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  • 1
    Online Resource
    Online Resource
    The Effect of Keystone Individuals on Collective Outcomes Can Be Mediated through Interactions or Behavioral Persistence
    University of Chicago Press ; 2016
    In:  The American Naturalist Vol. 188, No. 2 ( 2016-08), p. 240-252
    Details
    In: The American Naturalist, University of Chicago Press, Vol. 188, No. 2 ( 2016-08), p. 240-252
    Type of Medium: Online Resource
    ISSN: 0003-0147 , 1537-5323
    URL: Article
    DOI: 10.1086/687235
    RVK:
    WA 15000
    Language: English
    Publisher: University of Chicago Press
    Publication Date: 2016
    detail.hit.zdb_id: 1473832-6
    detail.hit.zdb_id: 207092-3
    detail.hit.zdb_id: 2669910-2
    SSG: 12
    SSG: 25
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  • 2
    Online Resource
    Online Resource
    The effect of individual variation on the structure and function of interaction networks in harvester ants
    The Royal Society ; 2011
    In:  Journal of The Royal Society Interface Vol. 8, No. 64 ( 2011-11-07), p. 1562-1573
    Details
    In: Journal of The Royal Society Interface, The Royal Society, Vol. 8, No. 64 ( 2011-11-07), p. 1562-1573
    Abstract: Social insects exhibit coordinated behaviour without central control. Local interactions among individuals determine their behaviour and regulate the activity of the colony. Harvester ants are recruited for outside work, using networks of brief antennal contacts, in the nest chamber closest to the nest exit: the entrance chamber. Here, we combine empirical observations, image analysis and computer simulations to investigate the structure and function of the interaction network in the entrance chamber. Ant interactions were distributed heterogeneously in the chamber, with an interaction hot-spot at the entrance leading further into the nest. The distribution of the total interactions per ant followed a right-skewed distribution, indicating the presence of highly connected individuals. Numbers of ant encounters observed positively correlated with the duration of observation. Individuals varied in interaction frequency, even after accounting for the duration of observation. An ant's interaction frequency was explained by its path shape and location within the entrance chamber. Computer simulations demonstrate that variation among individuals in connectivity accelerates information flow to an extent equivalent to an increase in the total number of interactions. Individual variation in connectivity, arising from variation among ants in location and spatial behaviour, creates interaction centres, which may expedite information flow.
    Type of Medium: Online Resource
    ISSN: 1742-5689 , 1742-5662
    URL: Article
    DOI: 10.1098/rsif.2011.0059
    Language: English
    Publisher: The Royal Society
    Publication Date: 2011
    detail.hit.zdb_id: 2156283-0
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  • 3
    Online Resource
    Online Resource
    Correction
    University of Chicago Press ; 2021
    In:  The American Naturalist Vol. 197, No. 3 ( 2021-03-01), p. 390-391
    Details
    In: The American Naturalist, University of Chicago Press, Vol. 197, No. 3 ( 2021-03-01), p. 390-391
    Type of Medium: Online Resource
    ISSN: 0003-0147 , 1537-5323
    URL: Article
    DOI: 10.1086/712423
    RVK:
    WA 15000
    Language: English
    Publisher: University of Chicago Press
    Publication Date: 2021
    detail.hit.zdb_id: 1473832-6
    detail.hit.zdb_id: 207092-3
    detail.hit.zdb_id: 2669910-2
    SSG: 12
    SSG: 25
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  • 4
    Online Resource
    Online Resource
    Counting the Ways to Decode Dynamic Signals
    American Association for the Advancement of Science (AAAS) ; 2014
    In:  Science Vol. 343, No. 6177 ( 2014-03-21), p. 1326-1327
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 343, No. 6177 ( 2014-03-21), p. 1326-1327
    Abstract: The role of biological signaling networks is to reliably transmit specific information about the extracellular environment to multiple intracellular downstream effectors, allowing the cell to adjust its physiological state to changing conditions. One mechanism that cells use to enhance the performance of signaling networks is the temporal modulation, or dynamics, of the transmitted signals ( 1 – 4 ). The key role that modulating temporal activity of the signal plays in information transmission makes signaling dynamics an attractive target for therapeutic approaches that interfere with the transmission of specific types of information through the network ( 5 ). The diversity of temporal modulation strategies seen in various signaling networks suggests that there is no single optimal strategy for making use of dynamic information. Therefore, to uncover the benefits of temporal modulation strategies, it is important to understand how the suitability of each type of signaling dynamics is matched to the nature of the particular information that is being transmitted. Some types of information are transmitted through frequency-modulated signals, whereas other types are transmitted through modulation of signal amplitude or duration. Work by Cai et al. ( 6 ) on page 1329 of this issue identifies how the social amoeba Dictyostelium discoideum decodes a temporally dynamic signal to coordinate its development in response to starvation.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1252247
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2014
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
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  • 5
    Online Resource
    Online Resource
    Loci specific epigenetic drug sensitivity
    Oxford University Press (OUP) ; 2020
    In:  Nucleic Acids Research Vol. 48, No. 9 ( 2020-05-21), p. 4797-4810
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 48, No. 9 ( 2020-05-21), p. 4797-4810
    Abstract: Therapeutic targeting of epigenetic modulators offers a novel approach to the treatment of multiple diseases. The cellular consequences of chemical compounds that target epigenetic regulators (epi-drugs) are complex. Epi-drugs affect global cellular phenotypes and cause local changes to gene expression due to alteration of a gene chromatin environment. Despite increasing use in the clinic, the mechanisms responsible for cellular changes are unclear. Specifically, to what degree the effects are a result of cell-wide changes or disease related locus specific effects is unknown. Here we developed a platform to systematically and simultaneously investigate the sensitivity of epi-drugs at hundreds of genomic locations by combining DNA barcoding, unique split-pool encoding, and single cell expression measurements. Internal controls are used to isolate locus specific effects separately from any global consequences these drugs have. Using this platform we discovered wide-spread loci specific sensitivities to epi-drugs for three distinct epi-drugs that target histone deacetylase, DNA methylation and bromodomain proteins. By leveraging ENCODE data on chromatin modification, we identified features of chromatin environments that are most likely to be affected by epi-drugs. The measurements of loci specific epi-drugs sensitivities will pave the way to the development of targeted therapy for personalized medicine.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkaa210
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1472175-2
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  • 6
    Online Resource
    Online Resource
    Author response
    eLife Sciences Publications, Ltd ; 2015
    In:  eLife Vol. 4 ( 2015-10-08)
    Details
    In: eLife, eLife Sciences Publications, Ltd, Vol. 4 ( 2015-10-08)
    Abstract: The human body is made up of many different types of cell that are each specialized to perform particular roles. Although each cell type has the same set of genes, the level of activity (or “expression”) of these genes varies between each type. Additionally, gene expression in cells of the same type can vary due to randomness in the regulation of genes. Although variation in gene expression between cells can allow populations of cells to adapt to a changing environment, variability can also cause problems when many different cells need to work together. A system called “paracrine signaling” allows cells to communicate with each other by releasing signaling molecules that bind to and activate surrounding cells. The distance that this molecule travels, or the “paracrine communication distance”, determines how many surrounding cells each cell can communicate with to coordinate their responses. However, it is not clear what impact paracrine signaling has on the variability between cells, or what limitations there are on the size of the paracrine communication distance. Cells that are damaged during wounding immediately release a molecule called ATP, which acts as a danger signal to activate the wound healing process in the surrounding cells. The release of ATP from wounded cells forms a spatial gradient in the surrounding healthy cells and stimulates the release of molecules called growth factors that are required for the healing process. Here, Handly et al. developed a new device to study the responses of human cells to a wound and used it in combination with a computational model to measure the impact of paracrine communication on these responses. The experiments show that paracrine signaling by the growth factor EGF reduces the variability in the responses of cells to the ATP signal. However, this reduction is limited by the size of the paracrine communication distance. Paracrine communication distances that are too small or too large either do not provide adequate reduction in variability or result in “over-averaging”. Handly et al.’s findings show that there is an optimal level of paracrine signaling during wounding that helps to coordinate the response in nearby cells without inappropriately over-averaging the signal.
    Type of Medium: Online Resource
    ISSN: 2050-084X
    URL: Article
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    DOI: 10.7554/eLife.09652
    DOI: 10.7554/eLife.09652.001
    DOI: 10.7554/eLife.09652.002
    DOI: 10.7554/eLife.09652.003
    DOI: 10.7554/eLife.09652.004
    DOI: 10.7554/eLife.09652.005
    DOI: 10.7554/eLife.09652.006
    DOI: 10.7554/eLife.09652.007
    DOI: 10.7554/eLife.09652.008
    DOI: 10.7554/eLife.09652.009
    DOI: 10.7554/eLife.09652.010
    DOI: 10.7554/eLife.09652.011
    DOI: 10.7554/eLife.09652.012
    DOI: 10.7554/eLife.09652.013
    DOI: 10.7554/eLife.09652.014
    DOI: 10.7554/eLife.09652.015
    DOI: 10.7554/eLife.09652.016
    DOI: 10.7554/eLife.09652.017
    DOI: 10.7554/eLife.09652.018
    DOI: 10.7554/eLife.09652.019
    DOI: 10.7554/eLife.09652.020
    DOI: 10.7554/eLife.09652.021
    Language: English
    Publisher: eLife Sciences Publications, Ltd
    Publication Date: 2015
    detail.hit.zdb_id: 2687154-3
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  • 7
    Online Resource
    Online Resource
    Accurate information transmission through dynamic biochemical signaling networks
    American Association for the Advancement of Science (AAAS) ; 2014
    In:  Science Vol. 346, No. 6215 ( 2014-12-12), p. 1370-1373
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 346, No. 6215 ( 2014-12-12), p. 1370-1373
    Abstract: Cells need to process information about their external environment reliably to survive. However, variation, or noise, in biochemical reactions, or in the states of individual cells, make it hard for a cell to detect concentration, rather than just the presence or absence of an activating ligand. Selimkhanov et al. show that cellular signaling circuits get around this problem by continually monitoring signals over time. Such dynamic responses in cultured human cells more effectively distinguish signals from noise and thus avoid loss of information transmitted to the cell from external signals. Science , this issue p. 1370
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1254933
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2014
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
    SSG: 11
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  • 8
    Online Resource
    Online Resource
    Distinct cellular states determine calcium signaling response
    EMBO ; 2016
    In:  Molecular Systems Biology Vol. 12, No. 12 ( 2016-12)
    Details
    In: Molecular Systems Biology, EMBO, Vol. 12, No. 12 ( 2016-12)
    Abstract: image Single‐cell measurements of calcium responses to ATP , in combination with analyses of the full distribution of kinetic parameters, reveal the existence of three major distinct cellular states within the population. Calcium signaling response to ATP is used as a model to analyze whether distinct cellular response states coexist. Single‐cell parameter fitting of a differential equations model of calcium response to ATP identifies a unique kinetic signature for each single cell. Cells can be classified into three distinct cell states. Each of the three states has a distinct feedback motif that connects calcium concentration to IP 3R activity.
    Type of Medium: Online Resource
    ISSN: 1744-4292 , 1744-4292
    URL: Article
    DOI: 10.15252/msb.20167137
    Language: English
    Publisher: EMBO
    Publication Date: 2016
    detail.hit.zdb_id: 2193510-5
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  • 9
    Online Resource
    Online Resource
    Quantifying the phenotypic information in mRNA abundance
    EMBO ; 2022
    In:  Molecular Systems Biology Vol. 18, No. 8 ( 2022-08)
    Details
    In: Molecular Systems Biology, EMBO, Vol. 18, No. 8 ( 2022-08)
    Type of Medium: Online Resource
    ISSN: 1744-4292 , 1744-4292
    URL: Article
    DOI: 10.15252/msb.202211001
    Language: English
    Publisher: EMBO
    Publication Date: 2022
    detail.hit.zdb_id: 2193510-5
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  • 10
    Online Resource
    Online Resource
    Identifying chromatin features that regulate gene expression distribution
    Springer Science and Business Media LLC ; 2020
    In:  Scientific Reports Vol. 10, No. 1 ( 2020-11-25)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2020-11-25)
    Abstract: Gene expression variability, differences in the number of mRNA per cell across a population of cells, is ubiquitous across diverse organisms with broad impacts on cellular phenotypes. The role of chromatin in regulating average gene expression has been extensively studied. However, what aspects of the chromatin contribute to gene expression variability is still underexplored. Here we addressed this problem by leveraging chromatin diversity and using a systematic investigation of randomly integrated expression reporters to identify what aspects of chromatin microenvironment contribute to gene expression variability. Using DNA barcoding and split-pool decoding, we created a large library of isogenic reporter clones and identified reporter integration sites in a massive and parallel manner. By mapping our measurements of reporter expression at different genomic loci with multiple epigenetic profiles including the enrichment of transcription factors and the distance to different chromatin states, we identified new factors that impact the regulation of gene expression distributions.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-020-77638-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2615211-3
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