This paper presents the definition, solution and validation of a stochastic model of the budding yeast cell cycle, based on Stochastic Petri Nets (SPN). A specific family of SPNs is selected for building a stochastic version of a well-established deterministic model. We describe the procedure followed in defining the SPN model from the deterministic ODE model, a procedure that can be largely automated. The validation of the SPN model is conducted with respect to both the results provided by the deterministic one and the experimental results available from literature. The SPN model catches the behavior of the wild type budding yeast cells and a variety of mutants. We show that the stochastic model matches some characteristics of budding yeast cells that cannot be found with the deterministic model. The SPN model fine-tunes the simulation results, enriching the breadth and the quality of its outcome.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.jtbi.2008.07.019 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
In the later stages of Parkinson's disease (PD), patients often manifest levodopa-induced dyskinesia (LID), compromising their quality of life. The pathophysiology underlying LID is poorly understood, and treatment options are limited. To move toward filling this treatment gap, the intrinsic and synaptic changes in striatal spiny projection neurons (SPNs) triggered by the sustained elevation of dopamine (DA) during dyskinesia were characterized using electrophysiological, pharmacological, molecular and behavioral approaches.
View Article and Find Full Text PDFWhen do we find a third neural response to visual symmetry?
Cortex
December 2024
Department of Psychological Sciences, University of Liverpool, Liverpool, UK.
The human visual system is tuned to symmetry, and the neural response to visual symmetry has been well studied. One line of research measures an Event Related Potential (ERP) component called the Sustained Posterior Negativity (SPN). Amplitude is more negative at posterior electrodes when participants see symmetrical patterns compared to asymmetrical patterns.
View Article and Find Full Text PDFFBP1 controls liver cancer evolution from senescent MASH hepatocytes.
Nature
January 2025
Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA.
Article Synopsis
- Hepatocellular carcinoma (HCC) arises from liver cells (hepatocytes) that are damaged and undergoing compensatory growth, particularly due to metabolic disorders like MASH.
- The tumor-suppressive effects of p53 and the anti-cancer role of the enzyme FBP1 are undermined in HCC, as FBP1 is commonly degraded and suppressed in tumors.
- Key metabolic pathways involving AKT and NRF2 play a role in reversing the effects of cellular senescence, boosting the growth of HCC cells and leading to the accumulation of genetic mutations that contribute to cancer progression.
The neural mechanisms of emotional flexibility influenced by the emotional valence shift direction and preparation effect.
Int J Psychophysiol
December 2024
School of Psychology, Shaanxi Normal University, Xi'an, Shaanxi 710062, China. Electronic address:
Emotional flexibility refers to an individual's ability to change emotional responses in constantly changing environments to adapt to different situations. This study aims to use the Emotional Switching Task (EST) paradigm, combined with Electroencephalogram (EEG) technology and behavioral experiments, to explore the impact of emotional valence shift directions and preparation effects on the switching cost of emotional flexibility. The results found that when individuals switch from positive emotional valence to positive emotional valence, the switching cost is smaller than other transition directions.
View Article and Find Full Text PDFCell-type-specific auditory responses in the striatum are shaped by feedforward inhibition.
Cell Rep
December 2024
Department of Psychiatry and Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA. Electronic address:
The posterior "tail" region of the striatum receives dense innervation from sensory brain regions and is important for behaviors that require sensorimotor integration. The output neurons of the striatum, D1 and D2 striatal projection neurons (SPNs), which make up the direct and indirect pathways, are thought to play distinct functional roles, although it remains unclear if these neurons show cell-type-specific differences in their response to sensory stimuli. Here, we examine the strength of synaptic inputs onto D1 and D2 SPNs following the stimulation of upstream auditory pathways.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!