Parameter inference for a stochastic kinetic model of expanded polyglutamine proteins.

The presence of protein aggregates in cells is a known feature of many human age-related diseases, such as Huntington's disease. Simulations using fixed parameter values in a model of the dynamic evolution of expanded polyglutaime (PolyQ) proteins in cells have been used to gain a better understanding of the biological system. However, there is considerable uncertainty about the values of some of the parameters governing the system. Currently, appropriate values are chosen by ad hoc attempts to tune the parameters so that the model output matches experimental data. The problem is further complicated by the fact that the data only offer a partial insight into the underlying biological process: the data consist only of the proportions of cell death and of cells with inclusion bodies at a few time points, corrupted by measurement error. Developing inference procedures to estimate the model parameters in this scenario is a significant task. The model probabilities corresponding to the observed proportions cannot be evaluated exactly, and so they are estimated within the inference algorithm by repeatedly simulating realizations from the model. In general such an approach is computationally very expensive, and we therefore construct Gaussian process emulators for the key quantities and reformulate our algorithm around these fast stochastic approximations. We conclude by highlighting appropriate values of the model parameters leading to new insights into the underlying biological processes.

TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis.

MOTIVATION: The analysis of longitudinal datasets and construction of gene regulatory networks (GRNs) provide a valuable means to disentangle the complexity of microRNA (miRNA)-mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal miRNA-mRNA datasets. RESULTS: We present TimiRGeN, an R package that uses time point-based differential expression results to identify miRNA-mRNA interactions influencing signaling pathways of interest. miRNA-mRNA interactions can be visualized in R or exported to PathVisio or Cytoscape. The output can be used for hypothesis generation and directing in vitro or further in silico work such as GRN construction. AVAILABILITY AND IMPLEMENTATION: TimiRGeN is available for download on Bioconductor (https://bioconductor.org/packages/TimiRGeN) and requires R v4.0.2 or newer and BiocManager v3.12 or newer. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A computer simulation approach to assessing therapeutic intervention points for the prevention of cytokine-induced cartilage breakdown.

OBJECTIVE: To use a novel computational approach to examine the molecular pathways involved in cartilage breakdown and to use computer simulation to test possible interventions for reducing collagen release. METHODS: We constructed a computational model of the relevant molecular pathways using the Systems Biology Markup Language, a computer-readable format of a biochemical network. The model was constructed using our experimental data showing that interleukin-1 (IL-1) and oncostatin M (OSM) act synergistically to up-regulate collagenase protein levels and activity and initiate cartilage collagen breakdown. Simulations were performed using the COPASI software package. RESULTS: The model predicted that simulated inhibition of JNK or p38 MAPK, and overexpression of tissue inhibitor of metalloproteinases 3 (TIMP-3) led to a reduction in collagen release. Overexpression of TIMP-1 was much less effective than that of TIMP-3 and led to a delay, rather than a reduction, in collagen release. Simulated interventions of receptor antagonists and inhibition of JAK-1, the first kinase in the OSM pathway, were ineffective. So, importantly, the model predicts that it is more effective to intervene at targets that are downstream, such as the JNK pathway, rather than those that are close to the cytokine signal. In vitro experiments confirmed the effectiveness of JNK inhibition. CONCLUSION: Our study shows the value of computer modeling as a tool for examining possible interventions by which to reduce cartilage collagen breakdown. The model predicts that interventions that either prevent transcription or inhibit the activity of collagenases are promising strategies and should be investigated further in an experimental setting.

Design and chemical evaluation of reduced machine-yield cigarettes.

Experimental cigarettes (ECs) were made by combining technological applications that individually reduce the machine measured yields of specific toxicants or groups of toxicants in mainstream smoke (MS). Two tobacco blends, featuring a tobacco substitute sheet or a tobacco blend treatment, were combined with filters containing an amine functionalised resin (CR20L) and/or a polymer-derived, high activity carbon adsorbent to generate three ECs with the potential for generating lower smoke toxicant yields than conventional cigarettes. MS yields of smoke constituents were determined under 4 different smoking machine conditions. Health Canada Intense (HCI) machine smoking conditions gave the highest MS yields for nicotine-free dry particulate matter and for most smoke constituents measured. Toxicant yields from the ECs were compared with those from two commercial comparator cigarettes, three scientific control cigarettes measured contemporaneously and with published data on 120 commercial cigarettes. The ECs were found to generate some of the lowest machine yields of toxicants from cigarettes for which published HCI smoke chemistry data are available; these comparisons therefore confirm that ECs with reduced MS machine toxicant yields compared to commercial cigarettes can be produced. The results encourage further work examining human exposure to toxicants from these cigarettes, including human biomarker studies.

The use of a novel tobacco-substitute sheet and smoke dilution to reduce toxicant yields in cigarette smoke.

The Institute of Medicine encouraged the pursuit and development of potential reduced-exposure products, tobacco products that substantially reduce exposure to one or more tobacco toxicants and can reasonably be expected to reduce the risk of one or more specific diseases or other adverse health effects. One approach to reducing smoke toxicant yields is to dilute the smoke with glycerol. We report chemical, biological and human exposure data related to experimental cigarettes containing up to 60% of a novel glycerol containing "tobacco-substitute" sheet. Analysis of mainstream smoke from experimental cigarettes showed reductions in yields of most measured constituents, other than some volatile species. In vitro toxicological tests showed reductions in the activity of smoke particulates in proportion to their glycerol content. Human exposure to nicotine was reduced by a mean of 18% as determined by filter studies and by 14% using 24h urinary biomarker analysis. Smoke particulate exposures were reduced by a mean of 29% in filter studies and NNK exposure by similar amounts based on urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol concentrations. These results show that reducing exposure to some smoke toxicants is possible using a tobacco-substitute sheet, although some smoke toxicants, and the sensory attributes of the smoke, remain as technical challenges.

Modelling the checkpoint response to telomere uncapping in budding yeast.

One of the DNA damage-response mechanisms in budding yeast is temporary cell-cycle arrest while DNA repair takes place. The DNA damage response requires the coordinated interaction between DNA repair and checkpoint pathways. Telomeres of budding yeast are capped by the Cdc13 complex. In the temperature-sensitive cdc13-1 strain, telomeres are unprotected over a specific temperature range leading to activation of the DNA damage response and subsequently cell-cycle arrest. Inactivation of cdc13-1 results in the generation of long regions of single-stranded DNA (ssDNA) and is affected by the activity of various checkpoint proteins and nucleases. This paper describes a mathematical model of how uncapped telomeres in budding yeast initiate the checkpoint pathway leading to cell-cycle arrest. The model was encoded in the Systems Biology Markup Language (SBML) and simulated using the stochastic simulation system Biology of Ageing e-Science Integration and Simulation (BASIS). Each simulation follows the time course of one mother cell keeping track of the number of cell divisions, the level of activity of each of the checkpoint proteins, the activity of nucleases and the amount of ssDNA generated. The model can be used to carry out a variety of in silico experiments in which different genes are knocked out and the results of simulation are compared to experimental data. Possible extensions to the model are also discussed.

Modelling antipredator vigilance and flight response in group foragers when warning signals are ambiguous.

The trade-off between feeding and vigilance in flocks of birds has been extensively studied and modelled. An assumption of many models is that if one bird spots the predator, it gives a signal and the rest of the flock takes flight. However, it has been observed that birds do not always respond to signals and in fact many signals turn out to be false alarms. Since taking flight is both costly in time and energy, it may be advantageous for birds not to respond to all alarm calls. A model is developed to show under what circumstances birds should respond to a signal. The model predicts that under most, but not all, circumstances, birds should respond to multiple detections but not to single detections. The model also predicts that if birds respond to all flights, they will have to compensate for the time lost to feeding and the greater energy requirement of spending more time in flight, by being less vigilant, and they have a lower probability of survival than birds which only respond to multiple detections.

A spatial model of antipredator vigilance.

Many species of animals have to perform two contradictory tasks: feeding, and avoiding becoming food for others. A large number of theoretical and empirical studies have investigated the trade-off between feeding and antipredator vigilance, especially in birds. An important factor which has been neglected in these studies is that of the area occupied by the flock. If individuals feed close together, competition increases and feeding rates decrease. However, if individuals space themselves widely, then vigilance efficiency goes down and there is an increased predation risk. We develop a vigilance model which allows birds to control the area the flock occupies as well as their vigilance rate. The optimal strategy is found for the birds under a variety of environmental conditions. In particular the effect of each environmental parameter on this optimum is considered in turn. How the model can be adapted for different bird species is also investigated.

Comparison of the measurement of serum cotinine levels by gas chromatography and radioimmunoassay.

Standard cotinine solutions, controls and human serum samples containing cotinine have been measured by both radioimmunoassay (RIA) and gas chromatographic (GC) techniques. Cross-checks on standards and controls showed good agreement. However, for samples containing greater than 50 ng ml-1 of cotinine, RIA gave results on average 60% higher than GC. Determinations by using RIA and GC on samples containing less than 7 ng ml-1 of cotinine gave no significant correlation. The importance of the age of the serum sample has been investigated, and it is suggested that the age may affect the determination when dealing with low levels of cotinine.

Considerations of the chemical complexity of ETS with regard to inhalation studies.

Any inhalation study that investigates environmental tobacco smoke, ETS, is considering a very complex entity. ETS contains numerous chemicals that are continuously changing both in their absolute concentration, in the ratio of concentration between one and another, and even in their particulate to vapour phase distribution. Moreover, when considering ETS in real-life situations, many of the chemical components of ETS will be present as a result of sources other than tobacco smoking. This paper emphasises that the chemical and physical nature of ETS must be considered in the design and interpretation of any inhalation study on ETS, and illustrates the difficulty in defining precisely what constitutes ETS in such studies.