Diffusion-based DNA target colocalization by thermodynamic mechanisms

In eukaryotic cell nuclei, a variety of DNA interactions with nuclear elements occur, which, in combination with intra- and inter- chromosomal cross-talks, shape a functional 3D architecture. In some cases they are organized by active, i.e. actin/myosin, motors. More often, however, they have been related to passive diffusion mechanisms. Yet, the crucial questions on how DNA loci recognize their target and are reliably shuttled to their destination by Brownian diffusion are still open. Here, we complement the current experimental scenario by considering a physics model, in which the interaction between distant loci is mediated by diffusing bridging molecules. We show that, in such a system, the mechanism underlying target recognition and colocalization is a thermodynamic switch-like process (a phase transition) that only occurs if the concentration and affinity of binding molecules is above a threshold, or else stable contacts are not possible. We also briefly discuss the kinetics of this "passive-shuttling" process, as produced by random diffusion of DNA loci and their binders, and derive predictions based on the effects of genomic modifications and deletions

Froth-like minimizers of a non local free energy functional with competing interactions

We investigate the ground and low energy states of a one dimensional non local free energy functional describing at a mean field level a spin system with both ferromagnetic and antiferromagnetic interactions. In particular, the antiferromagnetic interaction is assumed to have a range much larger than the ferromagnetic one. The competition between these two effects is expected to lead to the spontaneous emergence of a regular alternation of long intervals on which the spin profile is magnetized either up or down, with an oscillation scale intermediate between the range of the ferromagnetic and that of the antiferromagnetic interaction. In this sense, the optimal or quasi-optimal profiles are "froth-like": if seen on the scale of the antiferromagnetic potential they look neutral, but if seen at the microscope they actually consist of big bubbles of two different phases alternating among each other. In this paper we prove the validity of this picture, we compute the oscillation scale of the quasi-optimal profiles and we quantify their distance in norm from a reference periodic profile. The proof consists of two main steps: we first coarse grain the system on a scale intermediate between the range of the ferromagnetic potential and the expected optimal oscillation scale; in this way we reduce the original functional to an effective "sharp interface" one. Next, we study the latter by reflection positivity methods, which require as a key ingredient the exact locality of the short range term. Our proof has the conceptual interest of combining coarse graining with reflection positivity methods, an idea that is presumably useful in much more general contexts than the one studied here.Comment: 38 pages, 2 figure

Phospholipase C–mediated hydrolysis of PIP2 releases ERM proteins from lymphocyte membrane

Mechanisms controlling the disassembly of ezrin/radixin/moesin (ERM) proteins, which link the cytoskeleton to the plasma membrane, are incompletely understood. In lymphocytes, chemokine (e.g., SDF-1) stimulation inactivates ERM proteins, causing their release from the plasma membrane and dephosphorylation. SDF-1–mediated inactivation of ERM proteins is blocked by phospholipase C (PLC) inhibitors. Conversely, reduction of phosphatidylinositol 4,5-bisphosphate (PIP2) levels by activation of PLC, expression of active PLC mutants, or acute targeting of phosphoinositide 5-phosphatase to the plasma membrane promotes release and dephosphorylation of moesin and ezrin. Although expression of phosphomimetic moesin (T558D) or ezrin (T567D) mutants enhances membrane association, activation of PLC still relocalizes them to the cytosol. Similarly, in vitro binding of ERM proteins to the cytoplasmic tail of CD44 is also dependent on PIP2. These results demonstrate a new role of PLCs in rapid cytoskeletal remodeling and an additional key role of PIP2 in ERM protein biology, namely hydrolysis-mediated ERM inactivation

Mixed-species plantations of eucalyptus with nitrogen fixing trees: a review

Mixed-species plantations of Eucalyptus with a nitrogen (N2) fixing species have the potential to increase productivity while maintaining soil fertility, compared to Eucalyptus monocultures. However, it is difficult to predict combinations of species and sites that will lead to these benefits. We review the processes and interactions occurring in mixed plantations, 5 and the influence of species or site attributes, to aid the selection of successful combinations of species and sites. Successful mixtures, where productivity is increased over that of monocultures, have often developed stratified canopies, such that the less shade-tolerant species overtops the more shadetolerant species. Successful mixtures also have significantly higher rates of N and P cycling than 10 Eucalyptus monocultures. It is therefore important to select N2-fixing species with readily decomposable litter and high rates of nutrient cycling, as well as high rates of N2-fixation. While the dynamics of N2-fixation in tree stands are not well understood, it appears as though eucalypts can benefit from fixed N as early as the first or second year following plantation establishment. A meta-analysis of 18 published studies revealed several trials in which mixtures were significantly 15 (

The Lancet Psychiatry Commission : a blueprint for protecting physical health in people with mental illness

No abstract available

Actin foci facilitate activation of the phospholipase C-γ in primary T lymphocytes via the WASP pathway

Wiscott Aldrich Syndrome protein (WASP) deficiency results in defects in calcium ion signaling, cytoskeletal regulation, gene transcription and overall T cell activation. The activation of WASP constitutes a key pathway for actin filament nucleation. Yet, when WASP function is eliminated there is negligible effect on actin polymerization at the immunological synapse, leading to gaps in our understanding of the events connecting WASP and calcium ion signaling. Here, we identify a fraction of total synaptic F-actin selectively generated by WASP in the form of distinct F-actin ‘foci’. These foci are polymerized de novo as a result of the T cell receptor (TCR) proximal tyrosine kinase cascade, and facilitate distal signaling events including PLCγ1 activation and subsequent cytoplasmic calcium ion elevation. We conclude that WASP generates a dynamic F-actin architecture in the context of the immunological synapse, which then amplifies the downstream signals required for an optimal immune response. DOI: http://dx.doi.org/10.7554/eLife.04953.00