Chemical master equation and Langevin regimes for a gene transcription model

Gene transcription models must take account of intrinsic stochasticity. The Chemical Master Equation framework is based on modelling assumptions that are highly appropriate for this context, and the Stochastic Simulation Algorithm (also known as Gillespie's algorithm) allows for practical simulations to be performed. However, for large networks and/or fast reactions, such computations can be prohibitatively expensive. The Chemical Langevin regime replaces the massive ordinary dierential equation system with a small stochastic dierential equation system that is more amenable to computation. Although the transition from Chemical Master Equation to Chemical Langevin Equation can be justied rigorously in the large system size limit, there is very little guidance available about how closely the two models match for a xed system. Here, we consider a transcription model from the recent literature and show that it is possible to compare rst and second moments in the two stochastic settings. To analyse the Chemical Master Equation we use some recent work of Gadgil, Lee and Othmer, and to analyse the Chemical Langevin Equation we use Ito's Lemma. We nd that there is a perfect match|both modelling regimes give the same means, variances and correlations for all components in the system. The model that we analyse involves 'unimolecular reactions', and we nish with some numerical simulations involving dimerization to show that the means and variances in the two regimes can also be close when more general 'bimolecular reactions' are involved

Percutaneous management of long and diffused coronary lesions using newer generation drug-eluting stents in routine clinical practice : long-term outcomes and complication predictors

Long and diffuse coronary lesions (LDCLs) are routinely subjected to percutaneous management, but long‑term clinical outcomes and complication predictors with the use of contemporary stents and techniques remain undetermined. Long and diffuse coronary lesion was defined as a lesion requiring an implantation of 30 mm or longer total stent(s) length (TSL) into one coronary artery (bailouts excluded). There were 290 LDCL interventions with the use of newer generation drug‑eluting stents (DESs cobalt chromium everolimus- or zotarolimus-eluting stents) performed between January 2013 and January 2016. The mean (SD) TSL was 55.5 (16.8) mm. The use of intravascular ultrasound / optical coherence tomography was 17.1%, rotablation, 6.9%, and noncompliant balloon, 88.9%. The median (range) follow‑up duration was 831 (390-1373) days. All‑cause mortality and cardiac death rates were 11.7% and 6.9%, respectively. The myocardial infarction (MI) rate was 6.6%, including target‑vessel MI in 4.1%. The rate of clinically‑driven repeat revascularization was 13.8%, and of definite or probable LDCL stent thrombosis, 7.2%. Overall patient‑oriented adverse event rate (any death, MI, or repeat revascularization) was 25.5%, and device‑oriented rate (cardiac death, target vessel‑MI, or target lesion restenosis), 13.4%. Adverse outcome predictors were chronic kidney disease, acute coronary syndrome as an indication for the procedure, chronic heart failure with reduced left ventricular ejection fraction, multivessel disease, and coexisting peripheral artery disease, but not lesion‑related factors, such as bifurcation, calcification, chronic total occlusion, or TSL. Adverse outcomes following contemporary LDCL management using newer generation DESs in routine clinical practice are associated with clinical patient characteristics rather than lesion characteristics or TSL. We identified high‑risk patient cohorts that may benefit from enhanced surveillance

Stochasticity in the miR-9/Hes1 oscillatory network can account for clonal heterogeneity in the timing of differentiation.

Recent studies suggest that cells make stochastic choices with respect to differentiation or division. However, the molecular mechanism underlying such stochasticity is unknown. We previously proposed that the timing of vertebrate neuronal differentiation is regulated by molecular oscillations of a transcriptional repressor, HES1, tuned by a post-transcriptional repressor, miR-9. Here, we computationally model the effects of intrinsic noise on the Hes1/miR-9 oscillator as a consequence of low molecular numbers of interacting species, determined experimentally. We report that increased stochasticity spreads the timing of differentiation in a population, such that initially equivalent cells differentiate over a period of time. Surprisingly, inherent stochasticity also increases the robustness of the progenitor state and lessens the impact of unequal, random distribution of molecules at cell division on the temporal spread of differentiation at the population level. This advantageous use of biological noise contrasts with the view that noise needs to be counteracted

Tourette’s disorder and other tic disorders in DSM-5: a comment

Classification of tic disorders will be revised in the forthcoming edition of the Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5). We do not support the suggestion to move tic disorders to “Anxiety and Obsessive–Compulsive Disorders”, if the section “Disorders Usually First Diagnosed in Infancy, Childhood, or Adolescence” is not retained. Other than that, most proposed changes of the criteria for tic disorders contain a number of welcome improvements, e.g., the more unified definition of tics including the removal of the term “stereotyped” and the better capture of the temporal pattern of tics (e.g., removal of the maximum 3 months criterion for a tic-free period in chronic tic disorders). But, unfortunately there are some inconsistencies in detail, e.g., the unification of diagnostic criteria for tic disorders had not been consistently pursued in transient tic disorder. In sum, the proposed DSM-5 criteria could be seen as an important step forward particularly in clinical routine. However, continued research is needed to justify the existing and proposed classification of tic disorders as well as to better clarify what other changes should be made in the DSM-5 and beyond

Daily living skills scale: Development and preliminary validation of a new, open-source assessment of daily living skills

Autistic individuals and individuals with a range of other neurodevelopmental conditions (NDD) often present with lower levels of daily living skills (DLS) when compared to their neurotypical peers. Importantly, lower levels of DLS have been linked to a range of negative outcomes, including lower rates of post-secondary education, lower employment rates, and higher daily support needs across autism and NDD. However, there are currently no open-source informant-reported instruments for capturing key aspects of DLS. This study describes the development, refinement, and initial psychometric evaluation of a new, relatively brief (53-item). Daily Living Skills Scale (DLSS) in a sample of 1,361 children aged 2–17 years, Confirmatory Factor Analysis demonstrated an excellent fit of unidimensional model to the data (CFI = 0.953, TLI = 0.951, RMSEA = 0.073 [95% CI: 0.071–0.074]). The single-factor CFA model showed evidence of measurement invariance of factor loadings, thresholds, and residual variance (strict invariance) across sex, age, race, and ethnicity. Model reliability and internal consistency were excellent (ω = 0.98; α = 0.97). Conditional reliability estimates indicated very good reliability (= 0.80) for the total DLS scale from very low (θ = −4.2) to high (θ = +2.4) scores. Conceptually derived self-care, homecare, and community participation subscales also showed strong reliability and internal consistency. With further replication, the EFS has excellent potential for wide adoption across research and clinical contexts

Three-Dimensional Traction Force Microscopy: A New Tool for Quantifying Cell-Matrix Interactions

The interactions between biochemical processes and mechanical signaling play important roles during various cellular processes such as wound healing, embryogenesis, metastasis, and cell migration. While traditional traction force measurements have provided quantitative information about cell matrix interactions in two dimensions, recent studies have shown significant differences in the behavior and morphology of cells when placed in three-dimensional environments. Hence new quantitative experimental techniques are needed to accurately determine cell traction forces in three dimensions. Recently, two approaches both based on laser scanning confocal microscopy have emerged to address this need. This study highlights the details, implementation and advantages of such a three-dimensional imaging methodology with the capability to compute cellular traction forces dynamically during cell migration and locomotion. An application of this newly developed three-dimensional traction force microscopy (3D TFM) technique to single cell migration studies of 3T3 fibroblasts is presented to show that this methodology offers a new quantitative vantage point to investigate the three-dimensional nature of cell-ECM interactions

Matrix Rigidity Induces Osteolytic Gene Expression of Metastatic Breast Cancer Cells

Nearly 70% of breast cancer patients with advanced disease will develop bone metastases. Once established in bone, tumor cells produce factors that cause changes in normal bone remodeling, such as parathyroid hormone-related protein (PTHrP). While enhanced expression of PTHrP is known to stimulate osteoclasts to resorb bone, the environmental factors driving tumor cells to express PTHrP in the early stages of development of metastatic bone disease are unknown. In this study, we have shown that tumor cells known to metastasize to bone respond to 2D substrates with rigidities comparable to that of the bone microenvironment by increasing expression and production of PTHrP. The cellular response is regulated by Rho-dependent actomyosin contractility mediated by TGF-ß signaling. Inhibition of Rho-associated kinase (ROCK) using both pharmacological and genetic approaches decreased PTHrP expression. Furthermore, cells expressing a dominant negative form of the TGF-ß receptor did not respond to substrate rigidity, and inhibition of ROCK decreased PTHrP expression induced by exogenous TGF-ß. These observations suggest a role for the differential rigidity of the mineralized bone microenvironment in early stages of tumor-induced osteolysis, which is especially important in metastatic cancer since many cancers (such as those of the breast and lung) preferentially metastasize to bone

Stochastic Responses May Allow Genetically Diverse Cell Populations to Optimize Performance with Simpler Signaling Networks

Two theories have emerged for the role that stochasticity plays in biological responses: first, that it degrades biological responses, so the performance of biological signaling machinery could be improved by increasing molecular copy numbers of key proteins; second, that it enhances biological performance, by enabling diversification of population-level responses. Using T cell biology as an example, we demonstrate that these roles for stochastic responses are not sufficient to understand experimental observations of stochastic response in complex biological systems that utilize environmental and genetic diversity to make cooperative responses. We propose a new role for stochastic responses in biology: they enable populations to make complex responses with simpler biochemical signaling machinery than would be required in the absence of stochasticity. Thus, the evolution of stochastic responses may be linked to the evolvability of different signaling machineries.National Institutes of Health (U.S.). Pioneer Awar

Cell division and death inhibit glassy behaviour of confluent tissues

We investigate the effects of cell division and apopotosis on collective dynamics in two-dimensional epithelial tissues. Our model includes three key ingredients observed across many epithelia, namely cell-cell adhesion, cell death and a cell division process that depends on the surrounding environment. We show a rich non-equilibrium phase diagram depending on the ratio of cell death to cell division and on the adhesion strength. For large apopotosis rates, cells die out and the tissue disintegrates. As the death rate decreases, however, we show, consecutively, the existence of a gas-like phase, a gel-like phase, and a dense confluent (tissue) phase. Most striking is the observation that the tissue is self-melting through its own internal activity, ruling out the existence of any glassy phase.Comment: 9 pages, 10 figure