Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair.

DNA double-strand breaks are lesions that form during metabolism, DNA replication and exposure to mutagens. When a double-strand break occurs one of a number of repair mechanisms is recruited, all of which have differing propensities for mutational events. Despite DNA repair being of crucial importance, the relative contribution of these mechanisms and their regulatory interactions remain to be fully elucidated. Understanding these mutational processes will have a profound impact on our knowledge of genomic instability, with implications across health, disease and evolution. Here we present a new method to model the combined activation of non-homologous end joining, single strand annealing and alternative end joining, following exposure to ionising radiation. We use Bayesian statistics to integrate eight biological data sets of double-strand break repair curves under varying genetic knockouts and confirm that our model is predictive by re-simulating and comparing to additional data. Analysis of the model suggests that there are at least three disjoint modes of repair, which we assign as fast, slow and intermediate. Our results show that when multiple data sets are combined, the rate for intermediate repair is variable amongst genetic knockouts. Further analysis suggests that the ratio between slow and intermediate repair depends on the presence or absence of DNA-PKcs and Ku70, which implies that non-homologous end joining and alternative end joining are not independent. Finally, we consider the proportion of double-strand breaks within each mechanism as a time series and predict activity as a function of repair rate. We outline how our insights can be directly tested using imaging and sequencing techniques and conclude that there is evidence of variable dynamics in alternative repair pathways. Our approach is an important step towards providing a unifying theoretical framework for the dynamics of DNA repair processes

A computational method for the investigation of multistable systems and its application to genetic switches

BACKGROUND: Genetic switches exhibit multistability, form the basis of epigenetic memory, and are found in natural decision making systems, such as cell fate determination in developmental pathways. Synthetic genetic switches can be used for recording the presence of different environmental signals, for changing phenotype using synthetic inputs and as building blocks for higher-level sequential logic circuits. Understanding how multistable switches can be constructed and how they function within larger biological systems is therefore key to synthetic biology. RESULTS: Here we present a new computational tool, called StabilityFinder, that takes advantage of sequential Monte Carlo methods to identify regions of parameter space capable of producing multistable behaviour, while handling uncertainty in biochemical rate constants and initial conditions. The algorithm works by clustering trajectories in phase space, and iteratively minimizing a distance metric. Here we examine a collection of models of genetic switches, ranging from the deterministic Gardner toggle switch to stochastic models containing different positive feedback connections. We uncover the design principles behind making bistable, tristable and quadristable switches, and find that rate of gene expression is a key parameter. We demonstrate the ability of the framework to examine more complex systems and examine the design principles of a three gene switch. Our framework allows us to relax the assumptions that are often used in genetic switch models and we show that more complex abstractions are still capable of multistable behaviour. CONCLUSIONS: Our results suggest many ways in which genetic switches can be enhanced and offer designs for the construction of novel switches. Our analysis also highlights subtle changes in correlation of experimentally tunable parameters that can lead to bifurcations in deterministic and stochastic systems. Overall we demonstrate that StabilityFinder will be a valuable tool in the future design and construction of novel gene networks

In vivo confinement promotes collective migration of neural crest cells

Collective cell migration is fundamental throughout development and in many diseases. Spatial confinement using micropatterns has been shown to promote collective cell migration in vitro, but its effect in vivo remains unclear. Combining computational and experimental approaches, we show that the in vivo collective migration of neural crest cells (NCCs) depends on such confinement. We demonstrate that confinement may be imposed by the spatiotemporal distribution of a nonpermissive substrate provided by versican, an extracellular matrix molecule previously proposed to have contrasting roles: barrier or promoter of NCC migration. We resolve the controversy by demonstrating that versican works as an inhibitor of NCC migration and also acts as a guiding cue by forming exclusionary boundaries. Our model predicts an optimal number of cells in a given confinement width to allow for directional migration. This optimum coincides with the width of neural crest migratory streams analyzed across different species, proposing an explanation for the highly conserved nature of NCC streams during development

Ultra-processed food consumption and obesity in the Australian adult population

Background: Rapid simultaneous increases in ultra-processed food sales and obesity prevalence have been observed worldwide, including in Australia. Consumption of ultra-processed foods by the Australian population was previously shown to be systematically associated with increased risk of intakes of nutrients outside levels recommended for the prevention of obesity. This study aims to explore the association between ultra-processed food consumption and obesity among the Australian adult population and stratifying by age group, sex and physical activity level. Methods: A cross-sectional analysis of anthropometric and dietary data from 7411 Australians aged ≥20 years from the National Nutrition and Physical Activity Survey 2011–2012 was performed. Food consumption was evaluated through 24-h recall. The NOVA system was used to identify ultra-processed foods, i.e. industrial formulations manufactured from substances derived from foods and typically added of flavours, colours and other cosmetic additives, such as soft drinks, confectionery, sweet or savoury packaged snacks, microwaveable frozen meals and fast food dishes. Measured weight, height and waist circumference (WC) data were used to calculate the body mass index (BMI) and diagnosis of obesity and abdominal obesity. Regression models were used to evaluate the association of dietary share of ultra-processed foods (quintiles) and obesity indicators, adjusting for socio-demographic variables, physical activity and smoking. Results: Significant (P-trend ≤ 0.001) direct dose–response associations between the dietary share of ultra-processed foods and indicators of obesity were found after adjustment. In the multivariable regression analysis, those in the highest quintile of ultra-processed food consumption had significantly higher BMI (0.97 kg/m2; 95% CI 0.42, 1.51) and WC (1.92 cm; 95% CI 0.57, 3.27) and higher odds of having obesity (OR = 1.61; 95% CI 1.27, 2.04) and abdominal obesity (OR = 1.38; 95% CI 1.10, 1.72) compared with those in the lowest quintile of consumption. Subgroup analyses showed that the trend towards positive associations for all obesity indicators remained in all age groups, sex and physical activity level. Conclusion: The findings add to the growing evidence that ultra-processed food consumption is associated with obesity and support the potential role of ultra-processed foods in contributing to obesity in Australia

Directional collective cell migration emerges as a property of cell interactions.

Collective cell migration is a fundamental process, occurring during embryogenesis and cancer metastasis. Neural crest cells exhibit such coordinated migration, where aberrant motion can lead to fatality or dysfunction of the embryo. Migration involves at least two complementary mechanisms: contact inhibition of locomotion (a repulsive interaction corresponding to a directional change of migration upon contact with a reciprocating cell), and co-attraction (a mutual chemoattraction mechanism). Here, we develop and employ a parameterized discrete element model of neural crest cells, to investigate how these mechanisms contribute to long-range directional migration during development. Motion is characterized using a coherence parameter and the time taken to reach, collectively, a target location. The simulated cell group is shown to switch from a diffusive to a persistent state as the response-rate to co-attraction is increased. Furthermore, the model predicts that when co-attraction is inhibited, neural crest cells can migrate into restrictive regions. Indeed, inhibition of co-attraction in vivo and in vitro leads to cell invasion into restrictive areas, confirming the prediction of the model. This suggests that the interplay between the complementary mechanisms may contribute to guidance of the neural crest. We conclude that directional migration is a system property and does not require action of external chemoattractants

Monitoring Cognitive and Emotional Processes Through Pupil and Cardiac Response During Dynamic Versus Logical Task

The paper deals with the links between physiological measurements and cognitive and emotional functioning. As long as the operator is a key agent in charge of complex systems, the definition of metrics able to predict his performance is a great challenge. The measurement of the physiological state is a very promising way but a very acute comprehension is required; in particular few studies compare autonomous nervous system reactivity according to specific cognitive processes during task performance and task related psychological stress is often ignored. We compared physiological parameters recorded on 24 healthy subjects facing two neuropsychological tasks: a dynamic task that require problem solving in a world that continually evolves over time and a logical task representative of cognitive processes performed by operators facing everyday problem solving. Results showed that the mean pupil diameter change was higher during the dynamic task; conversely, the heart rate was more elevated during the logical task. Finally, the systolic blood pressure seemed to be strongly sensitive to psychological stress. A better taking into account of the precise influence of a given cognitive activity and both workload and related task-induced psychological stress during task performance is a promising way to better monitor operators in complex working situations to detect mental overload or pejorative stress factor of error

A case of panuveitis with hypopyon due to presumed ocular leishmaniasis in a HIV patient.

BACKGROUND: Post-kala-azar dermal leishmaniasis is a well-known immunologic cutaneous reaction. There are few case reports of ocular leishmaniasis. It is a sight-threatening condition that needs to be rapidly recognized and treated to avoid permanent visual loss. Ocular leishmaniasis panuveitis can present with severe inflammation in patients with highly active anti-retroviral therapy (HAART)-induced immune reconstitution syndrome. FINDINGS: A case of a 40-year-old man, human immunodeficiency virus (HIV) positive on HAART, with a presumed diagnosis of ocular leishmaniasis, is presented. He had a past history of visceral leishmaniasis and was referred to the uveitis service with rapidly worsening panuveitis and counting fingers vision in both eyes. On empirical anti-leishmania therapy and systemic steroids, the visual acuity of the left eye improved to 6/9 but remained poor in the right eye. Based on the medical history, improvement with therapy and the exclusion of other common infections, a presumed diagnosis of ocular leishmaniasis-related panuveitis was made. CONCLUSIONS: A major immune reaction against lingering parasites may play a key role in the pathogenesis of this sight-threatening and rapidly progressive condition. Both the infection and the immune reaction should be treated

Seeing the woods for the trees: the problem of information inefficiency and information overload on operator performance

One of the recurring questions in designing dynamic control environments is whether providing more information leads to better operational decisions. The idea of having every piece of information is increasingly tempting (and in safety critical domains often mandatory) but has become a potential obstacle for designers and operators. The present research study examined this challenge of appropriate information design and usability within a railway control setting. A laboratory study was conducted to investigate the presentation of different levels of information (taken from data processing framework, Dadashi et al., 2014) and the association with, and potential prediction of, the performance of a human operator when completing a cognitively demanding problem solving scenario within railways. Results indicated that presenting users only with information corresponding to their cognitive task, and in the absence of other, non task-relevant information, improves the performance of their problem solving/alarm handling. Knowing the key features of interest to various agents (machine or human) and using the data processing framework to guide the optimal level of information required by each of these agents could potentially lead to safer and more usable designs

Impacts of climate change on plant diseases – opinions and trends

There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases in the coming decades. This review addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies on the impacts of climate change on plant health. Sudden Oak Death is used as an introductory case study: Californian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronicity between host cambium activity and pathogen colonization rate. A summary of observed and predicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Prediction and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertainty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to interdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in mountain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (including our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycorrhiza, using long-term and large-scale datasets and considering various plant disease control methods