Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human α-thrombin

: The long-range communication between the two exosites of human α-thrombin (thrombin) tightly modulates the protein-effector interactions. Duplex/quadruplex aptamers represent an emerging class of very effective binders of thrombin. Among them, NU172 and HD22 aptamers are at the forefront of exosite I and II recognition, respectively. The present study investigates the simultaneous binding of these two aptamers by combining a structural and dynamics approach. The crystal structure of the ternary complex formed by the thrombin with NU172 and HD22_27mer provides a detailed view of the simultaneous binding of these aptamers to the protein, inspiring the design of novel bivalent thrombin inhibitors. The crystal structure represents the starting model for molecular dynamics studies, which point out the cooperation between the binding at the two exosites. In particular, the binding of an aptamer to its exosite reduces the intrinsic flexibility of the other exosite, that preferentially assumes conformations similar to those observed in the bound state, suggesting a predisposition to interact with the other aptamer. This behaviour is reflected in a significant increase of the anticoagulant activity of NU172 when the inactive HD22_27mer is bound to exosite II, providing a clear evidence of the synergic action of the two aptamers

Comparison of Bayesian optimization and the reduction of resonance driving terms in the optimization of the dynamic aperture of the BESSY III MBA lattice

HZB is currently designing the lattice for BESSY III, the successor of the 1.7 GeV electron storage ring running in Berlin since 1998. HZB follows a deterministic lattice design strategy, where the natural substructures of a non-hybrid MBA lattice are optimized separately. The substructures consist of only a few parameters, that can be derived from the strategic goals of the project. In the next step, the focusing and de-focusing sextupole families are split up, to optimize the longitudinal and the transverse apertures. The paper compares two approaches to select the optimal sextupole strengths. The first one is multi-objective Bayesian optimization, where the dynamic aperture volume from tracking simulations is used as an objective to be maximized. The second approach does not involve tracking and minimizes the geometric and chromatic resonance driving terms. The comparison of the two results includes their quality in terms of the size of the achievable 3D dynamic aperture and the computational effort involved

Pending issues in protection, productivity growth, and poverty reduction

This paper selectively synthesizes much of the research on Latin American and Caribbean labor markets in recent years. Several themes emerge that are particularly relevant to ongoing policy dialogues. First, labor legislation matters, but markets may be less segmented than previously thought. The impetus to voluntary informality, which appears to be a substantial fraction of the sector, implies that the design of social safety nets and labor legislation needs to take a more integrated view of the labor market, taking into account the cost-benefit analysis workers and firms make about whether to interact with formal institutions. Second, the impact of labor market institutions on productivity growth has probably been underemphasized. Draconian firing restrictions increase litigation and uncertainty surrounding worker separations, reduce turnover and job creation, and poorly protect workers. But theory and anecdotal evidence also suggest that they, and other related state or union induced rigidities, may have an even greater disincentive effect on technological adoption, which accounts for half of economic growth. Finally, institutions can affect poverty and equity, although the effects seem generally small and channels are not always clear. Overall, the present constellation of labor regulations serves workers and firms poorly and both could benefit from substantial reform.Labor Markets,Labor Standards,Economic Theory&Research,Work&Working Conditions,Labor Management and Relations

Polyelectrolyte/surfactant films: from 2D to 3D structural control

Reversible control of the 3D structure of polyelectrolyte/surfactant films at the air/water interface is showcased. A recently discovered mechanism is exploited to form highly efficient, stable and biocompatible films by spreading aggregates composed of poly-L-lysine and sodium dodecyl sulfate on the surface of water. Reversible control of: (1) the surface monolayer coverage, (2) the switching on or off discrete extended structures, and (3) the extended structure coverage is demonstrated for the first time. The intricacy by which the film structures can be controlled is unprecedented and opens exciting potential to optimize film properties by chemical design for novel biomedical transfer applications.We thank the Institut Laue-Langevin for beam time on FIGARO (DOIs: https://doi.org/10.5291/ILL-DATA.9-12-614 and https://doi.org/10.5291/ILL-DATA.9-12-631), Simon Wood for technical assistance and the Partnership for Soft Condensed Matter (PSCM) for lab support. IV acknowledges the financial support from the Hungarian National Research, Development and Innovation Office (NKFIH K116629). AM acknowledges the financial support from MICINN under grant PID2021-129054NA-I00 and the IKUR Strategy of the Basque Government.Peer reviewe

The LogiSmile Project - Piloting autonomous vehicles for last-mile Logistics in european cities

The use of autonomous technologies for last-mile logistics has the potential to reduce operation costs, cut emissions from the delivery sector, improve safety levels in communities, and provide efficient delivery solutions in areas which experience access regulations. Unfortunately, the implementation of real-life, economically-sustainable, and safe use cases in open urban environments remains scarce, especially in Europe. As a consequence, there is a real need for pilot tests of innovative delivery schemes based on autonomous technologies, not only in numerical simulations, but also in representative urban settings throughout Europe. In this paper, we will present the LogiSmile project, in which a consortium of European partners is piloting a transport management system for autonomous last-mile logistics. Beyond describing the delivery characteristics and use cases of this system, we also highlight the lessons learnt during the course of the project about managing innovation in the urban mobility field, gathering insight form the innovation triple helix (academia, industry and public sector).Peer ReviewedPostprint (published version

Seven benzimidazole pesticides combined at sub-threshold levels induce micronuclei in vitro

This article is made available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http:// creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Benzimidazoles act by disrupting microtubule polymerisation and are capable of inducing the formation of micronuclei. Considering the similarities in their mechanisms of action (inhibition of microtubule assembly by binding to the colchicine-binding site on tubulin monomers), combination effects according to the principles of concentration addition might occur. If so, it is to be expected that several benzimidazoles contribute to micronucleus formation even when each single one is present at or below threshold levels. This would have profound implications for risk assessment, but the idea has never been tested rigorously. To fill this gap, we analysed micronucleus frequencies for seven benzimidazoles, including the fungicide benomyl, its metabolite carbendazim, the anthelmintics albendazole, albendazole oxide, flubendazole, mebendazole and oxibendazole. Thiabendazole was also tested but was inactive. We used the cytochalasin-blocked micronucleus assay with CHO-K1 cells according to OECD guidelines, and employed an automated micronucleus scoring system based on image analysis to establish quantitative concentration–response relationships for the seven active benzimidazoles. Based on this information, we predicted additive combination effects for a mixture of the seven benzimidazoles by using the concepts of concentration addition and independent action. The observed effects of the mixture agreed very well with those predicted by concentration addition. Independent action underestimated the observed combined effects by a large margin. With a mixture that combined all benzimidazoles at their estimated threshold concentrations for micronucleus induction, micronucleus frequencies of ~15.5% were observed, correctly anticipated by concentration addition. On the basis of independent action, this mixture was expected to produce no effects. Our data provide convincing evidence that concentration addition is applicable to combinations of benzimidazoles that form micronuclei by disrupting microtubule polymerisation. They present a rationale for grouping these chemicals together for the purpose of cumulative risk assessment.United Kingdom Food Standards Agenc

Engineering phosphatidylinositol-4,5-bisphosphate model membranes enriched in endocytic cargo: a neutron reflectometry, AFM and QCM-D structural study

The combination of in vitro models of biological membranes based on solid-supported lipid bilayers (SLBs) and of surface sensitive techniques, such as neutron reflectometry (NR), atomic force microscopy (AFM) and quartz crystal microbalance with dissipation monitoring (QCM-D), is well suited to provide quantitative information about molecular level interactions and lipid spatial distributions. In this work, cellular plasma membranes have been mimicked by designing complex SLB, containing phosphatidylinositol 4,5-bisphosphate (PtdIns4,5P2) lipids as well as incorporating synthetic lipo-peptides that simulate the cytoplasmic tails of transmembrane proteins. The QCM-D results revealed that the adsorption and fusion kinetics of PtdIns4,5P2 are highly dependent of Mg2+. Additionally, it was shown that increasing concentrations of PtdIns4,5P2 leads to the formation of SLBs with higher homogeneity. The presence of PtdIns4,5P2 clusters was visualized by AFM. NR provided important insights about the structural organization of the various components within the SLB, highlighting that the leaflet symmetry of these SLBs is broken by the presence of CD4-derived cargo peptides. Finally, we foresee our study to be a starting point for more sophisticated in vitro models of biological membranes with the incorporation of inositol phospholipids and synthetic endocytic motifs.publishe

A low-latency feedback system for the control of horizontal betatron oscillations

Reinforcement learning (RL) algorithms are investigated at KIT as an option to control the beam dynamics at storage rings. These methods require specialized hardware to satisfy throughput and latency constraints dictated by the timescale of the relevant phenomena. The KINGFISHER platform, based on the novel Xilinx Versal Adaptive Compute and Acceleration Platform, is an ideal candidate to deploy RL-on-a-chip thanks to its ability to execute computationally intensive and low latency feedback loops in the order of tens of microseconds. In this publication, we will present the integration of the KINGFISHER system at the Karlsruhe Research Accelerator (KARA), as a proof-of-principle turn-by-turn control feedback loop, to control induced transversal oscillations of an electron beam