissions of ozone-depleting substances (ODSs). ODSs are also greenhouse gases that contribute to the radiative forcing of climate change. Using historical...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0610328104

    authors: Velders GJ,Andersen SO,Daniel JS,Fahey DW,McFarland M

    更新日期:2007-03-20 00:00:00

  • Distinct gating mechanism of SOC channel involving STIM-Orai coupling and an intramolecular interaction of Orai in Caenorhabditis elegans.

    abstract::Store-operated calcium entry (SOCE), an important mechanism of Ca2+ signaling in a wide range of cell types, is mediated by stromal interaction molecule (STIM), which senses the depletion of endoplasmic reticulum Ca2+ stores and binds and activates Orai channels in the plasma membrane. This inside-out mechanism of Ca2...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1714986115

    authors: Kim KM,Wijerathne T,Hur JH,Kang UJ,Kim IH,Kweon YC,Lee AR,Jeong SJ,Lee SK,Lee YY,Sim BW,Lee JH,Baig C,Kim SU,Chang KT,Lee KP,Park CY

    更新日期:2018-05-15 00:00:00