A nonequilibrium strategy for fast target search on the genome

Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "chromophoresis", the dynamics of DNA-binding proteins up or down gradients in the density of epigenetic marks, or colours (biochemical tags on the genome). We focus on a set of proteins that deposit marks from which they are repelled---a case which is only encountered away from thermodynamic equilibrium. For suitable ranges of kinetic parameter values, chromophoretic proteins can perform unidirectional motion and are optimally redistributed along the genome. Importantly, they can also locally unravel a region of the genome which is collapsed due to self-interactions and "dive" deep into its core, for a striking enhancement of the efficiency of target search on such an inaccessible substrate. We discuss the potential relevance of chromophoresis for the location of DNA lesions.Comment: 5 pages, 5 figure

Work fluctuations of self-propelled particles in the phase separated state

We study the large deviations of the distribution P(W_\tau) of the work associated with the propulsion of individual active brownian particles in a time interval \tau, in the region of the phase diagram where macroscopic phase separation takes place. P(W_\tau) is characterised by two peaks, associated to particles in the gaseous and in the clusterised phases, and two separate non-convex branches. Accordingly, the generating function of W_\tau cumulants displays a double singularity. We discuss the origin of such non-convex branches in terms of the peculiar dynamics of the system phases, and the relation between the observation time \tau and the typical persistence times of the particles in the two phases.Comment: 7 pages, 5 figure

Analysis of overload and sensorless control capability of PM-assisted synchronous reluctance machines

Synchronous reluctance machines are a valid alternative to induction motors for industrial applications requiring variable speed regulation. To mitigate the well-known downside of their lower power factor, permanent-magnetassisted topologies are adopted. Both high-strength rare-earth magnets and low cost ferrite magnets can be used in such machines. Their design and optimization procedures have been discussed in related literature. This paper compares synchronous reluctance machines assisted with NdFeB and ferrite magnets, focusing on torque overload capability and feasibility of saliencybased position estimation algorithms. Three prototypes were realized and tested. They all have the stator of a commercial induction motor, and three custom synchronous reluctance rotors with same laminations: one has no magnets, the other two have NdFeB and ferrite magnets respectively, designed to give the same torque at rated current. Results from simulations and experiments are presented, focusing on torque and demagnetization limits in the over-current loading range. Moreover, the feasibility of saliency-based sensorless methods is investigated, both at high and low current loads. The results of the paper suggest that the ferrite-assisted solution is the candidate solution for replacing induction motors in variable speed applications

Inviscid limit of the active interface equations

We present a detailed solution of the active interface equations in the inviscid limit. The active interface equations were previously introduced as a toy model of membrane-protein systems: they describe a stochastic interface where growth is stimulated by inclusions which themselves move on the interface. In the inviscid limit, the equations reduce to a pair of coupled conservation laws. After discussing how the inviscid limit is obtained, we turn to the corresponding Riemann problem: the solution of the set of conservation laws with discontinuous initial condition. In particular, by considering two physically meaningful initial conditions, a giant trough and a giant peak in the interface, we elucidate the generation of shock waves and rarefaction fans in the system. Then, by combining several Riemann problems, we construct an oscillating solution of the active interface with periodic boundaries conditions. The existence of this oscillating state reflects the reciprocal coupling between the two conserved quantities in our system.Comment: 22 pages, 11 figure

Quantification of the starling population, estimation and mapping of the damage to olive crops in the apulia region

The presence of wildlife in areas with a high concentration of farming activities can create a conflict between conservation objectives and productive purposes. Near Brindisi (Apulia, S-E Italy), a substantial amount of cash compensation claims for damages reported by local farmers and attributed to starlings (Sturnus vulgaris) has been registered. The aim of this study was to quantify the starling population wintering in the Apulia region, in order to assess the potential damage to crop production caused by this species. Our analysis was conducted over three years and included three main activities: a study of starling abundance and movements, the identification of areas and crops affected by damages, and a determination of the damage to the agricultural system in terms of quantity and concentration (heatmap). The study showed a loss of expected production that was coherent with the eating capacity of starlings wintering in the region. This means a loss, in terms of gross profitable production, of around 550,000 euros concentrated in a few narrow areas close to the roosts. Results on species behavior, damage quantification, and mapping are useful elements aimed to activate trade-off measures to preserve production and protection objectives, and to allow policymakers to address enforcement interventions and to establish parameters for financial compensation

RNA Docking and Local Translation Regulate Site-Specific Axon Remodeling In Vivo

Nascent proteins can be positioned rapidly at precise subcellular locations by local protein synthesis (LPS) to facilitate localized growth responses. Axon arbor architecture, a major determinant of synaptic connectivity, is shaped by localized growth responses, but it is unknown whether LPS influences these responses in vivo. Using high-resolution live imaging, we examined the spatiotemporal dynamics of RNA and LPS in retinal axons during arborization in vivo. Endogenous RNA tracking reveals that RNA granules dock at sites of branch emergence and invade stabilized branches. Live translation reporter analysis reveals that de novo ß-actin hotspots colocalize with docked RNA granules at the bases and tips of new branches. Inhibition of axonal ß-actin mRNA translation disrupts arbor dynamics primarily by reducing new branch emergence and leads to impoverished terminal arbors. The results demonstrate a requirement for LPS in building arbor complexity and suggest a key role for pre-synaptic LPS in assembling neural circuits.This work was supported by Cambridge Trust, Croucher Foundation, Sir Edward Youde Memorial Fund (H.H.-W.W.), Gates Cambridge (J.Q.L.), Fundac¸ a˜ o para a Cieˆ ncia e Tecnologia (C.M.R.), Wellcome Trust Senior Investigator Award (100329/Z/ 12/Z) (W.A.H.), EPSRC Grant (EP/H018301/1), MRC Grant (MR/K015850/1 and MR/K02292X/1), Wellcome Trust (089703/Z/09/Z) (C.F.K.), Wellcome Trust Programme Grant (085314/Z/08/Z), and ERC Advanced Grant (322817) (C.E.H.)

Single Molecule Translation Imaging Visualizes the Dynamics of Local β-Actin Synthesis in Retinal Axons

Local mRNA translation occurs in growing axons enabling precise control of the proteome in response to signals. To measure quantitatively the spatiotemporal dynamics of protein synthesis in growth cones, we further developed a technique for single molecule translation imaging (SMTI). We report that Netrin-1 triggers a burst of β-actin synthesis at multiple non-repetitive sites, particularly in the periphery. The response is remarkably rapid starting within 20 seconds of cue application.This work was supported by grants from the Leverhulme Trust, the Engineering and Physical Sciences Research Council, UK (grant EP/H018301/1), the Medical Research Council (grant MR/K015850/1, and MR/K02292X/1), the Wellcome Trust (089703/Z/09/Z) (C.F.K.), Sir Edward Youde Memorial Fund, Croucher Foundation, Cambridge Trust (H.H.W.) Gates Cambridge Scholarship (J.Q.L.), Wellcome Trust Studentship (V.U.), European Research Council Advanced Grant (322817), the Wellcome Trust (085314/Z/08/Z) (C.E.H.)

A simple cytofluorimetric score may optimize testing for biallelic CEBPA mutations in patients with acute myeloid leukemia

Acute myeloid leukemia with biallelic mutation of CEBPA (CEBPA-dm AML) is a distinct good prognosis entity recognized by WHO 2016 classification. However, testing for CEBPA mutation is challenging, due to the intrinsic characteristics of the mutation itself. Indeed, molecular analysis cannot be performed with NGS technique and requires Sanger sequencing. The association of recurrent mutations or translocations with specific immunophenotypic patterns has been already reported in other AML subtypes. The aim of this study was the development of a specific cytofluorimetric score (CEBPA-dm score), in order to distinguish patients who are unlikely to harbor the mutation. To this end, the correlation of CEBPA-dm score with the presence of the mutation was analyzed in 50 consecutive AML patients with normal karyotype and without NPM1 mutation (that is mutually exclusive with CEBPA mutation). One point each was assigned for expression of HLA DR, CD7, CD13, CD15, CD33, CD34 and one point for lack of expression of CD14. OS was not influenced by sex, age and CEBPA-dm score. Multivariate OS analysis showed that CEBPA-dm (p < 0.02) and FLT3-ITD (p < 0.01) were the strongest independent predictors of OS. With a high negative predictive value (100%), CEBPA-dm score < 6 was able to identify patients who are unlikely to have the mutation. Therefore, the application of this simple score might optimize the use of expensive and time-consuming diagnostic and prognostic assessment in the baseline work up of AML patients

On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons.

Ribosome assembly occurs mainly in the nucleolus, yet recent studies have revealed robust enrichment and translation of mRNAs encoding many ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Here, we report a physical and functional interaction between locally synthesized RPs and ribosomes in the axon. We show that axonal RP translation is regulated through a sequence motif, CUIC, that forms an RNA-loop structure in the region immediately upstream of the initiation codon. Using imaging and subcellular proteomics techniques, we show that RPs synthesized in axons join axonal ribosomes in a nucleolus-independent fashion. Inhibition of axonal CUIC-regulated RP translation decreases local translation activity and reduces axon branching in the developing brain, revealing the physiological relevance of axonal RP synthesis in vivo. These results suggest that axonal translation supplies cytoplasmic RPs to maintain/modify local ribosomal function far from the nucleolus in neurons.This work was supported by Wellcome Trust Grants (085314/Z/08/Z and 203249/Z/16/Z) to C.E.H. and (100329/Z/12/Z) to W.A.H., European Research Council Advanced Grant (322817) to C.E.H., Champalimaud Vision Award to C.E.H. and by the Netherlands Organization for Scientific Research (NWO Rubicon 019.161LW.033) to M.K. CFK acknowledges funding from the UK Engineering and Physical Sciences Research Council, EPSRC (grants EP/L015889/1 and EP/H018301/1), the Wellcome Trust (grants 3-3249/Z/16/Z and 089703/Z/09/Z) and the UK Medical Research Council, MRC (grants MR/K015850/1 and MR/K02292X/1) and Infinitus (China) Ltd