Multiprotein DNA looping

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switch-like transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.Comment: 11 pages, 4 figure

Thinning of beech forests stocking on shallow calcareous soil maintains soil C and N stocks in the long run

Sustainable forest management should avoid disturbance and volatilization of the soil carbon (C) and nitrogen (N) stocks both under present and projected future climate. Earlier studies have shown that thinning of European beech forests induces a strong initial perturbation of the soil C and N cycles in shallow Rendzic Leptosol, which consists of lower soil N retention and strongly enhanced gaseous losses observed over several years. Persistence of these effects could decrease soil organic matter (SOM) levels and associated soil functions such as erosion protection, nutrient retention, and fertility. Therefore, we resampled untreated control and thinned stands a decade after thinning at sites representing both typical present day and projected future climatic conditions for European beech forests. We determined soil organic C and total N stocks, as well as δ13C and δ15N as integrators of changes in soil C and N cycles. Thinning did not alter these parameters at any of the sampled sites, indicating that initial effects on soil C and N cycles constitute short-term perturbations. Consequently, thinning may be considered a sustainable beech forest management strategy with regard to the maintenance of soil organic C and total N stocks both under present and future climat

Conservation Laws in Smooth Particle Hydrodynamics: the DEVA Code

We describe DEVA, a multistep AP3M-like-SPH code particularly designed to study galaxy formation and evolution in connection with the global cosmological model. This code uses a formulation of SPH equations which ensures both energy and entropy conservation by including the so-called \bn h terms. Particular attention has also been paid to angular momentum conservation and to the accuracy of our code. We find that, in order to avoid unphysical solutions, our code requires that cooling processes must be implemented in a non-multistep way. We detail various cosmological simulations which have been performed to test our code and also to study the influence of the \bn h terms. Our results indicate that such correction terms have a non-negligible effect on some cosmological simulations, especially on high density regions associated either to shock fronts or central cores of collapsed objects. Moreover, they suggest that codes paying a particular attention to the implementation of conservation laws of physics at the scales of interest, can attain good accuracy levels in conservation laws with limited computational resources.Comment: 36 pages, 10 figures. Accepted for publication in The Astrophysical Journa

Positive and negative feedbacks and free-scale pattern distribution in rural-population dynamics

Depopulation of rural areas is a widespread phenomenon that has occurred in most industrialized countries, and has contributed significantly to a reduction in the productivity of agro-ecological resources. In this study, we identified the main trends in the dynamics of rural populations in the Central Pyrenees in the 20th C and early 21st C, and used density independent and density dependent models and identified the main factors that have influenced the dynamics. In addition, we investigated the change in the power law distribution of population size in those periods. Populations exhibited density-dependent positive feedback between 1960 and 2010, and a long-term positive correlation between agricultural activity and population size, which has resulted in a free-scale population distribution that has been disrupted by the collapse of the traditional agricultural society and by emigration to the industrialized cities. We concluded that complex socio-ecological systems that have strong feedback mechanisms can contribute to disruptive population collapses, which can be identified by changes in the pattern of population distribution

Critical thinking: the ARDESOS-DIAPROVE programme in dialogue with the Inference to the Best and Only explanation

[EN]In our daily lives, we are often faced with the need to explain various phenomena, but we do not always select the most accurate explanation. For example, let us consider a “toxic” relationship with physical and psychological abuse, where one of the partners is reluctant to end it. Explanations for this situation can range from emotional or economic dependency to irrational hypotheses such as witchcraft. Surprisingly, some people may turn to the latter explanation and consequently seek ineffective solutions, such as visiting a witch doctor instead of a psychologist. This choice of an inappropriate explanation can lead to actions that are not only ineffective but potentially harmful. This example underscores the importance of inference to the best explanation (IBE) in everyday decision making. IBE involves selecting the hypothesis that would best explain the available body of data or evidence, a process that is crucial to making sound decisions but is also vulnerable to bias and errors of judgment. Within this context, the purpose of our article is to explore how the IBE process and the selection of appropriate explanations impact decision making and problem solving in real life. To this end, we systematically analyze the role of IBE in the ARDESOS-DIAPROVE program, evaluating how this approach can enhance the teaching and practice of critical thinking

The influence of the da Vinci surgical robot on electromagnetic tracking in a clinical environment

Robot-assisted surgery is increasingly used in surgery for cancer. Reduced overview and loss of anatomical orientation are challenges that might be solved with image-guided surgical navigation using electromagnetic tracking (EMT). However, the robot’s presence may distort the electromagnetic field, affecting EMT accuracy. The aim of this study was to evaluate the robot’s influence on EMT accuracy. For this purpose, two different electromagnetic field generators were used inside a clinical surgical environment: a table top field generator (TTFG) and a planar field generator (PFG). The position and orientation of sensors within the electromagnetic field were measured using an accurate in-house developed 3D board. Baseline accuracy was measured without the robot, followed by stepwise introduction of potential distortion sources (robot and robotic instruments). The absolute accuracy was determined within the entire 3D board and in the clinical working volume. For the baseline setup, median errors in the entire tracking volume within the 3D board were 0.9 mm and 0.3° (TTFG), and 1.1 mm and 0.4° (PFG). Adding the robot and instruments did not affect the TTFG’s position accuracy (p = 0.60), while the PFG’s accuracies decreased to 1.5 mm and 0.7° (p &lt; 0.001). For both field generators, when adding robot and instruments, accuracies inside the clinical working volume were higher compared to the entire tracking 3D board volume, 0.7 mm and 0.3° (TTFG), and 1.1 mm and 0.7° (PFG). Introduction of a surgical robot and robotic instruments shows limited distortion of the EMT field, allowing sufficient accuracy for surgical navigation in robotic procedures.</p

Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension

We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Non-linear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding processComment: 13 pages, 3 figure

Plant-plant interactions scale up to produce vegetation spatial patterns: The influence of long- and short-term process

Vegetation spatial patterns emerge in response to feedback interactions between organisms and their environment, because of the redistribution of water and nutrients around the plant canopy or as a consequence of facilitation/competition interactions at the plant level, even in the absence of pre-existing substratum heterogeneities. It has been suggested that changes in vegetation spatial patterns are a signal of transition shift in ecosystems. Understanding the factors that lead to aggregated spatial patterns and control the transition to random distributions requires that environmental and species information is taken into account. In this study, we investigated the relative contributions of aridity (a long-term process), to which vegetation is adapted, and the area covered by bare soil (short-term process) to plant-plant associations and their contribution to aggregated spatial patterns. The study was conducted in a gradient of aridity ranging from that in subalpine grassland habitats in the Pyrenees and Sierra Nevada mountains to that in the semiarid steppes of Cabo de Gata and the middle Ebro Valley in Spain. We compared sites that differed in aridity and a geophysical feature (north- vs. south-facing slope). We observed that the relative contribution of aridity and bare soil to plant-plant facilitation and vegetation aggregation differed in subalpine and semiarid areas. Facilitation in subalpine habitats had a marked effect on aggregated spatial patterns, while aridity contributed to disruption of these patterns. Conversely, in semiarid habitats, the disruption of aggregated patterns was mainly promoted by an increase in bare soil area rather than in aridity. In semiarid habitats, the higher level of stress on south-facing slopes increased facilitation interactions relative to north-facing slopes, although this did not enhance the persistence of aggregated spatial patterns. We conclude that the use of aggregated spatial patterns as an indicator of ecosystem shift must distinguish and separately take account of long-term processes to which vegetation adapt, and short-term process