Temporal transitions in post-mitotic neurons throughout the C. elegans nervous system [ChIP-seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE181288 | GEO | 2021/10/25
REPOSITORIES: GEO
Similar Datasets
Project description:The nervous system of animals is functional at early postembryonic stages but undergoes extensive anatomical and functional changes throughout postembryonic development to eventually form a fully mature nervous system at adulthood. The molecular changes in post-mitotic neurons across post-embryonic development and the genetic programs that control these temporal transitions are not well understood. Using the model organism C. elegans, we comprehensively characterized the distinct functional states (locomotor behavior) and corresponding distinct molecular states (transcriptome) of the post-mitotic nervous system across temporal transitions from early post-embryonic periods to adulthood. We observed pervasive changes in gene expression, many of which controlled by the conserved heterochronic miRNA lin-4/mir-125 and its target, the transcription factor lin-14. The functional relevance of these molecular, lin-4/lin-14 controlled transitions are exemplified by a novel neuropeptide, nlp-45, which confers temporally controlled anti-exploratory activities. Our studies provide new insights into a perhaps generalizable regulatory mechanism that alters neuron-type specific gene batteries to modulate distinct behaviors states, and also provides a rich atlas of post-embryonic molecular changes to uncover additional regulatory mechanisms.
2021-10-25 | GSE158274 | GEO
Project description:Edelstein1996 - EPSP ACh species
Model of a nicotinic Excitatory Post-Synaptic Potential in a Torpedo electric organ. Acetylcholine is represented explicitely as a molecular species.
This model has initially been encoded using StochSim.
This model is described in the article:
A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions.
Edelstein SJ, Schaad O, Henry E, Bertrand D, Changeux JP.
Biol. Cybern. 1996 Nov; 75(5):361-79
Abstract:
Nicotinic acetylcholine receptors are transmembrane oligomeric proteins that mediate interconversions between open and closed channel states under the control of neurotransmitters. Fast in vitro chemical kinetics and in vivo electrophysiological recordings are consistent with the following multi-step scheme. Upon binding of agonists, receptor molecules in the closed but activatable resting state (the Basal state, B) undergo rapid transitions to states of higher affinities with either open channels (the Active state, A) or closed channels (the initial Inactivatable and fully Desensitized states, I and D). In order to represent the functional properties of such receptors, we have developed a kinetic model that links conformational interconversion rates to agonist binding and extends the general principles of the Monod-Wyman-Changeux model of allosteric transitions. The crucial assumption is that the linkage is controlled by the position of the interconversion transition states on a hypothetical linear reaction coordinate. Application of the model to the peripheral nicotine acetylcholine receptor (nAChR) accounts for the main properties of ligand-gating, including single-channel events, and several new relationships are predicted. Kinetic simulations reveal errors inherent in using the dose-response analysis, but justify its application under defined conditions. The model predicts that (in order to overcome the intrinsic stability of the B state and to produce the appropriate cooperativity) channel activation is driven by an A state with a Kd in the 50 nM range, hence some 140-fold stronger than the apparent affinity of the open state deduced previously. According to the model, recovery from the desensitized states may occur via rapid transit through the A state with minimal channel opening, thus without necessarily undergoing a distinct recovery pathway, as assumed in the standard 'cycle' model. Transitions to the desensitized states by low concentration 'pre-pulses' are predicted to occur without significant
channel opening, but equilibrium values of IC50 can be obtained only with long pre-pulse times. Predictions are also made concerning allosteric effectors and their possible role in coincidence detection. In terms of future developments, the analysis presented here provides a physical basis for constructing more biologically realistic models of synaptic modulation that may be applied to artificial neural networks.
This model is hosted on BioModels Database
and identified by: BIOMD0000000002
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
2024-09-02 | BIOMD0000000002 | BioModels
Project description:Temporal transitions in post-mitotic neurons throughout the C. elegans nervous system
| PRJNA664707 | ENA
Project description:Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem cell states. The two states that bookend the pluripotency continuum, naïve and primed, are well characterized, but our understanding of the intermediate states and the transitions between them remain incomplete. To address this gap in knowledge, using a previously validated system to induce naive mouse embryonic stem cells (ESCs) to post-implantation pre-grastrulating epiblast-like cells (EpiLCs), we generated comprehensive high-temporal-resolution maps of the proteome, phosphoproteome, transcriptome, and epigenome of ESCs transitioning from naïve to primed pluripotency. Our data provide a comprehensive molecular description of the phased progression of pluripotency and a foundation for investigating mechanisms that regulate pluripotent state transitions.
2019-04-04 | GSE117896 | GEO
Project description:Dutta-Roy2015 - Opening of the multiple AMPA
receptor conductance states
This model is described in the article:
Ligand-dependent opening of
the multiple AMPA receptor conductance States: a concerted
model.
Dutta-Roy R, Rosenmund C, Edelstein
SJ, Le Novère N.
PLoS ONE 2015; 10(1): e0116616
Abstract:
Modulation of the properties of AMPA receptors at the
post-synaptic membrane is one of the main suggested mechanisms
underlying fast synaptic transmission in the central nervous
system of vertebrates. Electrophysiological recordings of
single channels stimulated with agonists showed that both
recombinant and native AMPA receptors visit multiple
conductance states in an agonist concentration dependent
manner. We propose an allosteric model of the multiple
conductance states based on concerted conformational
transitions of the four subunits, as an iris diaphragm. Our
model predicts that the thermodynamic behaviour of the
conductance states upon full and partial agonist stimulations
can be described with increased affinity of receptors as they
progress to higher conductance states. The model also predicts
the existence of AMPA receptors in non-liganded conductive
substates. However, the probability of spontaneous openings
decreases with increasing conductances. Finally, we predict
that the large conductance states are stabilized within the
rise phase of a whole-cell EPSC in glutamatergic hippocampal
neurons. Our model provides a mechanistic link between ligand
concentration and conductance states that can explain
thermodynamic and kinetic features of AMPA receptor gating.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000569.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000569 | BioModels
Project description:Pdgfra+ oligodendrocyte precursor cells (OPCs) arise in distinct specification waves during embryo- genesis in the central nervous system (CNS). It is unclear whether there is a correlation between these waves and different oligodendrocyte (OL) states at adult stages. Here, we present bulk and single-cell transcriptomics resources providing insights on how transitions between these states occur. We found that post-natal OPCs from brain and spinal cord present similar transcriptional signatures. Moreover, post-natal OPC progeny of E13.5 Pdgfra+ cells present electrophysiological and transcriptional profiles similar to OPCs derived from subsequent specification waves, indicating that Pdgfra+ pre- OPCs rewire their transcriptional network during development. Single-cell RNA-seq and lineage tracing indicates that a subset of E13.5 Pdgfra+ cells originates cells of the pericyte lineage. Thus, our results indicate that embryonic Pdgfra+ cells in the CNS give rise to distinct post-natal cell lineages, including OPCs with convergent transcriptional profiles in different CNS regions.
2018-07-21 | GSE95093 | GEO
Project description:Temporal transitions in post-mitotic neurons throughout the C. elegans nervous system [ChIP-seq]
| PRJNA751424 | ENA
Project description:Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem-cell states. The two states that bookend the pluripotency continuum, naïve and primed, are well characterized, but our understanding of the intermediate states and transitions between them remain incomplete. Here, we dissect the dynamics of pluripotent state transitions underlying pre- to post-implantation epiblast differentiation. Through comprehensive mapping of the proteome, phosphoproteome, transcriptome, and epigenome of embryonic stem cells transitioning from naïve to primed pluripotency, we find that rapid, acute, and widespread changes to the phosphoproteome precede ordered changes to the epigenome, transcriptome, and proteome. Reconstruction of kinase-substrate networks reveals signaling cascades, dynamics, and crosstalk. Distinct waves of global proteomic changes mark discrete phases of pluripotency, with cell state-specific surface markers tracking pluripotent state transitions. Our data provide new insights into the multi-layered control of the phased progression of pluripotency and a foundation for modeling mechanisms regulating pluripotent state transitions (www.stemcellatlasorg).
2019-05-07 | PXD010621 | Pride
Project description:Edelstein1996 - EPSP ACh event
Model of a nicotinic Excitatory Post-Synaptic Potential in a
Torpedo electric organ. Acetylcholine is not represented
explicitely, but by an event that changes the constants of
transition from unliganded to liganded.
This model has initially been encoded using StochSim.
This model is described in the article:
A kinetic mechanism for
nicotinic acetylcholine receptors based on multiple allosteric
transitions.
Edelstein SJ, Schaad O, Henry E,
Bertrand D, Changeux JP.
Biol Cybern 1996 Nov; 75(5):
361-379
Abstract:
Nicotinic acetylcholine receptors are transmembrane
oligomeric proteins that mediate interconversions between open
and closed channel states under the control of
neurotransmitters. Fast in vitro chemical kinetics and in vivo
electrophysiological recordings are consistent with the
following multi-step scheme. Upon binding of agonists, receptor
molecules in the closed but activatable resting state (the
Basal state, B) undergo rapid transitions to states of higher
affinities with either open channels (the Active state, A) or
closed channels (the initial Inactivatable and fully
Desensitized states, I and D). In order to represent the
functional properties of such receptors, we have developed a
kinetic model that links conformational interconversion rates
to agonist binding and extends the general principles of the
Monod-Wyman-Changeux model of allosteric transitions. The
crucial assumption is that the linkage is controlled by the
position of the interconversion transition states on a
hypothetical linear reaction coordinate. Application of the
model to the peripheral nicotine acetylcholine receptor (nAChR)
accounts for the main properties of ligand-gating, including
single-channel events, and several new relationships are
predicted. Kinetic simulations reveal errors inherent in using
the dose-response analysis, but justify its application under
defined conditions. The model predicts that (in order to
overcome the intrinsic stability of the B state and to produce
the appropriate cooperativity) channel activation is driven by
an A state with a Kd in the 50 nM range, hence some 140-fold
stronger than the apparent affinity of the open state deduced
previously. According to the model, recovery from the
desensitized states may occur via rapid transit through the A
state with minimal channel opening, thus without necessarily
undergoing a distinct recovery pathway, as assumed in the
standard 'cycle' model. Transitions to the desensitized states
by low concentration 'pre-pulses' are predicted to occur
without significant channel opening, but equilibrium values of
IC50 can be obtained only with long pre-pulse times.
Predictions are also made concerning allosteric effectors and
their possible role in coincidence detection. In terms of
future developments, the analysis presented here provides a
physical basis for constructing more biologically realistic
models of synaptic modulation that may be applied to artificial
neural networks.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000001.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000001 | BioModels
Project description:The developmental origins of health and adult disease (DOHaD) hypothesis states that exposure to various environmental stressors early in life can elicit changes to the genome and epigenome thereby resulting in an increased susceptibility of a disease state during adulthood. Atrazine, a common herbicide used throughout the Midwestern United States for control of weeds on various crops frequently contaminates potable water supplies and is a suspected endocrine disrupting chemical. Studies suggest atrazine elicits reproductive dysfunction through the hypothalamus-pituitary-gonadal (HPG) axis. In previous studies, zebrafish were exposed to 0.3, 3, or 30 parts per billion (ppb; ug/L) atrazine through embryogenesis, rinsed, and allowed to mature to adulthood. A decrease in spawning was observed in adults with an embryonic exposure. In addition, adult females had an increase in progesterone and ovarian follicular atresia, alterations in levels of a serotonin metabolite and serotonin turnover in brain tissue, and transcriptome alterations in brain and ovarian tissue supporting neuroendocrine alterations from an embryonic atrazine exposure were reported. Furthermore, offspring of the exposed population exhibited morphological alterations. As reproductive dysfunction may also be influenced by males, this study assessed transcriptomic profiles of brain and testes, morphology, histology, and hormone levels in adult males exposed to atrazine during embryogenesis. Transcriptomic profiles of adult male brain tissue revealed alterations in genes associated with cell to cell signaling and interaction of neurotransmission, cell morphology, cellular assembly and organization of neurites, cellular function and maintenance of neuritogenesis and synaptogenesis, and molecular transport of hormones. In addition, the transcriptomic profiles of adult male testes tissue demonstrated alterations in genes associated with lipid metabolism, molecular transport of steroids, small molecule biochemistry of lipids, and cell morphology. The embryonic atrazine exposure resulted in no alterations in body or testes weight, gonadosomatic index, testes histology, or levels of 11-ketotestosterone or testosterone in adult male zebrafish. Thus, although the transcriptomics data indicate later-in-life alterations on the neuroendocrine system of adult males exposed to atrazine during embryogenesis, analysis of additional endpoints is needed to determine functional impairments. We treated zebrafish embryos from approximately 1 hour post fertilization through 72 hours post fertilization (embryogenesis) to 0, 0.3, 3, or 30 parts per billion (ppb) atrazine. Following the 72 hour exposure period, larave were rinsed and allowed to mature under normal conditions until adulthood (5-6 months post fertilization). At this time, zebrafish were bred weekly for three weeks in order to initiate breeding cycles. Following this peroid, gonadal tissue was disseceted and processed for transcriptomic analysis.
2016-07-01 | E-GEOD-72243 | biostudies-arrayexpress