Functionalization of a protosynaptic gene expression network

Conaco, Cecilia; Bassett, Danielle S.; Zhou, Hongjun; Arcila, Mary Luz; Degnan, Sandie M.; Degnan, Bernard M.; Kosik, Kenneth S.

doi:10.1073/pnas.1201890109

Cited by 65 publications

(73 citation statements)

References 42 publications

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“…But knowing whether PSD genes occur and function together in sponges would help determine when components of a proper PSD arose. In this vein, correlation analysis by Conaco et al (Conaco et al, 2012) suggested that although there is a lack of global coregulation of the entire set of PSD genes, small modules are coexpressed. But there is some circularity in this reasoning, because the same analysis suggests there is no co-regulation of epithelial genes in sponges based on the fact that the authors did not consider sponges to possess proper epithelia.…”

Section: Conducting Pathways and Effectorsmentioning

confidence: 99%

Elements of a ‘nervous system’ in sponges

Leys

2015

Journal of Experimental Biology

128

123

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Genomic and transcriptomic analyses show that sponges possess a large repertoire of genes associated with neuronal processes in other animals, but what is the evidence these are used in a coordination or sensory context in sponges? The very different phylogenetic hypotheses under discussion today suggest very different scenarios for the evolution of tissues and coordination systems in early animals. The sponge genomic 'toolkit' either reflects a simple, pre-neural system used to protect the sponge filter or represents the remnants of a more complex signalling system and sponges have lost cell types, tissues and regionalization to suit their current suspensionfeeding habit. Comparative transcriptome data can be informative but need to be assessed in the context of knowledge of sponge tissue structure and physiology. Here, I examine the elements of the sponge neural toolkit including sensory cells, conduction pathways, signalling molecules and the ionic basis of signalling. The elements described do not fit the scheme of a loss of sophistication, but seem rather to reflect an early specialization for suspension feeding, which fits with the presumed ecological framework in which the first animals evolved.

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Section: Conducting Pathways and Effectorsmentioning

confidence: 99%

Elements of a ‘nervous system’ in sponges

Leys

2015

Journal of Experimental Biology

128

123

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“…For example, γ-aminobutyric acid (GABA), glutamate and nitric oxide (NO) have all been detected in sponges and shown to regulate cell behavior (Ellwanger et al, 2007;Elliott and Leys, 2010). A recent transcriptome profiling of the sponge A. queenslandica revealed the expression of wide repertoire of components active in synapses found in the vertebrate nervous systems (Conaco et al, 2012). In the social amoeba Dictysotelium, disruption of a glutamate receptor by homologous recombination reveals a role for glutamate signaling in the suppression of cell division (Taniura et al, 2006), while GABA induces terminal differentiation of spores through a GABA B receptor (Anjard and Loomis, 2006).…”

Section: Introductionmentioning

confidence: 99%

Neurotransmitter-mediated control of neurogenesis in the adult vertebrate brain

et al. 2013

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SummaryIt was long thought that no new neurons are added to the adult brain. Similarly, neurotransmitter signaling was primarily associated with communication between differentiated neurons. Both of these ideas have been challenged, and a crosstalk between neurogenesis and neurotransmitter signaling is beginning to emerge. In this Review, we discuss neurotransmitter signaling as it functions at the intersection of stem cell research and regenerative medicine, exploring how it may regulate the formation of new functional neurons and outlining interactions with other signaling pathways. We consider evolutionary and cross-species comparative aspects, and integrate available results in the context of normal physiological versus pathological conditions. We also discuss the potential role of neurotransmitters in brain size regulation and implications for cell replacement therapies. Key words: Adult neurogenesis, Homeostasis, Neural stem cell, Neurotransmitter, Regeneration IntroductionIn the brain, signaling via neurotransmitters, small molecules released by neurons to communicate with other cells, has primarily been associated with the function rather than with the formation of neurons. However, several reports have identified roles for neurotransmitters in cell fate determination in a wide range of species both within and outside the central nervous system (CNS). A thorough discussion on the evolutionary origin of neurotransmitter signaling is outside the scope of this Review, but it is important to note that both neurotransmitters and their receptors (see Table 1) are present and functionally important in organisms without a nervous system. For example, γ-aminobutyric acid (GABA), glutamate and nitric oxide (NO) have all been detected in sponges and shown to regulate cell behavior (Ellwanger et al., 2007;Elliott and Leys, 2010). A recent transcriptome profiling of the sponge A. queenslandica revealed the expression of wide repertoire of components active in synapses found in the vertebrate nervous systems (Conaco et al., 2012). In the social amoeba Dictysotelium, disruption of a glutamate receptor by homologous recombination reveals a role for glutamate signaling in the suppression of cell division (Taniura et al., 2006), while GABA induces terminal differentiation of spores through a GABA B receptor (Anjard and Loomis, 2006). GABA and glutamate appear to play opposing roles in spore induction (Fountain, 2010) in Dictyostelium, indicating that the apparent antagonistic relationship between glutamate and GABA signaling was established prior to the evolution of synaptic communication in the CNS.Furthermore, neurotransmitters control cell proliferation during development long before the onset of neurogenesis in mammals, as exemplified by GABA signaling in the early embryo (Andäng et al., 2008). Once developmental neurogenesis is initiated, neurotransmitter signaling has an impact on several aspects of neurogenesis, including proliferation, migration and differentiation in various locations in the CNS, such as the tele...

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“…Mh, In the last decade, extensive research on complexity in networks has evidenced (among many results [1, 2]) the widespread of modular structures and the importance of quasi-independent communities in many research areas such as neuroscience [3,4], biochemistry [5] and genetics [6], just to cite a few. In particular, the modular, hierarchical architecture of cortical neural networks has nowadays been analyzed in depths [7], yet the beauty revealed by this investigation is not captured by the statistical mechanics of neural networks, nor standard ones (i.e.…”

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confidence: 99%

Retrieval Capabilities of Hierarchical Networks: From Dyson to Hopfield

Agliari¹,

Barra²,

Galluzzi³

et al. 2015

Phys. Rev. Lett.

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We consider statistical-mechanics models for spin systems built on hierarchical structures, which provide a simple example of non-mean-field framework. We show that the coupling decay with spin distance can give rise to peculiar features and phase diagrams much richer that their mean-field counterpart. In particular, we consider the Dyson model, mimicking ferromagnetism in lattices, and we prove the existence of a number of meta-stabilities, beyond the ordered state, which get stable in the thermodynamic limit. Such a feature is retained when the hierarchical structure is coupled with the Hebb rule for learning, hence mimicking the modular architecture of neurons, and gives rise to an associative network able to perform both as a serial processor as well as a parallel processor, depending crucially on the external stimuli and on the rate of interaction decay with distance; however, those emergent multitasking features reduce the network capacity with respect to the mean-field counterpart. The analysis is accomplished through statistical mechanics, graph theory, signal-to-noise technique and numerical simulations in full consistency. Our results shed light on the biological complexity shown by real networks, and suggest future directions for understanding more realistic models.PACS numbers: 07.05. Mh, In the last decade, extensive research on complexity in networks has evidenced (among many results [1, 2]) the widespread of modular structures and the importance of quasi-independent communities in many research areas such as neuroscience [3,4], biochemistry [5] and genetics [6], just to cite a few. In particular, the modular, hierarchical architecture of cortical neural networks has nowadays been analyzed in depths [7], yet the beauty revealed by this investigation is not captured by the statistical mechanics of neural networks, nor standard ones (i.e. performing serial processing) [8,9] neither multitasking ones (i.e. performing parallel processing) [10,11]. In fact, these models are intrinsically mean-field, thus lacking a proper definition of metric distance among neurons.Hierarchical structures have been proposed in the past as (relatively) simple models for ferromagnetic transitions beyond the mean-field scenario -the Dyson hierarchical model (DHM) [12]-and are currently experiencing a renewal interest for understanding glass transitions in finite dimension [13,14]. Therefore, times are finally ripe for approaching neural networks embedded in a nonmean-field architecture, and this letter summarizes our findings on associative neural networks where the Hebbian kernel is coupled with the Dyson topology.First, we start studying the DHM mixing the AmitGutfreund-Sompolinsky ansatz approach [9] (to select candidable retrievable states) with the interpolation technique (to check their thermodynamic stability) and we show that, as soon as ergodicity is broken, beyond the ferromagnetic/pure state (largely discussed in the past, see e.g., [15,16]), a number of metastable states suddenly appear and become stable in the ...

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Functionalization of a protosynaptic gene expression network

Cited by 65 publications

References 42 publications

Elements of a ‘nervous system’ in sponges

Elements of a ‘nervous system’ in sponges

Neurotransmitter-mediated control of neurogenesis in the adult vertebrate brain

Retrieval Capabilities of Hierarchical Networks: From Dyson to Hopfield

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