The interplay of intrinsic and extrinsic bounded noises in biomolecular networks

Extrinsic fluctuations in the p53 cycle

Fluctuations are inherent to biological systems, arising from the stochastic nature of molecular interactions, and influence various aspects of system behavior, stability, and robustness. These fluctuations can be categorized as intrinsic, stemming from the system's inherent structure and dynamics, and extrinsic, arising from external factors, such as temperature variations. Understanding the interplay between these fluctuations is crucial for obtaining a comprehensive understanding of biological phenomena. However, studying these effects poses significant computational challenges. In this study, we used an underexplored methodology to analyze the effect of extrinsic fluctuations in stochastic systems using ordinary differential equations instead of solving the master equation with stochastic parameters. By incorporating temperature fluctuations into reaction rates, we explored the impact of extrinsic factors on system dynamics. We constructed a master equation and calculated the equations for the dynamics of the first two moments, offering computational efficiency compared with directly solving the chemical master equation. We applied this approach to analyze a biological oscillator, focusing on the p53 model and its response to temperature-induced extrinsic fluctuations. Our findings underscore the impact of extrinsic fluctuations on the nature of oscillations in biological systems, with alterations in oscillatory behavior depending on the characteristics of extrinsic fluctuations. We observed an increased oscillation amplitude and frequency of the p53 concentration cycle. This study provides valuable insights into the effects of extrinsic fluctuations on biological oscillations and highlights the importance of considering them in more complex systems to prevent unwanted scenarios related to health issues.

Species interactions drive continuous assembly of freshwater communities in stochastic environments

Understanding the factors driving the maintenance of long-term biodiversity in changing environments is essential for improving restoration and sustainability strategies in the face of global environmental change. Biodiversity is shaped by both niche and stochastic processes, however the strength of deterministic processes in unpredictable environmental regimes is highly debated. Since communities continuously change over time and space-species persist, disappear or (re)appear-understanding the drivers of species gains and losses from communities should inform us about whether niche or stochastic processes dominate community dynamics. Applying a nonparametric causal discovery approach to a 30-year time series containing annual abundances of benthic invertebrates across 66 locations in New Zealand rivers, we found a strong negative causal relationship between species gains and losses directly driven by predation indicating that niche processes dominate community dynamics. Despite the unpredictable nature of these system, environmental noise was only indirectly related to species gains and losses through altering life history trait distribution. Using a stochastic birth-death framework, we demonstrate that the negative relationship between species gains and losses can not emerge without strong niche processes. Our results showed that even in systems that are dominated by unpredictable environmental variability, species interactions drive continuous community assembly.

The chemical Langevin equation for biochemical systems in dynamic environments

Modelling and simulation of complex biochemical reaction networks form cornerstones of modern biophysics. Many of the approaches developed so far capture temporal fluctuations due to the inherent stochasticity of the biophysical processes, referred to as intrinsic noise. Stochastic fluctuations, however, predominantly stem from the interplay of the network with many other - and mostly unknown - fluctuating processes, as well as with various random signals arising from the extracellular world; these sources contribute extrinsic noise. Here we provide a computational simulation method to probe the stochastic dynamics of biochemical systems subject to both intrinsic and extrinsic noise. We develop an extrinsic chemical Langevin equation-a physically motivated extension of the chemical Langevin equation- to model intrinsically noisy reaction networks embedded in a stochastically fluctuating environment. The extrinsic CLE is a continuous approximation to the Chemical Master Equation (CME) with time-varying propensities. In our approach, noise is incorporated at the level of the CME, and can account for the full dynamics of the exogenous noise process, irrespective of timescales and their mismatches. We show that our method accurately captures the first two moments of the stationary probability density when compared with exact stochastic simulation methods, while reducing the computational runtime by several orders of magnitude. Our approach provides a method that is practical, computationally efficient and physically accurate to study systems that are simultaneously subject to a variety of noise sources.

Multiple epidemic waves as the outcome of stochastic SIR epidemics with behavioral responses: a hybrid modeling approach

In the behavioral epidemiology (BE) of infectious diseases, little theoretical effort seems to have been devoted to understand the possible effects of individuals' behavioral responses during an epidemic outbreak in small populations. To fill this gap, here we first build general, behavior implicit, SIR epidemic models including behavioral responses and set them within the framework of nonlinear feedback control theory. Second, we provide a thorough investigation of the effects of different types of agents' behavioral responses for the dynamics of hybrid stochastic SIR outbreak models. In the proposed model, the stochastic discrete dynamics of infection spread is combined with a continuous model describing the agents' delayed behavioral response. The delay reflects the memory mechanisms with which individuals enact protective behavior based on past data on the epidemic course. This results in a stochastic hybrid system with time-varying transition probabilities. To simulate such system, we extend Gillespie's classic stochastic simulation algorithm by developing analytical formulas valid for our classes of models. The algorithm is used to simulate a number of stochastic behavioral models and to classify the effects of different types of agents' behavioral responses. In particular this work focuses on the effects of the structure of the response function and of the form of the temporal distribution of such response. Among the various results, we stress the appearance of multiple, stochastic epidemic waves triggered by the delayed behavioral response of individuals.

Model-based optimization of combination protocols for irradiation-insensitive cancers

Alternations in the p53 regulatory network may render cancer cells resistant to the radiation-induced apoptosis. In this theoretical study we search for the best protocols combining targeted therapy with radiation to treat cancers with wild-type p53, but having downregulated expression of PTEN or overexpression of Wip1 resulting in resistance to radiation monotherapy. Instead of using the maximum tolerated dose paradigm, we exploit stochastic computational model of the p53 regulatory network to calculate apoptotic fractions for both normal and cancer cells. We consider combination protocols, with irradiations repeated every 12, 18, 24, or 36 h to find that timing between Mdm2 inhibitor delivery and irradiation significantly influences the apoptotic cell fractions. We assume that uptake of the inhibitor is higher by cancer than by normal cells and that cancer cells receive higher irradiation doses from intersecting beams. These two assumptions were found necessary for the existence of protocols inducing massive apoptosis in cancer cells without killing large fraction of normal cells neighboring tumor. The best found protocols have irradiations repeated every 24 or 36 h with two inhibitor doses per irradiation cycle, and allow to induce apoptosis in more than 95% of cancer cells, killing less than 10% of normal cells.

Phenotypic selection through cell death: stochastic modelling of O-6-methylguanine-DNA methyltransferase dynamics

Glioblastoma (GBM) is the most aggressive malignant primary brain tumour with a median overall survival of 15 months. To treat GBM, patients currently undergo a surgical resection followed by exposure to radiotherapy and concurrent and adjuvant temozolomide (TMZ) chemotherapy. However, this protocol often leads to treatment failure, with drug resistance being the main reason behind this. To date, many studies highlight the role of O-6-methylguanine-DNA methyltransferase (MGMT) in conferring drug resistance. The mechanism through which MGMT confers resistance is not well studied-particularly in terms of computational models. With only a few reasonable biological assumptions, we were able to show that even a minimal model of MGMT expression could robustly explain TMZ-mediated drug resistance. In particular, we showed that for a wide range of parameter values constrained by novel cell growth and viability assays, a model accounting for only stochastic gene expression of MGMT coupled with cell growth, division, partitioning and death was able to exhibit phenotypic selection of GBM cells expressing MGMT in response to TMZ. Furthermore, we found this selection allowed the cells to pass their acquired phenotypic resistance onto daughter cells in a stable manner (as long as TMZ is provided). This suggests that stochastic gene expression alone is enough to explain the development of chemotherapeutic resistance.

Mutation and Selection in Bacteria: Modelling and Calibration

Temporal evolution of a clonal bacterial population is modelled taking into account reversible mutation and selection mechanisms. For the mutation model, an efficient algorithm is proposed to verify whether experimental data can be explained by this model. The selection–mutation model has unobservable fitness parameters, and, to estimate them, we use an Approximate Bayesian Computation algorithm. The algorithms are illustrated using in vitro data for phase variable genes of Campylobacter jejuni.

Incorporating extrinsic noise into the stochastic simulation of biochemical reactions: A comparison of approaches

The stochastic simulation algorithm (SSA) has been widely used for simulating biochemical reaction networks. SSA is able to capture the inherently intrinsic noise of the biological system, which is due to the discreteness of species population and to the randomness of their reciprocal interactions. However, SSA does not consider other sources of heterogeneity in biochemical reaction systems, which are referred to as extrinsic noise. Here, we extend two simulation approaches, namely, the integration-based method and the rejection-based method, to take extrinsic noise into account by allowing the reaction propensities to vary in time and state dependent manner. For both methods, new efficient implementations are introduced and their efficiency and applicability to biological models are investigated. Our numerical results suggest that the rejection-based method performs better than the integration-based method when the extrinsic noise is considered.

Influence of parameter perturbations on the reachability of therapeutic target in systems with switchings

Background

Examination of physiological processes and the influences of the drugs on them can be efficiently supported by mathematical modeling. One of the biggest problems is related to the exact fitting of the parameters of a model. Conditions inside the organism change dynamically, so the rates of processes are very difficult to estimate. Perturbations in the model parameters influence the steady state so a desired therapeutic goal may not be reached. Here we investigate the effect of parameter deviation on the steady state in three simple models of the influence of a therapeutic drug on its target protein. Two types of changes in the model parameters are taken into account: small perturbations in the system parameter values, and changes in the switching time of a specific parameter. Additionally, we examine the systems response in case of a drug concentration decreasing with time.

Results

The models which we analyze are simplified, because we want to avoid influences of complex dynamics on the results. A system with a negative feedback loop is the most robust and the most rapid, so it requires the largest drug dose but the effects are observed very quickly. On the other hand a system with positive feedback is very sensitive to changes, so small drug doses are sufficient to reach a therapeutic target. In systems without feedback or with positive feedback, perturbations in the model parameters have a bigger influence on the reachability of the therapeutic target than in systems with negative feedback. Drug degradation or inactivation in biological systems enforces multiple drug applications to maintain the level of a drug’s target under the desired threshold. The frequency of drug application should be fitted to the system dynamics, because the response velocity is tightly related to the therapeutic effectiveness and the time for achieving the goal.

Conclusions

Systems with different types of regulation vary in their dynamics and characteristic features. Depending on the feedback loop, different types of therapy may be the most appropriate, and deviations in the model parameters have different influences on the reachability of the therapeutic target.

External Noise and External Signal Induced Transition of Gene Switch and Coherence Resonance in the Genetic Regulatory System

The transition of gene switch induced by external noises (multiplicative external noise and additive external noise) and external signals is investigated in the genetic regulatory system. Results show that the state-to-state transition of gene switch as well as resonant behaviors, such as the explicit coherence resonance (ECR), implicit coherence resonance (ICR) and control parameter coherence biresonance (CPCBR), can appear when noises are injected into the genetic regulatory system. The ECR is increased with the increase of the control parameter value when starting from the supercritical Hopf bifurcation parameter point, and there exists a critical control parameter value for the occurrence of ECR. However, the ICR is decreased as the control parameter value is increased when starting from the subcritical Hopf bifurcation point. In particular, the coherence of ECR is higher and more sensitive to noise than that of ICR. When an external signal is introduced into the system, the enhancement or suppression of the CPCBR and the number of peaks strongly depend on the frequency and amplitude of the external signal. Furthermore, the gene regulation system can selectively enhance or decrease the noise-induced oscillation signals at preferred frequency and amplitude of an external signal.

A Paradoxical Evolutionary Mechanism in Stochastically Switching Environments

Organisms with environmental sensors that guide survival are considered more likely to be favored by natural selection if they possess more accurate sensors. In this paper, we develop a theoretical model which shows that under certain conditions of environmental stochasticity, selection actually favors sensors of lower accuracy. An analogy between this counter-intuitive phenomenon and the well-known Parrondo’s paradox is suggested.

Fluctuations in reactive networks subject to extrinsic noise studied in the framework of the chemical Langevin equation

Theoretical and experimental studies have shown that the fluctuations of in vivo systems break the fluctuation-dissipation theorem. One can thus ask what information is contained in the correlation functions of protein concentrations and how they relate to the response of the reactive network to a perturbation. Answers to these questions are of prime importance to extract meaningful parameters from the in vivo fluorescence correlation spectroscopy data. In this paper we study the fluctuations of the concentration of a reactive species involved in a cyclic network that is in a nonequilibrium steady state perturbed by a noisy force, taking into account both the breaking of detailed balance and extrinsic noises. Using a generic model for the network and the extrinsic noise, we derive a chemical Langevin equation that describes the dynamics of the system, we determine the expressions of the correlation functions of the concentrations, and we estimate the deviation of the fluctuation-dissipation theorem and the range of parameters in which an effective temperature can be defined.

Stochastic modeling suggests that noise reduces differentiation efficiency by inducing a heterogeneous drug response in glioma differentiation therapy

Background

Glioma differentiation therapy is a novel strategy that has been used to induce glioma cells to differentiate into glia-like cells. Although some advances in experimental methods for exploring the molecular mechanisms involved in differentiation therapy have been made, a model-based comprehensive analysis is still needed to understand these differentiation mechanisms and improve the effects of anti-cancer therapeutics. This type of analysis becomes necessary in stochastic cases for two main reasons: stochastic noise inherently exists in signal transduction and phenotypic regulation during targeted therapy and chemotherapy, and the relationship between this noise and drug efficacy in differentiation therapy is largely unknown.

Results

In this study, we developed both an additive noise model and a Chemical-Langenvin-Equation model for the signaling pathways involved in glioma differentiation therapy to investigate the functional role of noise in the drug response. Our model analysis revealed an ultrasensitive mechanism of cyclin D1 degradation that controls the glioma differentiation induced by the cAMP inducer cholera toxin (CT). The role of cyclin D1 degradation in human glioblastoma cell differentiation was then experimentally verified. Our stochastic simulation demonstrated that noise not only renders some glioma cells insensitive to cyclin D1 degradation during drug treatment but also induce heterogeneous differentiation responses among individual glioma cells by modulating the ultrasensitive response of cyclin D1. As such, the noise can reduce the differentiation efficiency in drug-treated glioma cells, which was verified by the decreased evolution of differentiation potential, which quantified the impact of noise on the dynamics of the drug-treated glioma cell population.

Conclusion

Our results demonstrated that targeting the noise-induced dynamics of cyclin D1 during glioma differentiation therapy can increase anti-glioma effects, implying that noise is a considerable factor in assessing and optimizing anti-cancer drug interventions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-016-0316-x) contains supplementary material, which is available to authorized users.

The role of stochastic gene switching in determining the pharmacodynamics of certain drugs: basic mechanisms

In this paper we analyze the impact of the stochastic fluctuation of genes between their ON and OFF states on the pharmacodynamics of a potentially large class of drugs. We focus on basic mechanisms underlying the onset of in vitro experimental dose-response curves, by investigating two elementary molecular circuits. Both circuits consist in the transcription of a gene and in the successive translation into the corresponding protein. Whereas in the first the activation/deactivation rates of the single gene copy are constant, in the second the protein, now a transcription factor, amplifies the deactivation rate, so introducing a negative feedback. The drug is assumed to enhance the elimination of the protein, and in both cases the success of therapy is assured by keeping the level of the given protein under a threshold for a fixed time. Our numerical simulations suggests that the gene switching plays a primary role in determining the sigmoidal shape of dose-response curves. Moreover, the simulations show interesting phenomena related to the magnitude of the average gene switching time and to the drug concentration. In particular, for slow gene switching a significant fraction of cells can respond also in the absence of drug or with drug concentrations insufficient for the response in a deterministic setting. For higher drug concentrations, the non-responding fraction exhibits a maximum at intermediate values of the gene switching rates. For fast gene switching, instead, the stochastic prediction follows the prediction of the deterministic approximation, with all the cells responding or non-responding according to the drug dose.

Gene switching rate determines response to extrinsic perturbations in the self-activation transcriptional network motif

Gene switching dynamics is a major source of randomness in genetic networks, also in the case of large concentrations of the transcription factors. In this work, we consider a common network motif - the positive feedback of a transcription factor on its own synthesis - and assess its response to extrinsic noises perturbing gene deactivation in a variety of settings where the network might operate. These settings are representative of distinct cellular types, abundance of transcription factors and ratio between gene switching and protein synthesis rates. By investigating noise-induced transitions among the different network operative states, our results suggest that gene switching rates are key parameters to shape network response to external perturbations, and that such response depends on the particular biological setting, i.e. the characteristic time scales and protein abundance. These results might have implications on our understanding of irreversible transitions for noise-related phenomena such as cellular differentiation. In addition these evidences suggest to adopt the appropriate mathematical model of the network in order to analyze the system consistently to the reference biological setting.

The limiting dynamics of a bistable molecular switch with and without noise

We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the absence of any noise, and then go on to consider the effects of either noise coming from bursting (transcription or translation), or Gaussian noise in molecular degradation rates when there is a dominant slow variable in the system. We show analytically how the steady state distribution in the population can range from a single unimodal distribution through a bimodal distribution and give the explicit analytic form for the invariant stationary density which is globally asymptotically stable. Rather remarkably, the behaviour of the stationary density with respect to the parameters characterizing the molecular behaviour of the bistable switch is qualitatively identical in the presence of noise coming from bursting as well as in the presence of Gaussian noise in the degradation rate. This implies that one cannot distinguish between either the dominant source or nature of noise based on the stationary molecular distribution in a population of cells. We finally show that the switch model with bursting but two dominant slow genes has an asymptotically stable stationary density.

Dynamics of simple gene-network motifs subject to extrinsic fluctuations

Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the biomolecular interaction networks. Most previous work has been focused on the intrinsic noise (IN) of these networks. Yet, especially for high-copy-number biomolecules, extrinsic or environmental noise (EN) has been experimentally shown to dominate the variation. Here, we develop an analytical formalism that allows for calculation of the effect of EN on gene-expression motifs. We introduce a method for modeling bounded EN as an auxiliary species in the master equation. The method is fully generic and is not limited to systems with small EN magnitudes. We focus our study on motifs that can be viewed as the building blocks of genetic switches: a nonregulated gene, a self-inhibiting gene, and a self-promoting gene. The role of the EN properties (magnitude, correlation time, and distribution) on the statistics of interest are systematically investigated, and the effect of fluctuations in different reaction rates is compared. Due to its analytical nature, our formalism can be used to quantify the effect of EN on the dynamics of biochemical networks and can also be used to improve the interpretation of data from single-cell gene-expression experiments.

Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks

Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling.

When studying how e.g. diseases spread in a population, intermittent contacts taking place between individuals—through which the infection spreads—are best described by a time-varying network. This object captures both their complex structure and dynamics, which crucially affect spreading in the population. The dynamical process in question is then usually studied by simulating it on the time-varying network representing the population. Such simulations are usually time-consuming, especially when they require exploration of different parameter values. We here show how to adapt an algorithm originally proposed in 1976 to simulate chemical reactions—the Gillespie algorithm—to speed up such simulations. Instead of checking at each time-step if each possible reaction takes place, as traditional rejection sampling algorithms do, the Gillespie algorithm determines what reaction takes place next and at what time. This offers a substantial speed gain by doing away with the many rejected trials of the traditional methods, with the added benefit of giving stochastically exact results. In practice this new temporal Gillespie algorithm is tens to hundreds of times faster than the current state-of-the-art, opening up for thorough characterization of spreading phenomena and fast large-scale applications such as the simulation of city- or world-wide epidemics.

Automatising the analysis of stochastic biochemical time-series

BACKGROUND

Mathematical and computational modelling of biochemical systems has seen a lot of effort devoted to the definition and implementation of high-performance mechanistic simulation frameworks. Within these frameworks it is possible to analyse complex models under a variety of configurations, eventually selecting the best setting of, e.g., parameters for a target system.

MOTIVATION

This operational pipeline relies on the ability to interpret the predictions of a model, often represented as simulation time-series. Thus, an efficient data analysis pipeline is crucial to automatise time-series analyses, bearing in mind that errors in this phase might mislead the modeller's conclusions.

RESULTS

For this reason we have developed an intuitive framework-independent Python tool to automate analyses common to a variety of modelling approaches. These include assessment of useful non-trivial statistics for simulation ensembles, e.g., estimation of master equations. Intuitive and domain-independent batch scripts will allow the researcher to automatically prepare reports, thus speeding up the usual model-definition, testing and refinement pipeline.

The pharmacodynamics of the p53-Mdm2 targeting drug Nutlin: the role of gene-switching noise

In this work we investigate, by means of a computational stochastic model, how tumor cells with wild-type p53 gene respond to the drug Nutlin, an agent that interferes with the Mdm2-mediated p53 regulation. In particular, we show how the stochastic gene-switching controlled by p53 can explain experimental dose-response curves, i.e., the observed inter-cell variability of the cell viability under Nutlin action. The proposed model describes in some detail the regulation network of p53, including the negative feedback loop mediated by Mdm2 and the positive loop mediated by PTEN, as well as the reversible inhibition of Mdm2 caused by Nutlin binding. The fate of the individual cell is assumed to be decided by the rising of nuclear-phosphorylated p53 over a certain threshold. We also performed in silico experiments to evaluate the dose-response curve after a single drug dose delivered in mice, or after its fractionated administration. Our results suggest that dose-splitting may be ineffective at low doses and effective at high doses. This complex behavior can be due to the interplay among the existence of a threshold on the p53 level for its cell activity, the nonlinearity of the relationship between the bolus dose and the peak of active p53, and the relatively fast elimination of the drug.

P53 is an antitumor gene regulating vital cellular functions such as repair of DNA damage, cellular suicide, and cell proliferation: in many tumors p53 is lowly expressed and/or mutated. Drugs targeting the biomolecular network of p53 are becoming important. The network includes the key proteins Mdm2 and PTEN, whose production is regulated by p53, and which, in turn, enact positive and negative feedbacks on p53. Drug Nutlin, inhibiting the p53 inhibitor Mdm2, might be important for tumors where p53 is underproduced but unmutated. We investigate the cellular mechanism of action of Nutlin. The basic concept of our mathematical model is that the experimentally observed cell-to-cell variability of Nutlin efficacy is caused by the randomness of gene activation/deactivation of Mdmd2 and PTEN. Indeed, the abundance/scarceness of p53 regulates the probability that the relative genes are active or inactive. The model reproduced the experimental cell-specific response to different doses of Nutlin (dose-response curves) in some types of tumor cells. Much clinical research focus on 'metronomic' drug delivery regimens, where instead of giving large doses with long intervals, smaller doses are frequently delivered. In our simulations, dose-splitting of Nutlin produced a response generally worse than the response to a single dose.

Mean field analysis of a spatial stochastic model of a gene regulatory network

A gene regulatory network may be defined as a collection of DNA segments which interact with each other indirectly through their RNA and protein products. Such a network is said to contain a negative feedback loop if its products inhibit gene transcription, and a positive feedback loop if a gene product promotes its own production. Negative feedback loops can create oscillations in mRNA and protein levels while positive feedback loops are primarily responsible for signal amplification. It is often the case in real biological systems that both negative and positive feedback loops operate in parameter regimes that result in low copy numbers of gene products. In this paper we investigate the spatio-temporal dynamics of a single feedback loop in a eukaryotic cell. We first develop a simplified spatial stochastic model of a canonical feedback system (either positive or negative). Using a Gillespie's algorithm, we compute sample trajectories and analyse their corresponding statistics. We then derive a system of equations that describe the spatio-temporal evolution of the stochastic means. Subsequently, we examine the spatially homogeneous case and compare the results of numerical simulations with the spatially explicit case. Finally, using a combination of steady-state analysis and data clustering techniques, we explore model behaviour across a subregion of the parameter space that is difficult to access experimentally and compare the parameter landscape of our spatio-temporal and spatially-homogeneous models.

Investigating the relation between stochastic differentiation, homeostasis and clonal expansion in intestinal crypts via multiscale modeling

Colorectal tumors originate and develop within intestinal crypts. Even though some of the essential phenomena that characterize crypt structure and dynamics have been effectively described in the past, the relation between the differentiation process and the overall crypt homeostasis is still only partially understood. We here investigate this relation and other important biological phenomena by introducing a novel multiscale model that combines a morphological description of the crypt with a gene regulation model: the emergent dynamical behavior of the underlying gene regulatory network drives cell growth and differentiation processes, linking the two distinct spatio-temporal levels. The model relies on a few a priori assumptions, yet accounting for several key processes related to crypt functioning, such as: dynamic gene activation patterns, stochastic differentiation, signaling pathways ruling cell adhesion properties, cell displacement, cell growth, mitosis, apoptosis and the presence of biological noise. We show that this modeling approach captures the major dynamical phenomena that characterize the regular physiology of crypts, such as cell sorting, coordinate migration, dynamic turnover, stem cell niche correct positioning and clonal expansion. All in all, the model suggests that the process of stochastic differentiation might be sufficient to drive the crypt to homeostasis, under certain crypt configurations. Besides, our approach allows to make precise quantitative inferences that, when possible, were matched to the current biological knowledge and it permits to investigate the role of gene-level perturbations, with reference to cancer development. We also remark the theoretical framework is general and may be applied to different tissues, organs or organisms.

A NAD(P) reductase like protein is the salicylic acid receptor in the appendix of the Sauromatum guttatum inflorescence

The mode of action of the thermogenic inducers (salicylic acid, aspirin, and 2,6-dihydroxybenzoic acid) in the appendix of the Sauromatum guttatum inflorescence is poorly understood. Using ESI-MS and light scattering analysis, we have demonstrated that NAD(P) reductase like protein (RL) is the salicylic acid receptor in the Sauromatum appendix. RL was self-assembled in water into a large unit with a hydrodynamic diameter of 800 nm. In the presence of 1 pM salicylic acid, RL exhibited discontinuous and reversible volume phase transitions. The volume phase changed from 800 to 300 nm diameter and vice versa. RL stayed at each volume phase for ~4-5 min with a fast relaxation time between the 2 phases. ESI-MS analysis of RL extracted from appendices treated with salicylic acid, aspirin, and 2,6-DHBA at a micromolar range demonstrated that these compounds are capable of inducing graded conformational changes that are concentration-dependent. A strong correlation between RL conformations and heat-production induced by salicylic acid was also observed. These preliminary findings reveal structural and conformational roles for RL by which plants regulate their temperature and synchronize their time keeping mechanisms.