Coarse-grained modelling of supercoiled RNA

We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.Comment: 8 pages + 5 pages Supplementary Materia

Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation

It is well established that gene regulation can be achieved through activator and repressor proteins that bind to DNA and switch particular genes on or off, and that complex metabolic networks deter- mine the levels of transcription of a given gene at a given time. Using three complementary computa- tional techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are con- strained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any require- ment for external signalling factors. Our models com- bine atomistic molecular dynamics (MD) with coarse- grained simulations and statistical mechanical calcu- lations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denatura- tion in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informa- tional transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles

Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix

Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other alternative structures. Various polymer models have been developed to capture these properties, with Monte-Carlo (MC) approaches dedicated to the inference of thermodynamic properties. In this chapter, we explain how to perform such Monte-Carlo simulations, following two objectives. On one hand, we present the self-avoiding supercoiled Worm-Like Chain (ssWLC) model, which is known to capture the folding properties of supercoiled DNA, and provide a detailed explanation of a standard MC simulation method. On the other hand, we explain how to extend this ssWLC model to include structural transitions of the helix.Comment: Book chapter to appear in The Bacterial Nucleoid, Methods and Protocols, Springer serie

Emotions and Food Consumption: Emotional Eating Behavior in a European Population

Emotion can reflect in the perception of food consumption. An increase in food intake during emotional and psychological conditions may have a negative impact on human health. The aim of this cross-sectional study was to determine the associations between food consumption, emotional eating behavior, and emotional conditions such as stress, depression, loneliness, boredom eating, maintaining vigilance and alertness, and emotional food consolation. We used a Motivations for Food Choices Questionnaire (Eating Motivations, EATMOT) to determine the emotional aspects of food consumption in 9052 respondents living in 12 European countries between October 2017 and March 2018. Ordinal linear regression was used to identify the associations between the emotional eating behavior and emotional conditions such as stress, depression, loneliness, emotional consolation, and reasons to improve physical and psychological conditions. The regression models confirmed the associations between food consumption, emotional conditions, and emotional eating behavior. Associations were found between the emotional eating behavior and stress (odds ratio (OR) = 1.30, 95% confidence interval (CI) = 1.07–1.60, p = 0.010), depressive mood (OR = 1.41, 95% CI = 1.40–1.43, p < 0.001), loneliness (OR = 1.60, 95% CI = 1.58–1.62, p < 0.001), boredom (OR = 1.37, 95% CI = 1.36–1.39, p < 0.001), and emotional consolation (OR = 1.55, 95% CI = 1.54–1.57, p < 0.001). Emotional eating was associated with an effort to improve physical and psychological conditions, such as controlling body weight (OR = 1.11, 95% CI = 1.10–1.12, p < 0.001), keeping awake and alert (OR = 1.19, 95% CI = 1.19–1.20, p < 0.001) and consumption to feel good (OR = 1.22, 95% CI = 1.21–1.22, p < 0.001). In conclusion, emotions might provoke emotional eating behavior. The appropriate way to handle stress, depression, or other emotional states is important in conditions of being emotionally overwhelmed. The public should be educated on how to handle different emotional states. The focus should be moved somehow from emotional eating and the consumption of unhealthy food to healthy lifestyle practices, including regular exercise and healthy eating habits. Thus, it is necessary to halt these negative health effects on human health through public health programs.info:eu-repo/semantics/publishedVersio

DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism

Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. Firstly, a twist-induced denaturation bubble must diffuse so that its midpoint is near the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must be large enough to allow one of the arms to form a small number of hairpin bonds. Once the first arm is partially formed, the second arm can rapidly grow to a similar size. Because bubbles can twist back on themselves, they need considerably fewer bases to resolve torsional stress than the final cruciform state does. The initially stabilised cruciform therefore continues to grow, which typically proceeds synchronously, reminiscent of the S-type mechanism of cruciform formation. By using umbrella sampling techniques we calculate, for different temperatures and superhelical densities, the free energy as a function of the number of bonds in each cruciform along the correlated but non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat

Investigation of the level of knowledge in different countries about edible insects : cluster segmentation

This study aimed to investigate the level of knowledge about edible insects (EIs) in a sample of people from thirteen countries (Croatia, Greece, Latvia, Lebanon, Lithuania, Mexico, Poland, Portugal, Romania, Serbia, Slovenia, Spain, and Turkey). Data collection was based on a questionnaire survey applied through online tools between July and November 2021. For data analysis, techniques such as factor analysis, cluster analysis, and chi-square tests were used, with a significance level of 5%. A total of 27 items were used to measure knowledge on a five-point Likert scale. Applying factor analysis with principal components and Varimax rotation, a solution that explains about 55% of variance was obtained. This accounts for four factors that retained 22 of the 27 initial items: F1 = Sustainability (8 items), F2 = Nutrition (8 items), F3 = Production Factors (2 items), and F4 = Health Concerns (4 items). Internal consistency was evaluated through Cronbach’s alpha. The cluster analysis consisted of the application of hierarchical methods followed by k-means and produced three clusters (1—‘fearful’, 2—‘farming,’ and 3—‘ecological’ individuals). The characterisation of the clusters revealed that age did not influence cluster membership, while sex, education, country, living environment, professional area, and income all influenced the composition of the clusters. While participants from Mexico and Spain were fewer in the ‘fearful’ cluster, in those from Greece, Latvia, Lebanon, and Turkey, the situation was opposed. Participants from rural areas were mostly in cluster 2, which also included a higher percentage of participants with lower income. Participants from professional areas linked with biology, food, and nutrition were mostly in cluster 3. In this way, we concluded that the level of knowledge about EIs is highly variable according to the individual characteristics, namely that the social and cultural influences of the different countries lead to distinct levels of knowledge and interpretation of information, thus producing divergent approaches to the consumption of insects—some more reluctant and measuring possible risks. In contrast, others consider EIs a good and sustainable protein-food alternative.info:eu-repo/semantics/publishedVersio

Machine Learning for Health: Algorithm Auditing & Quality Control

Developers proposing new machine learning for health (ML4H) tools often pledge to match or even surpass the performance of existing tools, yet the reality is usually more complicated. Reliable deployment of ML4H to the real world is challenging as examples from diabetic retinopathy or Covid-19 screening show. We envision an integrated framework of algorithm auditing and quality control that provides a path towards the effective and reliable application of ML systems in healthcare. In this editorial, we give a summary of ongoing work towards that vision and announce a call for participation to the special issue Machine Learning for Health: Algorithm Auditing & Quality Control in this journal to advance the practice of ML4H auditing