Probing the entanglement and locating knots in ring polymers: a comparative study of different arc closure schemes

The interplay between the topological and geometrical properties of a polymer ring can be clarified by establishing the entanglement trapped in any portion (arc) of the ring. The task requires to close the open arcs into a ring, and the resulting topological state may depend on the specific closure scheme that is followed. To understand the impact of this ambiguity in contexts of practical interest, such as knot localization in a ring with non trivial topology, we apply various closure schemes to model ring polymers. The rings have the same length and topological state (a trefoil knot) but have different degree of compactness. The comparison suggests that a novel method, termed the minimally-interfering closure, can be profitably used to characterize the arc entanglement in a robust and computationally-efficient way. This closure method is finally applied to the knot localization problem which is tackled using two different localization schemes based on top-down or bottom-up searches.Comment: 9 pages, 7 figures. Submitted to Progress of Theoretical Physic

Multiscale entanglement in ring polymers under spherical confinement

The interplay of geometrical and topological entanglement in semiflexible knotted polymer rings confined inside a spherical cavity is investigated using advanced numerical methods. By using stringent and robust algorithms for locating knots, we characterize how the knot length lk depends on the ring contour length, Lc and the radius of the confining sphere, Rc . In the no- and strong- confinement cases we observe weak knot localization and complete knot delocalization, respectively. We show that the complex interplay of lk, Lc and Rc that seamlessly bridges these two limits can be encompassed by a simple scaling argument based on deflection theory. The same argument is used to rationalize the multiscale character of the entanglement that emerges with increasing confinement.Comment: 9 pages 9 figure

Multiscale Entanglement in Spherically Confined DNA Rings

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KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers

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Digitalization and valorization of the genotypic and phenotypic information retained within the FEM grapevine germplasm

The maintenance and valorization of genetic diversity is an undoubtable resource for the viticulture of the future, since the climate crisis is forcing us to think of new, more resilient varieties. For this reason, the grapevine germplasm of the Fondazione Edmund Mach has been continuously expanded in the last decade to a total of 3,120 accessions, whose trueness-to-type has been verified by means of the universal set of nine microsatellites. About two thirds are V. vinifera subsp. vinifera accessions, while the rest consists of naturalized and selected hybrids, V. vinifera subsp. sylvestris, and pure species. The genetic material has also been characterized over three consecutive years for ampelographic, vine development, and biotic stress response traits to be exploited for experimental purposes. All the data and metadata have been digitalized and hosted in a SQL database, the FEMVitisDB, developed with an ontology driven paradigm to annotate the deposited information. The database was built following the MIAPPE checklist to ensure data FAIRness. A RESTful WebServiceAPI based on BrAPI and a web frontend were developed to easily explore the information in the repository. Findings about the captured genetic diversity, the identified unique profiles, and the scouted unknown and therefore novel genotypes will be discussed. The latter enrich the genetic asset of the grapevine community, towards the feeding of international databases. Where feasible, the first degree of parentage relationship has been reconstructed. Finally, the outcomes regarding the inferred phenological core collections will be introduced to provide an information arsenal for future ’omics analyses

Prognostication in palliative radiotherapy-ProPaRT: Accuracy of prognostic scores

BackgroundPrognostication can be used within a tailored decision-making process to achieve a more personalized approach to the care of patients with cancer. This prospective observational study evaluated the accuracy of the Palliative Prognostic score (PaP score) to predict survival in patients identified by oncologists as candidates for palliative radiotherapy (PRT). We also studied interrater variability for the clinical prediction of survival and PaP scores and assessed the accuracy of the Survival Prediction Score (SPS) and TEACHH score. Materials and methodsConsecutive patients were enrolled at first access to our Radiotherapy and Palliative Care Outpatient Clinic. The discriminating ability of the prognostic models was assessed using Harrell's C index, and the corresponding 95% confidence intervals (95% CI) were obtained by bootstrapping. ResultsIn total, 255 patients with metastatic cancer were evaluated, and 123 (48.2%) were selected for PRT, all of whom completed treatment without interruption. Then, 10.6% of the irradiated patients who died underwent treatment within the last 30 days of life. The PaP score showed an accuracy of 74.8 (95% CI, 69.5-80.1) for radiation oncologist (RO) and 80.7 (95% CI, 75.9-85.5) for palliative care physician (PCP) in predicting 30-day survival. The accuracy of TEACHH was 76.1 (95% CI, 70.9-81.3) and 64.7 (95% CI, 58.8-70.6) for RO and PCP, respectively, and the accuracy of SPS was 70 (95% CI, 64.4-75.6) and 72.8 (95% CI, 67.3-78.3). ConclusionAccurate prognostication can identify candidates for low-fraction PRT during the last days of life who are more likely to complete the planned treatment without interruption.All the scores showed good discriminating capacity; the PaP had the higher accuracy, especially when used in a multidisciplinary way

On the origin and propagation of the COVID-19 outbreak in the Italian Province of Trento, a tourist region of Northern Italy

15openInternationalItalian coauthor/editorBackground: Trentino is an Italian province with a tourism-based economy, bordering the regions of Lombardy and Veneto, where the two earliest and largest outbreaks of COVID-19 occurred in Italy. The earliest cases in Trentino were reported in the first week of March 2020, with most of the cases occurring in the winter sport areas in the Dolomites mountain range. The number of reported cases decreased over the summer months and was followed by a second wave in the autumn and winter of 2020. Methods: we performed high-coverage Oxford Nanopore sequencing of 253 positive SARS-CoV-2 swabs collected in Trentino between March and December 2020. Results: in this work, we analyzed genome sequences to trace the routes through which the virus entered the area, and assessed whether the autumnal resurgence could be attributed to lineages persisting undetected during summer, or as a consequence of new introductions. Conclusions: Comparing the draft genomes analyzed with a large selection of European sequences retrieved from GISAID we found that multiple introductions of the virus occurred at the early stage of the epidemics; the two epidemic waves were unrelated; the second wave was due to reintroductions of the virus in summer when traveling restrictions were upliftedopenBianco, Luca; Moser, Mirko; Silverj, Andrea; Micheletti, Diego; Lorenzin, Giovanni; Collini, Lucia; Barbareschi, Mattia; Lanzafame, Paolo; Segata, Nicola; Pindo, Massimo; Franceschi, Pietro; Rota-Stabelli, Omar; Rizzoli, Annapaola; Fontana, Paolo; Donati, ClaudioBianco, L.; Moser, M.; Silverj, A.; Micheletti, D.; Lorenzin, G.; Collini, L.; Barbareschi, M.; Lanzafame, P.; Segata, N.; Pindo, M.; Franceschi, P.; Rota-Stabelli, O.; Rizzoli, A.; Fontana, P.; Donati, C

Structure and dynamics of ring polymers: entanglement effects because of solution density and ring topology

The effects of entanglement in solutions and melts of unknotted ring polymers have been addressed by several theoretical and numerical studies. The system properties have been typically profiled as a function of ring contour length at fixed solution density. Here, we use a different approach to investigate numerically the equilibrium and kinetic properties of solutions of model ring polymers. Specifically, the ring contour length is maintained fixed, while the interplay of inter- and intra-chain entanglement is modulated by varying both solution density (from infinite dilution up to \approx 40 % volume occupancy) and ring topology (by considering unknotted and trefoil-knotted chains). The equilibrium metric properties of rings with either topology are found to be only weakly affected by the increase of solution density. Even at the highest density, the average ring size, shape anisotropy and length of the knotted region differ at most by 40% from those of isolated rings. Conversely, kinetics are strongly affected by the degree of inter-chain entanglement: for both unknots and trefoils the characteristic times of ring size relaxation, reorientation and diffusion change by one order of magnitude across the considered range of concentrations. Yet, significant topology-dependent differences in kinetics are observed only for very dilute solutions (much below the ring overlap threshold). For knotted rings, the slowest kinetic process is found to correspond to the diffusion of the knotted region along the ring backbone.Comment: 17 pages, 11 figure

Unifying view of mechanical and functional hotspots across class A GPCRs

G protein-coupled receptors (GPCRs) are the largest superfamily of signaling proteins. Their activation process is accompanied by conformational changes that have not yet been fully uncovered. Here, we carry out a novel comparative analysis of internal structural fluctuations across a variety of receptors from class A GPCRs, which currently has the richest structural coverage. We infer the local mechanical couplings underpinning the receptors' functional dynamics and finally identify those amino acids whose virtual deletion causes a significant softening of the mechanical network. The relevance of these amino acids is demonstrated by their overlap with those known to be crucial for GPCR function, based on static structural criteria. The differences with the latter set allow us to identify those sites whose functional role is more clearly detected by considering dynamical and mechanical properties. Of these sites with a genuine mechanical/dynamical character, the top ranking is amino acid 7x52, a previously unexplored, and experimentally verifiable key site for GPCR conformational response to ligand binding. \ua9 2017 Ponzoni et al