Nucleic Acids Res

Site-directed spin labeling is emerging as an essential tool to investigate the structural and dynamical features of RNA. We propose here an enzymatic method, which allows the insertion of a paramagnetic center at a specific position in an RNA molecule. The technique is based on a segmental approach using a ligation protocol with T4 RNA ligase 2. One transcribed acceptor RNA is ligated to a donor RNA in which a thio-modified nucleotide is introduced at its 5'-end by in vitro transcription with T7 RNA polymerase. The paramagnetic thiol-specific reagent is subsequently attached to the RNA ligation product. This novel strategy is demonstrated by introducing a paramagnetic probe into the 55 nucleotides long RNA corresponding to K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-Box leader RNA. The efficiency of the coupling reaction and the quality of the resulting spin-labeled RNA were assessed by Mass Spectrometry, Electron Paramagnetic Resonance (EPR) and Nuclear Magnetic Resonance (NMR). This method enables various combinations of isotopic segmental labeling and spin labeling schemes, a strategy that will be of particular interest to investigate the structural and dynamical properties of large RNA complexes by NMR and EPR spectroscopies

RNA Biol

The HIV-1 Vif protein plays an essential role in the regulation of the infectivity of HIV-1 virion and in vivo pathogenesis. Vif neutralizes the human DNA-editing enzyme APOBEC3 protein, an antiretroviral cellular factor from the innate immune system, allowing the virus to escape the host defence system. It was shown that Vif is packaged into viral particles through specific interactions with the viral genomic RNA. Conserved and structured sequences from the 5'-noncoding region, such as the Tat-responsive element (TAR) or the genomic RNA dimerization initiation site (DIS), are primary binding sites for Vif. In the present study we used isothermal titration calorimetry to investigate sequence and structure determinants important for Vif binding to short viral RNA corresponding to TAR and DIS stem-loops. We showed that Vif specifically binds TAR and DIS in the low nanomolar range. In addition, Vif primarily binds the TAR UCU bulge, but not the apical loop. Determinants for Vif binding to the DIS loop-loop complex are likely more complex and involve the self-complementary loop together with the upper part of the stem. These results suggest that Tat-TAR inhibitors or DIS small molecule binders might be also effective to disturb Vif-TAR and Vif-DIS binding in order to reduce Vif packaging into virions

Novel sheathless CE-MS interface as an original and powerful infusion platform for nanoESI study: from intact proteins to high molecular mass noncovalent complexes.:

Development of nano-electrospray (nanoESI) sources allowed to increase significantly the sensitivity which is often lacking when studying biological noncovalent assemblies. However, the flow rate used to infuse the sample into the mass spectrometer cannot be precisely controlled with nanoESI and the robustness of the system could represent an issue. In this study, we have used a sheathless capillary electrophoresis-mass spectrometry (CESI) prototype as a nanoESI infusion device. The hydrodynamic mobilization of the capillary content was characterized and the ability of the system to generate a stable electrospray under controlled flow rate conditions ranging from 4 up to 900 nL/min was demonstrated. The effect of the infusing flow rate on the detection of an intact model protein analyzed under native conditions was investigated. Results demonstrated a significant increase in sensitivity of 46-fold and a signal-to-noise ratio improvement of nearly 5-fold when using an infusing flow rate from 456.9 down to 13.7 nL/min. The CESI prototype was further used to detect successfully the β ring homodimer in its native conformation. Obtained results were compared with those achieved with conventional ESI. Intensity signals were increased by a factor of 5, while sample consumption decreased 80 times. β ring complexed with the P14 peptide was also studied. Finally, the CESI interface was used to observe the quaternary structure of native hemocyanins from Carcinus maenas crabs; this high molecular complex coexisting under various degrees of complexation and resulting in masses ranging from 445 kDa to 1.34 MD

Discovery, Timing, and Multiwavelength Observations of the Black Widow Millisecond Pulsar PSR J1555-2908

We report the discovery of PSR J1555-2908, a 1.79 ms radio and gamma-ray pulsar in a 5.6 hr binary system with a minimum companion mass of 0.052 $M_\odot$. This fast and energetic ($\dot E = 3 \times 10^{35}$ erg/s) millisecond pulsar was first detected as a gamma-ray point source in Fermi LAT sky survey observations. Guided by a steep spectrum radio point source in the Fermi error region, we performed a search at 820 MHz with the Green Bank Telescope that first discovered the pulsations. The initial radio pulse timing observations provided enough information to seed a search for gamma-ray pulsations in the LAT data, from which we derive a timing solution valid for the full Fermi mission. In addition to the radio and gamma-ray pulsation discovery and timing, we searched for X-ray pulsations using NICER but no significant pulsations were detected. We also obtained time-series r-band photometry that indicates strong heating of the companion star by the pulsar wind. Material blown off the heated companion eclipses the 820 MHz radio pulse during inferior conjunction of the companion for ~10% of the orbit, which is twice the angle subtended by its Roche lobe in an edge-on system.Comment: 15 pages, 6 figures, accepted by Ap

The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation

Crc is a key global translational regulator in Pseudomonads that orchestrates the hierarchy of induction of several catabolic pathways for amino acids, sugars, hydrocarbons or aromatic compounds. In the presence of amino acids, which are preferred carbon sources, Crc inhibits translation of the Pseudomonas putida alkS and benR mRNAs, which code for transcriptional regulators of genes required to assimilate alkanes (hydrocarbons) and benzoate (an aromatic compound), respectively. Crc binds to the 5′-end of these mRNAs, but the sequence and/or structure recognized, and the way in which it inhibits translation, were unknown. We have determined the secondary structure of the alkS mRNA 5′-end through its sensitivity to several ribonucleases and chemical reagents. Footprinting and band-shift assays using variant alkS mRNAs have shown that Crc specifically binds to a short unpaired A-rich sequence located adjacent to the alkS AUG start codon. This interaction is stable enough to prevent formation of the translational initiation complex. A similar Crc-binding site was localized at benR mRNA, upstream of the Shine–Dalgarno sequence. This allowed predicting binding sites at other Crc-regulated genes, deriving a consensus sequence that will help to validate new Crc targets and to discriminate between direct and indirect effects of this regulator

Discovery, Timing, and Multiwavelength Observations of the Black Widow Millisecond Pulsar PSR J1555-2908

We report the discovery of PSR J1555-2908, a 1.79 ms radio and gamma-ray pulsar in a 5.6 hr binary system with a minimum companion mass of 0.052 M ⊙. This fast and energetic ( Ė=3×1035 erg s-1) millisecond pulsar was first detected as a gamma-ray point source in Fermi Large Area Telescope (LAT) sky survey observations. Guided by a steep-spectrum radio point source in the Fermi error region, we performed a search at 820 MHz with the Green Bank Telescope that first discovered the pulsations. The initial radio pulse timing observations provided enough information to seed a search for gamma-ray pulsations in the LAT data, from which we derive a timing solution valid for the full Fermi mission. In addition to the discovery and timing of radio and gamma-ray pulsations, we searched for X-ray pulsations using NICER but no significant pulsations were detected. We also obtained time-series r-band photometry that indicates strong heating of the companion star by the pulsar wind. Material blown off the heated companion eclipses the 820 MHz radio pulse during inferior conjunction of the companion for ≈10% of the orbit, which is twice the angle subtended by its Roche lobe in an edge-on system. © 2022. The Author(s). Published by the American Astronomical Society

Towards a More Resilient Euro Area. Ideas from the 'Future Europe' Forum. CEPS Paperback, 18 June 2018

Much progress has been made in improving resilience of the single currency since the beginning of the crisis. But many important issues remain to be tackled. The leaders of euro-area member states are expected to use the European Union Summit on 28-29 June 2018 to take preliminary decisions about which additional reforms to pursue. The run-up to this meeting saw a lively debate involving economists and policymakers, albeit against a backdrop of rising Euroscepticism among and waning trust between European partners. ESMT and the German Council of Economic Experts (GCEE) initiated the ‘Future Europe’ forum in the summer of 2017, aiming to bring together a high-level group of economists to discuss economically sensible, legally sound, and politically feasible concepts that deserved to be taken forward. By offering a forum for discussion, we hoped to foster constructive dialogue. They chose an innovative video-conference format to bring experts together face to face without them having to leave their desks (or living rooms). Some 30 economists took part in a dozen such virtual meetings, and their contributions culminated in a publication, brought out jointly by the Centre for European Policy Studies (CEPS), ESMT and the GCEE. The ebookTowards a More Resilient Euro Area: Ideas from the ‘Future Europe’ forum gathers summaries of these economists’ proposals and the discussions they sparked. The main aim was not to produce a variant of the jointly-authored academic paper, but to foster a lively debate between economists who – as one participant put it – “agree somewhat, but not too much”. The publication as a result combines essays outlining an individual author’s thoughts with summaries of the informed, impassioned, and always respectful discussions during each forum. While each contribution can only be attributed to the respective author, each idea and thought is a valuable input that deserves to be considered by European governments as they set about the next euro-area reforms

Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic

The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of local transmission and long-distance dispersal events. Comparison of genomes before and during the pandemic peak shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, local molecular clock modeling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of origination through an intrasubtype reassortment.Peer Reviewe

Comparison of polychlorinated biphenyl levels across studies of human neurodevelopment.

Polychlorinated biphenyls (PCBs) are persistent pollutants that are ubiquitous in the food chain, and detectable amounts are in the blood of almost every person in most populations that have been examined. Extensive evidence from animal studies shows that PCBs are neurotoxins, even at low doses. Interpretation of human data regarding low-level, early-life PCB exposure and subsequent neurodevelopment is problematic because levels of exposure were not similarly quantified across studies. We expressed the exposure levels from 10 studies of PCB and neurodevelopment in a uniform manner using a combination of data from original investigators, laboratory reanalyses, calculations based on published data, and expert opinion. The mainstay of our comparison was the median level of PCB 153 in maternal pregnancy serum. The median concentration of PCB 153 in the 10 studies ranged from 30 to 450 ng/g serum lipid, and the median of the 10 medians was 110 ng/g. We found that (a)) the distribution of PCB 153 exposure in most studies overlapped substantially, (b)) exposure levels in the Faroe Islands study were about 3-4-fold higher than in most other studies, and (c)) the exposure levels in the two recent U.S. studies were about one-third of those in the four earlier U.S. studies or recent Dutch, German, and northern Québec studies. Our results will facilitate a direct comparison of the findings on PCBs and neurodevelopment when they are published for all 10 studies

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie