A coherent framework for multiresolution analysis of biological networks with "memory": Ras pathway, cell cycle, and immune system.

Abstract:

:Various biological processes exhibit characteristics that vary dramatically in response to different input conditions or changes in the history of the process itself. One of the examples studied here, the Ras-PKC-mitogen-activated protein kinase (MAPK) bistable pathway, follows two distinct dynamics (modes) depending on duration and strength of EGF stimulus. Similar examples are found in the behavior of the cell cycle and the immune system. A classification methodology, based on time-frequency analysis, was developed and tested on these systems to understand global behavior of biological processes. Contrary to most traditionally used statistical and spectral methods, our approach captures complex functional relations between parts of the systems in a simple way. The resulting algorithms are capable of analyzing and classifying sets of time-series data obtained from in vivo or in vitro experiments, or in silico simulation of biological processes. The method was found to be considerably stable under stochastic noise perturbation and, therefore, suitable for the analysis of real experimental data.

authors

Barbano PE,Spivak M,Feng J,Antoniotti M,Mishra B

doi

10.1073/pnas.0500554102

keywords:

subject

Has Abstract

pub_date

2005-05-03 00:00:00

pages

6245-50

issue

18

eissn

0027-8424

issn

1091-6490

pii

0500554102

journal_volume

102

pub_type

杂志文章
  • Heterogeneity in the development of the vertebra.

    abstract::Vertebrae are derived from the sclerotomal moities of the somites. Sclerotomal cells migrate ventrally to surround the notochord, where they form the vertebral body, and dorsolaterally to form the neural arch, which is dorsally closed by the spinous process. Precursor cells of the spinous process as well as superficia...

    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.91.22.10435

    authors: Monsoro-Burq AH,Bontoux M,Teillet MA,Le Douarin NM

    更新日期:1994-10-25 00:00:00

  • The induced prostaglandin E2 pathway is a key regulator of the respiratory response to infection and hypoxia in neonates.

    abstract::Infection during the neonatal period commonly induces apnea episodes, and the proinflammatory cytokine IL-1beta may serve as a critical mediator between these events. To determine the mechanism by which IL-1beta depresses respiration, we examined a prostaglandin E(2) (PGE(2))-dependent pathway in newborn mice and huma...

    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.0611468104

    authors: Hofstetter AO,Saha S,Siljehav V,Jakobsson PJ,Herlenius E

    更新日期:2007-06-05 00:00:00

  • Atlantic hurricane surge response to geoengineering.

    abstract::Devastating floods due to Atlantic hurricanes are relatively rare events. However, the frequency of the most intense storms is likely to increase with rises in sea surface temperatures. Geoengineering by stratospheric sulfate aerosol injection cools the tropics relative to the polar regions, including the hurricane Ma...

    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.1510530112

    authors: Moore JC,Grinsted A,Guo X,Yu X,Jevrejeva S,Rinke A,Cui X,Kravitz B,Lenton A,Watanabe S,Ji D

    更新日期:2015-11-10 00:00:00

  • Molecular forms of the putative enkephalin precursor BAM-12P in bovine adrenal, pituitary, and hypothalamus.

    abstract::A highly specific radioimmunoassay for one of the putative adrenomedullary [Met]enkephalin precursors, BAM-12P (Tyr-Gly-Gly-Phe-Met-Arg-Arg-Val-Gly-Arg-Pro-Glu-OH), has been developed. The BAM-12P antibodies recognize the COOH-terminal fragment of the peptide from Arg7 to Glu12 and do not crossreact with [Met5]- or [L...

    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.79.6.2023

    authors: Baird A,Ling N,Böhlen P,Benoit R,Klepper R,Guillemin R

    更新日期:1982-03-01 00:00:00

  • Isolation and characterization of three endosomal fractions from the liver of estradiol-treated rats.

    abstract::Three distinct endosomal fractions were isolated in high purity from livers of estradiol-treated rats. Each fraction had characteristic physical and ultrastructural properties, but the lipid composition and major proteins of their membranes were similar and differed from those derived from the Golgi apparatus. Injecte...

    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.84.19.6785

    authors: Belcher JD,Hamilton RL,Brady SE,Hornick CA,Jaeckle S,Schneider WJ,Havel RJ

    更新日期:1987-10-01 00:00:00

  • Kinetic isotope effects in Ras-catalyzed GTP hydrolysis: evidence for a loose transition state.

    abstract::A remote labeling method has been developed to determine (18)O kinetic isotope effects (KIEs) in Ras-catalyzed GTP hydrolysis. Substrate mixtures consist of (13)C-depleted GTP and [(18)O,(13)C]GTP that contains (18)O at phosphoryl positions of mechanistic interest and (13)C at all carbon positions of the guanosine moi...

    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.0401675101

    authors: Du X,Black GE,Lecchi P,Abramson FP,Sprang SR

    更新日期:2004-06-15 00:00:00

  • Expression cloning of rat renal Na+/SO4(2-) cotransport.

    abstract::Injection of rat kidney cortex mRNA into Xenopus laevis oocytes leads to a stimulation of Na(+)-dependent SO4(2-) uptake. Based on this information, we have isolated from a corresponding library a cDNA (NaSi-1) that is most likely related to a Na+/SO4(2-) cotransport system. NaSi-1 cRNA leads in a time- and dose-depen...

    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.90.17.8073

    authors: Markovich D,Forgo J,Stange G,Biber J,Murer H

    更新日期:1993-09-01 00:00:00

  • Murine Ly-6 multigene family is located on chromosome 15.

    abstract::Murine Ly-6-encoded molecules play an important role in the antigen-independent activation of lymphocytes. We have described the cloning of a cDNA encoding the protein component of an Ly-6 molecule. Hybridization studies indicated that this cDNA identified multiple DNA fragments on Southern blots. The banding pattern ...

    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.84.6.1638

    authors: LeClair KP,Rabin M,Nesbitt MN,Pravtcheva D,Ruddle FH,Palfree RG,Bothwell A

    更新日期:1987-03-01 00:00:00

  • Phorbol ester effects on neurotransmission: interaction with neurotransmitters and calcium in smooth muscle.

    abstract::Stimulation of the phosphatidylinositol cycle by neurotransmitters generates diacylglycerol, an activator of protein kinase C, which may regulate some forms of neurotransmission. Phorbol esters, potent inflammatory and tumor-promoting compounds, also activate protein kinase C. We demonstrate potent and selective effec...

    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.82.2.604

    authors: Baraban JM,Gould RJ,Peroutka SJ,Snyder SH

    更新日期:1985-01-01 00:00:00

  • A predictive, size-dependent continuum model for dense granular flows.

    abstract::Dense granular materials display a complicated set of flow properties, which differentiate them from ordinary fluids. Despite their ubiquity, no model has been developed that captures or predicts the complexities of granular flow, posing an obstacle in industrial and geophysical applications. Here we propose a 3D cons...

    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.1219153110

    authors: Henann DL,Kamrin K

    更新日期:2013-04-23 00:00:00

  • POU domain factor Brn-3b is required for the development of a large set of retinal ganglion cells.

    abstract::The three members of the Brn-3 family of POU domain transcription factors are found in highly restricted sets of central nervous system neurons. Within the retina, these factors are present only within subsets of ganglion cells. We show here that in the developing mouse retina, Brn-3b protein is first observed in pres...

    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.93.9.3920

    authors: Gan L,Xiang M,Zhou L,Wagner DS,Klein WH,Nathans J

    更新日期:1996-04-30 00:00:00

  • Relationships between the responses of triglyceride-rich lipoproteins in blood plasma containing apolipoproteins B-48 and B-100 to a fat-containing meal in normolipidemic humans.

    abstract::The concentration of triglyceride-rich lipoproteins containing apolipoprotein (apo) B-48 (chylomicrons) and apo B-100 (very low density lipoproteins) was measured in blood plasma of healthy young men after an ordinary meal containing one-third of daily energy and fat. Plasma obtained in the postabsorptive state and at...

    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.90.5.2069

    authors: Schneeman BO,Kotite L,Todd KM,Havel RJ

    更新日期:1993-03-01 00:00:00

  • Identification of transcription coactivator OCA-B-dependent genes involved in antigen-dependent B cell differentiation by cDNA array analyses.

    abstract::The tissue-specific transcriptional coactivator OCA-B is required for antigen-dependent B cell differentiation events, including germinal center formation. However, the identity of OCA-B target genes involved in this process is unknown. This study has used large-scale cDNA arrays to monitor changes in gene expression ...

    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.1033108100

    authors: Kim U,Siegel R,Ren X,Gunther CS,Gaasterland T,Roeder RG

    更新日期:2003-07-22 00:00:00

  • Freezing immunoglobulins to see them move.

    abstract::The issue of protein dynamics and its implications in the biological function of proteins are arousing greater and greater interest in different fields of molecular biology. In cryo-electron tomography experiments one may take several snapshots of a given biological macromolecule. In principle, a large enough collecti...

    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.0400119101

    authors: Bongini L,Fanelli D,Piazza F,De Los Rios P,Sandin S,Skoglund U

    更新日期:2004-04-27 00:00:00

  • Matrix-transmitted paratensile signaling enables myofibroblast-fibroblast cross talk in fibrosis expansion.

    abstract::While the concept of intercellular mechanical communication has been revealed, the mechanistic insights have been poorly evidenced in the context of myofibroblast-fibroblast interaction during fibrosis expansion. Here we report and systematically investigate the mechanical force-mediated myofibroblast-fibroblast cross...

    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.1910650117

    authors: Liu L,Yu H,Zhao H,Wu Z,Long Y,Zhang J,Yan X,You Z,Zhou L,Xia T,Shi Y,Xiao B,Wang Y,Huang C,Du Y

    更新日期:2020-05-19 00:00:00

  • Role of NADPH oxidase in arsenic-induced reactive oxygen species formation and cytotoxicity in myeloid leukemia cells.

    abstract::Arsenic has played a key medicinal role against a variety of ailments for several millennia, but during the past century its prominence has been displaced by modern therapeutics. Recently, attention has been drawn to arsenic by its dramatic clinical efficacy against acute promyelocytic leukemia. Although toxic reactiv...

    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.0306687101

    authors: Chou WC,Jie C,Kenedy AA,Jones RJ,Trush MA,Dang CV

    更新日期:2004-03-30 00:00:00

  • Enhancing the antitumor efficacy of a cell-surface death ligand by covalent membrane display.

    abstract::TNF superfamily death ligands are expressed on the surface of immune cells and can trigger apoptosis in susceptible cancer cells by engaging cognate death receptors. A recombinant soluble protein comprising the ectodomain of Apo2 ligand/TNF-related apoptosis-inducing ligand (Apo2L/TRAIL) has shown remarkable preclinic...

    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.1418962112

    authors: Nair PM,Flores H,Gogineni A,Marsters S,Lawrence DA,Kelley RF,Ngu H,Sagolla M,Komuves L,Bourgon R,Settleman J,Ashkenazi A

    更新日期:2015-05-05 00:00:00

  • Oxygen toxicity in a polyamine-depleted spe2 delta mutant of Saccharomyces cerevisiae.

    abstract::When a mutant of Saccharomyces cerevisiae (spe2 delta) that cannot make spermidine or spermine was incubated in a polyamine-deficient medium in oxygen, there was a rapid cessation of cell growth and associated cell death. In contrast, when the mutant cells were incubated in the polyamine-deficient medium in air or ana...

    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.90.10.4693

    authors: Balasundaram D,Tabor CW,Tabor H

    更新日期:1993-05-15 00:00:00

  • High-affinity transport of glutathione is part of a multicomponent system essential for mitochondrial function.

    abstract::Glutathione, an essential cellular antioxidant required for mitochondrial function, is not synthesized by mitochondria but is imported from the cytosol. Rat liver mitochondria have a multicomponent system that underlies the remarkable ability of mitochondria to take up and retain glutathione. At external glutathione l...

    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.87.18.7185

    authors: Mårtensson J,Lai JC,Meister A

    更新日期:1990-09-01 00:00:00

  • Public awareness, concerns, and priorities about anthropogenic impacts on marine environments.

    abstract::Numerous international bodies have advocated the development of strategies to achieve the sustainability of marine environments. Typically, such strategies are based on information from expert groups about causes of degradation and policy options to address them, but these strategies rarely take into account assessed ...

    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.1417344111

    authors: Gelcich S,Buckley P,Pinnegar JK,Chilvers J,Lorenzoni I,Terry G,Guerrero M,Castilla JC,Valdebenito A,Duarte CM

    更新日期:2014-10-21 00:00:00

  • Control of DEMETER DNA demethylase gene transcription in male and female gamete companion cells in Arabidopsis thaliana.

    abstract::The DEMETER (DME) DNA glycosylase initiates active DNA demethylation via the base-excision repair pathway and is vital for reproduction in Arabidopsis thaliana DME-mediated DNA demethylation is preferentially targeted to small, AT-rich, and nucleosome-depleted euchromatic transposable elements, influencing expression ...

    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.1620592114

    authors: Park JS,Frost JM,Park K,Ohr H,Park GT,Kim S,Eom H,Lee I,Brooks JS,Fischer RL,Choi Y

    更新日期:2017-02-21 00:00:00

  • Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins.

    abstract::Elucidating the mechanism of folding of polynucleotides depends on accurate estimates of free energy surfaces and a quantitative description of the kinetics of structure formation. Here, the kinetics of hairpin formation in single-stranded DNA are measured after a laser temperature jump. The kinetics are modeled as co...

    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.131477798

    authors: Ansari A,Kuznetsov SV,Shen Y

    更新日期:2001-07-03 00:00:00

  • Molecular heterogeneity of variant isovaleryl-CoA dehydrogenase from cultured isovaleric acidemia fibroblasts.

    abstract::Variants of isovaleryl-CoA dehydrogenase (IVDHase, EC 1.3.99.10) in 15 isovaleric acidemia fibroblast lines were analyzed using [35S]methionine labeling, immunoprecipitation with anti-rat IVDHase antiserum, and NaDodSo4/polyacrylamide gel electrophoresis. Five distinct variants of IVDHase were detected. The molecular ...

    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.82.20.7081

    authors: Ikeda Y,Keese SM,Tanaka K

    更新日期:1985-10-01 00:00:00

  • Nitrogen trifluoride global emissions estimated from updated atmospheric measurements.

    abstract::Nitrogen trifluoride (NF(3)) has potential to make a growing contribution to the Earth's radiative budget; however, our understanding of its atmospheric burden and emission rates has been limited. Based on a revision of our previous calibration and using an expanded set of atmospheric measurements together with an atm...

    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.1212346110

    authors: Arnold T,Harth CM,Mühle J,Manning AJ,Salameh PK,Kim J,Ivy DJ,Steele LP,Petrenko VV,Severinghaus JP,Baggenstos D,Weiss RF

    更新日期:2013-02-05 00:00:00

  • MicroRNA dysregulation to identify therapeutic target combinations for chronic lymphocytic leukemia.

    abstract::Loss of miR-15/16 is the most common genetic lesion in chronic lymphocytic leukemia (CLL), promoting overexpression of BCL2, which factors in leukemia pathogenesis. Indeed, an inhibitor of Bcl2, venetoclcax, is highly active in the treatment of patients with CLL. However, single-agent venetoclcax fails to eradicate mi...

    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.1708264114

    authors: Rassenti LZ,Balatti V,Ghia EM,Palamarchuk A,Tomasello L,Fadda P,Pekarsky Y,Widhopf GF 2nd,Kipps TJ,Croce CM

    更新日期:2017-10-03 00:00:00

  • Her6 regulates the neurogenetic gradient and neuronal identity in the thalamus.

    abstract::During vertebrate brain development, the onset of neuronal differentiation is under strict temporal control. In the mammalian thalamus and other brain regions, neurogenesis is regulated also in a spatially progressive manner referred to as a neurogenetic gradient, the underlying mechanism of which is unknown. Here we ...

    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.0910894106

    authors: Scholpp S,Delogu A,Gilthorpe J,Peukert D,Schindler S,Lumsden A

    更新日期:2009-11-24 00:00:00

  • Apparent dependence of interactions between cytochrome b5 and cytochrome b5 reductase upon translational diffusion in dimyristoyl lecithin liposomes.

    abstract::Dimyristoyl lecithin liposomes, containing cytochrome b5 reductase (NADH:ferricytochrome b5 oxidoreductase, EC 1.6.2.2) and varying amounts of cytochrome b5, were used to measure flavoprotein catalysis alone and catalysis requiring electron transfer between the reductase and cytochrome as a function of temperature. Wh...

    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.72.7.2658

    authors: Strittmatter P,Rogers MJ

    更新日期:1975-07-01 00:00:00

  • Functional neuroanatomical double dissociation of mnemonic and executive control processes contributing to working memory performance.

    abstract::We used event-related functional MRI to investigate the neural bases of two categories of mental processes believed to contribute to performance of an alphabetization working memory task: memory storage and memory manipulation. Our delayed-response tasks required memory for the identity and position-in-the-display of ...

    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.96.22.12959

    authors: Postle BR,Berger JS,D'Esposito M

    更新日期:1999-10-26 00:00:00

  • Human cytomegalovirus in a SCID-hu mouse: thymic epithelial cells are prominent targets of viral replication.

    abstract::Animal models of human cytomegalovirus (CMV) infections have not been available to study pathogenesis or to evaluate antiviral drugs. Severe combined immunodeficient mice implanted with human fetal tissues (SCID-hu) were found to support CMV replication and may provide a model for this species-specific virus. When con...

    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.90.1.104

    authors: Mocarski ES,Bonyhadi M,Salimi S,McCune JM,Kaneshima H

    更新日期:1993-01-01 00:00:00

  • Fermi surface nesting induced strong pairing in iron-based superconductors.

    abstract::The discovery of high-temperature superconductivity in iron pnictides raised the possibility of an unconventional superconducting mechanism in multiband materials. The observation of Fermi-surface (FS)-dependent nodeless superconducting gaps suggested that inter-FS interactions may play a crucial role in superconducti...

    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.0900469106

    authors: Terashima K,Sekiba Y,Bowen JH,Nakayama K,Kawahara T,Sato T,Richard P,Xu YM,Li LJ,Cao GH,Xu ZA,Ding H,Takahashi T

    更新日期:2009-05-05 00:00:00