InSiDDe: A server for designing artificial disordered proteins

InSiDDe (In Silico Disorder Design) is a program for the in silico design of intrinsically disordered proteins of desired length and disorder probability. The latter is assessed using IUPred and spans values ranging from 0.55 to 0.95 with 0.05 increments. One to ten artificial sequences per query, each made of 50 to 200 residues, can be generated by InSiDDe. We describe the rationale used to set up InSiDDe and show that an artificial sequence of 100 residues with an IUPred score of 0.6 designed by InSiDDe could be recombinantly expressed in E. coli at high levels without degradation when fused to a natural molecular recognition element (MoRE). In addition, the artificial fusion protein exhibited the expected behavior in terms of binding modulation of the specific partner recognized by the MoRE. To the best of our knowledge, InSiDDe is the first publicly available software for the design of intrinsically disordered protein (IDP) sequences. InSiDDE is publicly available online

Late Devonian (Frasnian) Asteropygine trilobites from the Frasnes area, southern border of Dinant synclinorium, Belgium

The Frasnian representatives of Asteropyginae in the Frasnes area (south Belgium) have long been relatively well-documented when compared to other trilobites in the Devonian of the Ardennes (Belgium, northern France). However, examination of the type material and new collecting by the authors indicate that a taxonomic review has become necessary. Two new species of Bradocryphaeus are recorded, B. vanherlei sp. nov. and B. neptuni sp. nov.; one additional species, B. sp. 20, is known from the pygidium alone. New material is recorded of Bradocryphaeus maillieuxi (Richter & Richter), which has hitherto been scantily illustrated in the literature. The cephalon of Heliopyge helios (Richter & Richter) is redescribed on the basis of new specimens and its holotype pygidium refigured

Experimental observation of bias-dependent non-local Andreev reflection

We investigate transport through hybrid structures consisting of two normal metal leads connected via tunnel barriers to one common superconducting electrode. We find clear evidence for the occurrence of non-local Andreev reflection and elastic cotunneling through superconductor when the separation of the tunnel barrier is comparable to the superconducting coherence length. The probability of the two processes is energy dependent, with elastic cotunneling dominating at low energy and non-local Andreev reflection at higher energies. The energy scale of the crossover is found to be the Thouless energy of the superconductor, which indicates the phase coherence of the processes. Our results are relevant for the realization of recently proposed entangler devices.Comment: 4 pages, 4 figures. Accepted for publication in PR

Current-current correlations in hybrid superconducting and normal metal multiterminal structures

We consider a hybrid system consisting of two normal metal leads weakly connected to a superconductor. Current-current correlations of the normal leads are studied in the tunneling limit at subgap voltages and temperatures. We find that only two processes contribute to the cross-correlation: the crossed Andreev reflection (emission of electrons in different leads) and the elastic cotunneling. Both processes are possible due to the finite size of the Cooper pair. Noise measurements can thus be used to probe directly the superconducting wave function without the drawbacks appearing in average current measurements where the current is dominated by direct Andreev reflection processes. By tuning the voltages it is possible to change the sign of the cross correlation. Quantitative predictions are presented both in the diffusive and ballistic regimes.Comment: 7 pages, 2 Figure

A comparative analysis of the two main documents used in small and medium-sized enterprises in France and Québec as a framework for improving occupational health and safety

Context and background: In France as in Québec, occupational health and safety (OHS) has become a national priority. While organizations in these two societies differ slightly, preventive measures are the same, and legislation requires that the chosen approach to improving OHS be reduced to writing, even in small and medium-sized enterprises. Prevention is managed through existing structures within companies and is documented by the employer. Such documentation is mandatory and allows the company to manage its risks and to monitor the hazards associated its activities. The principal document used for this purpose is known as the “Document unique” in France and the “Programme de prevention” in Québec. Motivation: The aim of this concise review of the literature is to compare the “Document unique” and the “Programme de prevention” and thereby help experts develop a universal document that combines the best features of the French and Québécois versions. Methods: Differences between these two documents are noted. Through comparative analysis, we explain how prevention, the regulatory context and the field of application are defined in each case. We then discuss the helpful features and the limitations inherent in both documents and conclude with a table of comparison. Results and conclusions: The advantages and inconveniences appear to be similar for both documents. There are nevertheless opportunities to combine the best features of the Document unique and the Programme de prévention in order to obtain an improved guide for the writing of a complete accident prevention and OHS policy appreciated by employers and employees alike

Halorubrum pleomorphic virus-6 Membrane Fusion Is Triggered by an S-Layer Component of Its Haloarchaeal Host

(1) Background: Haloarchaea comprise extremely halophilic organisms of the Archaea domain. They are single-cell organisms with distinctive membrane lipids and a protein-based cell wall or surface layer (S-layer) formed by a glycoprotein array. Pleolipoviruses, which infect haloarchaeal cells, have an envelope analogous to eukaryotic enveloped viruses. One such member, Halorubrum pleomorphic virus 6 (HRPV-6), has been shown to enter host cells through virus-cell membrane fusion. The HRPV-6 fusion activity was attributed to its VP4-like spike protein, but the physiological trigger required to induce membrane fusion remains yet unknown. (2) Methods: We used SDS-PAGE mass spectroscopy to characterize the S-layer extract, established a proteoliposome system, and used R18-fluorescence dequenching to measure membrane fusion. (3) Results: We show that the S-layer extraction by Mg2+ chelating from the HRPV-6 host, Halorubrum sp. SS7-4, abrogates HRPV-6 membrane fusion. When we in turn reconstituted the S-layer extract from Hrr. sp. SS7-4 onto liposomes in the presence of Mg2+, HRPV-6 membrane fusion with the proteoliposomes could be readily observed. This was not the case with liposomes alone or with proteoliposomes carrying the S-layer extract from other haloarchaea, such as Haloferax volcanii. (4) Conclusions: The S-layer extract from the host, Hrr. sp. SS7-4, corresponds to the physiological fusion trigger of HRPV-6

Halorubrum pleomorphic virus-6 Membrane Fusion Is Triggered by an S-Layer Component of Its Haloarchaeal Host

(1) Background: Haloarchaea comprise extremely halophilic organisms of the Archaea domain. They are single-cell organisms with distinctive membrane lipids and a protein-based cell wall or surface layer (S-layer) formed by a glycoprotein array. Pleolipoviruses, which infect haloarchaeal cells, have an envelope analogous to eukaryotic enveloped viruses. One such member, Halorubrum pleomorphic virus 6 (HRPV-6), has been shown to enter host cells through virus-cell membrane fusion. The HRPV-6 fusion activity was attributed to its VP4-like spike protein, but the physiological trigger required to induce membrane fusion remains yet unknown. (2) Methods: We used SDS-PAGE mass spectroscopy to characterize the S-layer extract, established a proteoliposome system, and used R18-fluorescence dequenching to measure membrane fusion. (3) Results: We show that the S-layer extraction by Mg2+ chelating from the HRPV-6 host, Halorubrum sp. SS7-4, abrogates HRPV-6 membrane fusion. When we in turn reconstituted the S-layer extract from Hrr. sp. SS7-4 onto liposomes in the presence of Mg2+, HRPV-6 membrane fusion with the proteoliposomes could be readily observed. This was not the case with liposomes alone or with proteoliposomes carrying the S-layer extract from other haloarchaea, such as Haloferax volcanii. (4) Conclusions: The S-layer extract from the host, Hrr. sp. SS7-4, corresponds to the physiological fusion trigger of HRPV-6

Structure and Dynamics of RNA Guanine Quadruplexes in SARS-CoV-2 Genome. Original Strategies against Emerging Viruses

Guanine quadruplex (G4) structures in the viral genome have a key role in modulating viruses' biological activity. While several DNA G4 structures have been experimentally resolved, RNA G4s are definitely less explored. We report the first calculated G4 structure of the RG-1 RNA sequence of SARS-CoV-2 genome, obtained by using a multiscale approach combining quantum and classical molecular modeling and corroborated by the excellent agreement between the corresponding calculated and experimental circular dichroism spectra. We prove the stability of the RG-1 G4 arrangement as well as its interaction with G4 ligands potentially inhibiting viral protein translation