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      Senomic view of the cell: Senome versus Genome

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          ABSTRACT

          In the legacy of Thomas Henry Huxley, and his ‘epigenetic’ philosophy of biology, cells are proposed to represent a trinity of three memory-storing media: Senome, Epigenome, and Genome that together comprise a cell-wide informational architecture. Our current preferential focus on the Genome needs to be complemented by a similar focus on the Epigenome and a here proposed Senome, representing the sum of all the sensory experiences of the cognitive cell and its sensing apparatus. Only then will biology be in a position to embrace the whole complexity of the eukaryotic cell, understanding its true nature which allows the communicative assembly of cells in the form of sentient multicellular organisms.

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          Chromatin remodelling during development.

          Lena Ho, Gerald R Crabtree (2010)
          New methods for the genome-wide analysis of chromatin are providing insight into its roles in development and their underlying mechanisms. Current studies indicate that chromatin is dynamic, with its structure and its histone modifications undergoing global changes during transitions in development and in response to extracellular cues. In addition to DNA methylation and histone modification, ATP-dependent enzymes that remodel chromatin are important controllers of chromatin structure and assembly, and are major contributors to the dynamic nature of chromatin. Evidence is emerging that these chromatin-remodelling enzymes have instructive and programmatic roles during development. Particularly intriguing are the findings that specialized assemblies of ATP-dependent remodellers are essential for establishing and maintaining pluripotent and multipotent states in cells.
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            Ephaptic coupling of cortical neurons.

            Costas Anastassiou, Rodrigo Perin, Henry Markram … (2011)
            The electrochemical processes that underlie neural function manifest themselves in ceaseless spatiotemporal field fluctuations. However, extracellular fields feed back onto the electric potential across the neuronal membrane via ephaptic coupling, independent of synapses. The extent to which such ephaptic coupling alters the functioning of neurons under physiological conditions remains unclear. To address this question, we stimulated and recorded from rat cortical pyramidal neurons in slices with a 12-electrode setup. We found that extracellular fields induced ephaptically mediated changes in the somatic membrane potential that were less than 0.5 mV under subthreshold conditions. Despite their small size, these fields could strongly entrain action potentials, particularly for slow (<8 Hz) fluctuations of the extracellular field. Finally, we simultaneously measured from up to four patched neurons located proximally to each other. Our findings indicate that endogenous brain activity can causally affect neural function through field effects under physiological conditions.
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              The origin of membrane bioenergetics.

              Nick Lane, William F. Martin (2012)
              Harnessing energy as ion gradients across membranes is as universal as the genetic code. We leverage new insights into anaerobe metabolism to propose geochemical origins that account for the ubiquity of chemiosmotic coupling, and Na(+)/H(+) transporters in particular. Natural proton gradients acting across thin FeS walls within alkaline hydrothermal vents could drive carbon assimilation, leading to the emergence of protocells within vent pores. Protocell membranes that were initially leaky would eventually become less permeable, forcing cells dependent on natural H(+) gradients to pump Na(+) ions. Our hypothesis accounts for the Na(+)/H(+) promiscuity of bioenergetic proteins, as well as the deep divergence between bacteria and archaea. Copyright © 2012 Elsevier Inc. All rights reserved.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Commun Integr Biol
                Journal ID (iso-abbrev): Commun Integr Biol
                Journal ID (publisher-id): KCIB
                Journal ID (publisher-id): kcib20
                Title: Communicative & Integrative Biology
                Publisher: Taylor & Francis
                ISSN (Electronic): 1942-0889
                Publication date Collection: 2018
                Publication date (Electronic): 10 August 2018
                Publication date PMC-release: 10 August 2018
                Volume: 11
                Issue: 3
                Pages: 1-9
                Affiliations
                [a ]IZMB, University of Bonn , Bonn, Germany
                [b ]Paradise Valley , USA
                Author notes
                CONTACT František Baluška unb15e@ 123456uni-bonn.de IZMB, University of Bonn , Kirschellee 1, 53115 Bonn, Germany
                Author information
                http://orcid.org/0000-0001-8763-7861
                http://orcid.org/0000-0003-1661-5416
                Article
                Publisher ID: 1489184
                DOI: 10.1080/19420889.2018.1489184
                PMC ID: 6132427
                PubMed ID: 30214674
                SO-VID: e92c0789-d720-4a81-8264-cf2bf1d2f55e
                Copyright © © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 21 March 2018
                Date accepted : 11 June 2018
                Page count
                Figures: 1, References: 149, Pages: 9
                Categories
                Subject: Review

                ScienceOpen disciplines: Molecular biology
                Keywords: cell,cognition,communication,genome,epigenome,evolution
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: cell, cognition, communication, genome, epigenome, evolution

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