379 research outputs found
Compositionality, stochasticity and cooperativity in dynamic models of gene regulation
We present an approach for constructing dynamic models for the simulation of
gene regulatory networks from simple computational elements. Each element is
called a ``gene gate'' and defines an input/output-relationship corresponding
to the binding and production of transcription factors. The proposed reaction
kinetics of the gene gates can be mapped onto stochastic processes and the
standard ode-description. While the ode-approach requires fixing the system's
topology before its correct implementation, expressing them in stochastic
pi-calculus leads to a fully compositional scheme: network elements become
autonomous and only the input/output relationships fix their wiring. The
modularity of our approach allows to pass easily from a basic first-level
description to refined models which capture more details of the biological
system. As an illustrative application we present the stochastic repressilator,
an artificial cellular clock, which oscillates readily without any cooperative
effects.Comment: 15 pages, 8 figures. Accepted by the HFSP journal (13/09/07
A self-organized model for cell-differentiation based on variations of molecular decay rates
Systemic properties of living cells are the result of molecular dynamics
governed by so-called genetic regulatory networks (GRN). These networks capture
all possible features of cells and are responsible for the immense levels of
adaptation characteristic to living systems. At any point in time only small
subsets of these networks are active. Any active subset of the GRN leads to the
expression of particular sets of molecules (expression modes). The subsets of
active networks change over time, leading to the observed complex dynamics of
expression patterns. Understanding of this dynamics becomes increasingly
important in systems biology and medicine. While the importance of
transcription rates and catalytic interactions has been widely recognized in
modeling genetic regulatory systems, the understanding of the role of
degradation of biochemical agents (mRNA, protein) in regulatory dynamics
remains limited. Recent experimental data suggests that there exists a
functional relation between mRNA and protein decay rates and expression modes.
In this paper we propose a model for the dynamics of successions of sequences
of active subnetworks of the GRN. The model is able to reproduce key
characteristics of molecular dynamics, including homeostasis, multi-stability,
periodic dynamics, alternating activity, differentiability, and self-organized
critical dynamics. Moreover the model allows to naturally understand the
mechanism behind the relation between decay rates and expression modes. The
model explains recent experimental observations that decay-rates (or turnovers)
vary between differentiated tissue-classes at a general systemic level and
highlights the role of intracellular decay rate control mechanisms in cell
differentiation.Comment: 16 pages, 5 figure
Infliximab: 12 years of experience
Rheumatoid arthritis (RA), ankylosing spondylitis (AS) and psoriatic arthritis (PsA) are immune-mediated conditions that share an inflammatory mechanism fuelled by excessive cytokines, particularly TNF. Control of inflammation and rapid suppression of cytokines are important in treating these diseases. With this understanding and the corresponding advent of TNF inhibitors, RA patients, AS patients and PsA patients have found more choices than ever before and have greater hope of sustained relief. As a widely used TNF inhibitor, infliximab has a deep and established record of efficacy and safety data. Extensive evidence - from randomised controlled clinical trials, large registries and postmarketing surveillance studies - shows that infliximab effectively treats the signs and symptoms, provides rapid and prolonged suppression of inflammation, prevents radiologically observable disease progression and offers an acceptable safety profile in RA, AS and PsA. In very recent studies, investigators have observed drug-free remission in some patients. Additionally, infliximab may interfere with rapidly progressing disease in RA by early addition to methotrexate in patients with signs of an aggressive course. Finally, infliximab has been shown to reduce PsA clinical manifestations such as nail involvement. With our current understanding, substantial data and increasing confidence regarding use in practice, infliximab can be considered a well-known drug in our continued campaign against inflammatory rheumatic diseases
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
Molecular Constraints on Synaptic Tagging and Maintenance of Long-Term Potentiation: A Predictive Model
Protein synthesis-dependent, late long-term potentiation (LTP) and depression
(LTD) at glutamatergic hippocampal synapses are well characterized examples of
long-term synaptic plasticity. Persistent increased activity of the enzyme
protein kinase M (PKM) is thought essential for maintaining LTP. Additional
spatial and temporal features that govern LTP and LTD induction are embodied in
the synaptic tagging and capture (STC) and cross capture hypotheses. Only
synapses that have been "tagged" by an stimulus sufficient for LTP and learning
can "capture" PKM. A model was developed to simulate the dynamics of key
molecules required for LTP and LTD. The model concisely represents
relationships between tagging, capture, LTD, and LTP maintenance. The model
successfully simulated LTP maintained by persistent synaptic PKM, STC, LTD, and
cross capture, and makes testable predictions concerning the dynamics of PKM.
The maintenance of LTP, and consequently of at least some forms of long-term
memory, is predicted to require continual positive feedback in which PKM
enhances its own synthesis only at potentiated synapses. This feedback
underlies bistability in the activity of PKM. Second, cross capture requires
the induction of LTD to induce dendritic PKM synthesis, although this may
require tagging of a nearby synapse for LTP. The model also simulates the
effects of PKM inhibition, and makes additional predictions for the dynamics of
CaM kinases. Experiments testing the above predictions would significantly
advance the understanding of memory maintenance.Comment: v3. Minor text edits to reflect published versio
Dynamic interaction between WT1 and BASP1 in transcriptional regulation during differentiation
The Wilmsβ tumour suppressor protein WT1 plays a central role in the development of the kidney and also other organs. WT1 can act as a transcription factor with highly context-specific activator and repressor functions. We previously identified Brain Acid Soluble Protein 1 (BASP1) as a transcriptional cosuppressor that can block the transcriptional activation function of WT1. WT1 and BASP1 are co-expressed during nephrogenesis and both proteins ultimately become restricted to the podocyte cells of the adult kidney. Here, we have analysed the WT1/BASP1 complex in a podocyte precursor cell line that can be induced to differentiate. Chromatin immunoprecipitation revealed that WT1 and BASP1 occupy the promoters of the Bak, c-myc and podocalyxin genes in podocyte precursor cells. During differentiation-dependent upregulation of podocalyxin expression BASP1 occupancy of the podocalyxin promoter is reduced compared to that of WT1. In contrast, the repressive WT1/BASP1 occupancy of the c-myc and Bak promoters is maintained and these genes are downregulated during the differentiation process. We provide evidence that the regulation of BASP1 promoter occupancy involves the sumoylation of BASP1. Our results reveal a dynamic cooperation between WT1 and BASP1 in the regulation of gene expression during differentiation
A Symmetric Dual Feedback System Provides a Robust and Entrainable Oscillator
Many organisms have evolved molecular clocks to anticipate daily changes in their environment. The molecular mechanisms by which the circadian clock network produces sustained cycles have extensively been studied and transcriptional-translational feedback loops are common structures to many organisms. Although a simple or single feedback loop is sufficient for sustained oscillations, circadian clocks implement multiple, complicated feedback loops. In general, different types of feedback loops are suggested to affect the robustness and entrainment of circadian rhythms
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