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DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA–enzyme interactions in biological systems. Here we use molecular dynamics simulations and a coarse-grained model of DNA to address the nanopore unzipping of DNA filaments that are knotted. This previously unaddressed problem is motivated by the fact that DNA knots inevitably occur in isolated equilibrated filaments and in vivo. We study how different types of tight knots in the DNA segment just outside the pore impact unzipping at different driving forces. We establish three main results. First, knots do not significantly affect the unzipping process at low forces. However, knotted DNAs unzip more slowly and heterogeneously than unknotted ones at high forces. Finally, we observe that the microscopic origin of the hindrance typically involves two concurrent causes: the topological friction of the DNA chain sliding along its knotted contour and the additional friction originating from the entanglement with the newly unzipped DNA. The results reveal a previously unsuspected complexity of the interplay of DNA topology and unzipping, which should be relevant for interpreting nanopore-based single-molecule unzipping experiments and improving the modeling of DNA transactions in vivo.

In addition to providing general constraints on probability distributions, fluctuation theorems allow us to infer essential information on the role played by temperature in heat exchange phenomena. In this numerical study, we measure the temperature of an out-of-equilibrium active bath using a fluctuation theorem that relates the fluctuations in the heat exchanged between two baths to their temperatures. Our setup consists of a single particle moving between two wells of a quartic potential accommodating two different baths. The heat exchanged between the two baths is monitored according to two definitions: as the kinetic energy carried by the particle whenever it jumps from one well to the other and as the work performed by the particle on one of the two baths when immersed in it. First, we consider two equilibrium baths at two different temperatures and verify that a fluctuation theorem featuring the baths temperatures holds for both heat definitions. Then, we introduce an additional Gaussian coloured noise in one of the baths, so as to make it effectively an active (out-of-equilibrium) bath. We find that a fluctuation theorem is still satisfied with both heat definitions. Interestingly, in this case the temperature obtained through the fluctuation theorem for the active bath corresponds to the kinetic temperature when considering the first heat definition, while it is larger with the second one. We interpret these results by looking at the particle jump phenomenology.

Here, the authors perform a large-scale, high-throughput biochemical assay to determine the compatibility of over 300,000 domain recombination variants of the inward rectifier K+ channel Kir2.1. They derive rules for designing domain insertion variants that fold and traffic to the cell surface and conclude that the insertion of domains at protein termini is evolutionary favoured.

Until recently, Deltex (DTX) proteins have been considered putative E3 ligases, based on the presence of an E3 RING domain in their protein coding sequence. The human DTX family includes DTX1, DTX2, DTX3, DTX3L and DTX4. Despite the fact that our knowledge of this class of E3-ubiquitin ligases is still at an early stage, our understanding of their role in oncogenesis is beginning to unfold. In fact, recently published studies allow us to define specific biological scenarios and further consolidate evidence-based working hypotheses. According to the current evidence, all DTX family members are involved in the regulation of Notch signaling, suggesting a phylogenetically conserved role in the regulation of this pathway. Indeed, additional evidence reveals a wider involvement of these proteins in other signaling complexes and cancer-promoting mechanisms beyond NOTCH signaling. DTX3, in particular, had been known to express two isoform variants (DTX3a and DTX3b). The recent identification and cloning of a third isoform variant in cancer (DTX3c), and its specific involvement in EphB4 degradation in cancer cells, sheds further light on this group of proteins and their specific role in cancer. Herein, we review the cumulative knowledge of this family of E3 Ubiquitin ligases with a specific focus on the potential oncogenic role of DTX isoforms in light of the rapidly expanding findings regarding this protein family’s cellular targets and regulated signaling pathways. Furthermore, using a comparative and bioinformatic approach, we here disclose a new putative motif of a member of this family which may help in understanding the biological and contextual differences between the members of these proteins.

Zika xrRNAs survive in host cells because they can be unwound and copied by replicases, but resist degradation by exonucleases. Here authors use atomistic models and simulations and uncover that pulling into a pore the xrRNA $${3}^{\prime}$$ 3′ end, as done by replicases, causes progressive unfolding; pulling the $${5}^{\prime}$$ 5′ end, as done by exonucleases, triggers molecular tightening.

The dataset presented here regard the analysis reported in the research article entitled “Comparison of different plasma actuation strategies for aeroelastic control on a linear compressor cascade” De Giorgi et al. (2021) [1]. These data are related to the Computational Fluid Dynamics (CFD) assessment of different plasma actuation strategies for the aeroelastic control of an aero engine compressor cascade in subsonic flow conditions. The authors evaluated the accuracy of numerical computations using experimental results. Here, both experimental and raw data of the CFD simulations are presented.

DNA polymerase θ is a polymerase-helicase essential for microhomology-mediated end-joining (MMEJ) or alternative end-joining of DNA. Here the authors use biochemical and biophysical methods to reveal how full-length human DNA polymerase θ performs MMEJ at the molecular level.

The data regard the analysis reported in the research article “Influence of actuation parameters of multi-DBD plasma actuators on the static and dynamic behavior of an airfoil in unsteady flow” [1]. The data are related to the study focused on the evaluation of the effects of an active flow control system on the performance of an airfoil in an unsteady flow, with particular focus on the influence of actuation parameters on the global performances. Keywords: Load alleviation, Plasma actuation, Active flow control, Oscillating airfoils, Actuation law, Stability control

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The present work focuses on the impact of dielectric barrier discharge (DBD) plasma actuators (PAs) on non-premixed lifted flame stabilization in a methane CH4-air Bunsen burner. Two coaxial DBD-PA configurations are considered. They are composed of a copper corona, installed on the outer surface of a quartz tube and powered with a high voltage sinusoidal signal, and a grounded needle installed along the burner axis. The two configurations differ in the standoff distance value, which indicates the positioning of the high frequency/high voltage (HV) electrode’s upper edge with respect to the needle tip. Experimental results highlight that flame reattachment is obtained at a lower dissipated power when using a negative standoff distance (i.e., placing the needle upstream with respect to the corona). At 11 kV peak-to-peak voltage and 20 kHz frequency, plasma actuation allowed for reattaching the flame with a very low dissipated power (of about 0.05 W). Numerical simulations of the electrostatic field confirmed that this negative standoff configuration has a beneficial effect on the momentum sources, which oppose the flow and show that the highest electric field extends into the inner quartz tube, as confirmed by experimental visualization close to the needle tip. The modeling predicted an increase in the gas temperature of about 21.8 °C and a slight modification of the fuel composition at the burner exit. This impacts the flame speed with a 10% increase close to the stoichiometric conditions with respect to the clean configuration.