313 research outputs found
Transfer Functions for Protein Signal Transduction: Application to a Model of Striatal Neural Plasticity
We present a novel formulation for biochemical reaction networks in the
context of signal transduction. The model consists of input-output transfer
functions, which are derived from differential equations, using stable
equilibria. We select a set of 'source' species, which receive input signals.
Signals are transmitted to all other species in the system (the 'target'
species) with a specific delay and transmission strength. The delay is computed
as the maximal reaction time until a stable equilibrium for the target species
is reached, in the context of all other reactions in the system. The
transmission strength is the concentration change of the target species. The
computed input-output transfer functions can be stored in a matrix, fitted with
parameters, and recalled to build discrete dynamical models. By separating
reaction time and concentration we can greatly simplify the model,
circumventing typical problems of complex dynamical systems. The transfer
function transformation can be applied to mass-action kinetic models of signal
transduction. The paper shows that this approach yields significant insight,
while remaining an executable dynamical model for signal transduction. In
particular we can deconstruct the complex system into local transfer functions
between individual species. As an example, we examine modularity and signal
integration using a published model of striatal neural plasticity. The modules
that emerge correspond to a known biological distinction between
calcium-dependent and cAMP-dependent pathways. We also found that overall
interconnectedness depends on the magnitude of input, with high connectivity at
low input and less connectivity at moderate to high input. This general result,
which directly follows from the properties of individual transfer functions,
contradicts notions of ubiquitous complexity by showing input-dependent signal
transmission inactivation.Comment: 13 pages, 5 tables, 15 figure
State based model of long-term potentiation and synaptic tagging and capture
Recent data indicate that plasticity protocols have not only synapse-specific but also more widespread effects. In particular, in synaptic tagging and capture (STC), tagged synapses can capture plasticity-related proteins, synthesized in response to strong stimulation of other synapses. This leads to long-lasting modification of only weakly stimulated synapses. Here we present a biophysical model of synaptic plasticity in the hippocampus that incorporates several key results from experiments on STC. The model specifies a set of physical states in which a synapse can exist, together with transition rates that are affected by high- and low-frequency stimulation protocols. In contrast to most standard plasticity models, the model exhibits both early- and late-phase LTP/D, de-potentiation, and STC. As such, it provides a useful starting point for further theoretical work on the role of STC in learning and memory
HDAC1 Inactivation Induces Mitotic Defect and Caspase-Independent Autophagic Cell Death in Liver Cancer
Histone deacetylases (HDACs) are known to play a central role in the regulation of several cellular properties interlinked with the development and progression of cancer. Recently, HDAC1 has been reported to be overexpressed in hepatocellular carcinoma (HCC), but its biological roles in hepatocarcinogenesis remain to be elucidated. In this study, we demonstrated overexpression of HDAC1 in a subset of human HCCs and liver cancer cell lines. HDAC1 inactivation resulted in regression of tumor cell growth and activation of caspase-independent autophagic cell death, via LC3B-II activation pathway in Hep3B cells. In cell cycle regulation, HDAC1 inactivation selectively induced both p21WAF1/Cip1 and p27Kip1 expressions, and simultaneously suppressed the expression of cyclin D1 and CDK2. Consequently, HDAC1 inactivation led to the hypophosphorylation of pRb in G1/S transition, and thereby inactivated E2F/DP1 transcription activity. In addition, we demonstrated that HDAC1 suppresses p21WAF1/Cip1 transcriptional activity through Sp1-binding sites in the p21WAF1/Cip1 promoter. Furthermore, sustained suppression of HDAC1 attenuated in vitro colony formation and in vivo tumor growth in a mouse xenograft model. Taken together, we suggest the aberrant regulation of HDAC1 in HCC and its epigenetic regulation of gene transcription of autophagy and cell cycle components. Overexpression of HDAC1 may play a pivotal role through the systemic regulation of mitotic effectors in the development of HCC, providing a particularly relevant potential target in cancer therapy
Resonant magnetic exciton mode in the heavy-fermion antiferromagnet CeB6
Resonant magnetic excitations are widely recognized as hallmarks of
unconventional superconductivity in copper oxides, iron pnictides, and
heavy-fermion compounds. Numerous model calculations have related these modes
to the microscopic properties of the pair wave function, but the mechanisms
underlying their formation are still debated. Here we report the discovery of a
similar resonant mode in the non-superconducting, antiferromagnetically ordered
heavy-fermion metal CeB6. Unlike conventional magnons, the mode is
non-dispersive, and its intensity is sharply concentrated around a wave vector
separate from those characterizing the antiferromagnetic order. The magnetic
intensity distribution rather suggests that the mode is associated with a
coexisting order parameter of the unusual antiferro-quadrupolar phase of CeB6,
which has long remained "hidden" to the neutron-scattering probes. The mode
energy increases continuously below the onset temperature for
antiferromagnetism, in parallel to the opening of a nearly isotropic spin gap
throughout the Brillouin zone. These attributes bear strong similarity to those
of the resonant modes observed in unconventional superconductors below their
critical temperatures. This unexpected commonality between the two disparate
ground states indicates the dominance of itinerant spin dynamics in the ordered
low-temperature phases of CeB6 and throws new light on the interplay between
antiferromagnetism, superconductivity, and "hidden" order parameters in
correlated-electron materials
Quantitative Analysis of Mechanisms That Govern Red Blood Cell Age Structure and Dynamics during Anaemia
Mathematical modelling has proven an important tool in elucidating and quantifying mechanisms that govern the age structure and population dynamics of red blood cells (RBCs). Here we synthesise ideas from previous experimental data and the mathematical modelling literature with new data in order to test hypotheses and generate new predictions about these mechanisms. The result is a set of competing hypotheses about three intrinsic mechanisms: the feedback from circulating RBC concentration to production rate of immature RBCs (reticulocytes) in bone marrow, the release of reticulocytes from bone marrow into the circulation, and their subsequent ageing and clearance. In addition we examine two mechanisms specific to our experimental system: the effect of phenylhydrazine (PHZ) and blood sampling on RBC dynamics. We performed a set of experiments to quantify the dynamics of reticulocyte proportion, RBC concentration, and erythropoietin concentration in PHZ-induced anaemic mice. By quantifying experimental error we are able to fit and assess each hypothesis against our data and recover parameter estimates using Markov chain Monte Carlo based Bayesian inference. We find that, under normal conditions, about 3% of reticulocytes are released early from bone marrow and upon maturation all cells are released immediately. In the circulation, RBCs undergo random clearance but have a maximum lifespan of about 50 days. Under anaemic conditions reticulocyte production rate is linearly correlated with the difference between normal and anaemic RBC concentrations, and their release rate is exponentially correlated with the same. PHZ appears to age rather than kill RBCs, and younger RBCs are affected more than older RBCs. Blood sampling caused short aperiodic spikes in the proportion of reticulocytes which appear to have a different developmental pathway than normal reticulocytes. We also provide evidence of large diurnal oscillations in serum erythropoietin levels during anaemia
Proteolysis of proBDNF Is a Key Regulator in the Formation of Memory
It is essential to understand the molecular processes underlying long-term memory to provide therapeutic targets of aberrant memory that produce pathological behaviour in humans. Under conditions of recall, fully-consolidated memories can undergo reconsolidation or extinction. These retrieval-mediated memory processes may rely on distinct molecular processes. The cellular mechanisms initiating the signature molecular events are not known. Using infusions of protein synthesis inhibitors, antisense oligonucleotide targeting brain-derived neurotrophic factor (BDNF) mRNA or tPA-STOP (an inhibitor of the proteolysis of BDNF protein) into the hippocampus of the awake rat, we show that acquisition and extinction of contextual fear memory depended on the increased and decreased proteolysis of proBDNF (precursor BDNF) in the hippocampus, respectively. Conditions of retrieval that are known to initiate the reconsolidation of contextual fear memory, a BDNF-independent memory process, were not correlated with altered proBDNF cleavage. Thus, the processing of BDNF was associated with the acquisition of new information and the updating of information about a salient stimulus. Furthermore, the differential requirement for the processing of proBDNF by tPA in distinct memory processes suggest that the molecular events actively engaged to support the storage and/or the successful retrieval of memory depends on the integration of ongoing experience with past learning
Synergistic Activation of Dopamine D1 and TrkB Receptors Mediate Gain Control of Synaptic Plasticity in the Basolateral Amygdala
Fear memory formation is thought to require dopamine, brain-derived neurotrophic factor (BDNF) and zinc release in the basolateral amygdala (BLA), as well as the induction of long term potentiation (LTP) in BLA principal neurons. However, no study to date has shown any relationship between these processes in the BLA. Here, we have used in vitro whole-cell patch clamp recording from BLA principal neurons to investigate how dopamine, BDNF, and zinc release may interact to modulate the LTP induction in the BLA. LTP was induced by either theta burst stimulation (TBS) protocol or spaced 5 times high frequency stimulation (5xHFS). Significantly, both TBS and 5xHFS induced LTP was fully blocked by the dopamine D1 receptor antagonist, SCH23390. LTP induction was also blocked by the BDNF scavenger, TrkB-FC, the zinc chelator, DETC, as well as by an inhibitor of matrix metalloproteinases (MMPs), gallardin. Conversely, prior application of the dopamine reuptake inhibitor, GBR12783, or the D1 receptor agonist, SKF39393, induced robust and stable LTP in response to a sub-threshold HFS protocol (2xHFS), which does not normally induce LTP. Similarly, prior activation of TrkB receptors with either a TrkB receptor agonist, or BDNF, also reduced the threshold for LTP-induction, an effect that was blocked by the MEK inhibitor, but not by zinc chelation. Intriguingly, the TrkB receptor agonist-induced reduction of LTP threshold was fully blocked by prior application of SCH23390, and the reduction of LTP threshold induced by GBR12783 was blocked by prior application of TrkB-FC. Together, our results suggest a cellular mechanism whereby the threshold for LTP induction in BLA principal neurons is critically dependent on the level of dopamine in the extracellular milieu and the synergistic activation of postsynaptic D1 and TrkB receptors. Moreover, activation of TrkB receptors appears to be dependent on concurrent release of zinc and activation of MMPs
A Model of Late Long-Term Potentiation Simulates Aspects of Memory Maintenance
Late long-term potentiation (L-LTP) appears essential for the formation of
long-term memory, with memories at least partly encoded by patterns of
strengthened synapses. How memories are preserved for months or years, despite
molecular turnover, is not well understood. Ongoing recurrent neuronal
activity, during memory recall or during sleep, has been hypothesized to
preferentially potentiate strong synapses, preserving memories. This hypothesis
has not been evaluated in the context of a mathematical model representing
biochemical pathways important for L-LTP. I incorporated ongoing activity into
two such models: a reduced model that represents some of the essential
biochemical processes, and a more detailed published model. The reduced model
represents synaptic tagging and gene induction intuitively, and the detailed
model adds activation of essential kinases by Ca. Ongoing activity was modeled
as continual brief elevations of [Ca]. In each model, two stable states of
synaptic weight resulted. Positive feedback between synaptic weight and the
amplitude of ongoing Ca transients underlies this bistability. A tetanic or
theta-burst stimulus switches a model synapse from a low weight to a high
weight stabilized by ongoing activity. Bistability was robust to parameter
variations. Simulations illustrated that prolonged decreased activity reset
synapses to low weights, suggesting a plausible forgetting mechanism. However,
episodic activity with shorter inactive intervals maintained strong synapses.
Both models support experimental predictions. Tests of these predictions are
expected to further understanding of how neuronal activity is coupled to
maintenance of synaptic strength.Comment: Accepted to PLoS One. 8 figures at en
F-Spondin/spon1b Expression Patterns in Developing and Adult Zebrafish
F-spondin, an extracellular matrix protein, is an important player in embryonic morphogenesis and CNS development, but its presence and role later in life remains largely unknown. We generated a transgenic zebrafish in which GFP is expressed under the control of the F-spondin (spon1b) promoter, and used it in combination with complementary techniques to undertake a detailed characterization of the expression patterns of F-spondin in developing and adult brain and periphery. We found that F-spondin is often associated with structures forming long neuronal tracts, including retinal ganglion cells, the olfactory bulb, the habenula, and the nucleus of the medial longitudinal fasciculus (nMLF). F-spondin expression coincides with zones of adult neurogenesis and is abundant in CSF-contacting secretory neurons, especially those in the hypothalamus. Use of this new transgenic model also revealed F-spondin expression patterns in the peripheral CNS, notably in enteric neurons, and in peripheral tissues involved in active patterning or proliferation in adults, including the endoskeleton of zebrafish fins and the continuously regenerating pharyngeal teeth. Moreover, patterning of the regenerating caudal fin following fin amputation in adult zebrafish was associated with F-spondin expression in the blastema, a proliferative region critical for tissue reconstitution. Together, these findings suggest major roles for F-spondin in the CNS and periphery of the developing and adult vertebrate
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