RNA structures regulating nidovirus RNA synthesis

Viruses depend on their host cell for the production of their progeny. The genetic information that is required to regulate this process is contained in the viral genome. In the case of plus-stranded RNA viruses, like nidoviruses, the RNA genome is directly involved in translation (resulting in the synthesis of viral enzymes), replication, transcription and encapsidation into progeny virions. The multifunctional nature of these viral RNA genomes requires the tight control of all these processes for which they are equipped with RNA sequence motifs and higher order RNA structures. At 25-32 kilobases, nidoviruses possess the largest known RNA genomes. One characteristic of nidoviruses is that in infected cells they produce a nested set of subgenomic (sg) mRNAs. The sg mRNAs of two nidovirus families, arteri- and coronaviruses, consist of two RNA stretches that are noncontiguous in the genome. It was demonstrated that primary and higher order RNA structures play a crucial role during the synthesis of these special sg mRNAs. The obtained knowledge of arterivirus RNA synthesis, formed the basis for an virus inhibitor study in which regulatory RNA sequences were targeted in an attempt to block virus replication in cell culture using phosphorodiamidate morpholino oligomers (P-PMOs).Leiden University Medical HospitalNWO-CW 99-010Moleculaire basis van virus pathogenese en antivirale strategiee

A Fourier optics approach to evaluate the astrometric performance of MICADO

We present our investigation into the impact of wavefront errors on high accuracy astrometry using Fourier Optics. MICADO, the upcoming near-IR imaging instrument for the Extremely Large Telescope, will offer capabilities for relative astrometry with an accuracy of 50 micro arcseconds ({\mu}as). Due to the large size of the point spread function (PSF) compared to the astrometric requirement, the detailed shape and position of the PSF on the detector must be well understood. Furthermore, because the atmospheric dispersion corrector of MICADO is a moving component within an otherwise mostly static instrument, it might not be sufficient to perform a simple pre-observation calibration. Therefore, we have built a Fourier Optics framework, allowing us to evaluate the small changes in the centroid position of the PSF as a function of wavefront error. For a complete evaluation, we model both the low order surface form errors, using Zernike polynomials, and the mid- and high-spatial frequencies, using Power Spectral Density analysis. The described work will then make it possible, performing full diffractive beam propagation, to assess the expected astrometric performance of MICADO.Comment: 13 pages, 13 figures, to be submitted to the SPIE Astronomical Telescopes & Instrumentation 2020 conferenc

A new structure model for the packaging signal in the genome of group IIa Coronaviruses

Biophysical Structural ChemistrySupramolecular & Biomaterials Chemistr

Differences in lung clearance index and functional residual capacity between two commercial multiple-breath nitrogen washout devices in healthy children and adults

Contains fulltext : 221454.pdf (publisher's version ) (Open Access

Roles of Trm9- and ALKBH8-like proteins in the formation of modified wobble uridines in Arabidopsis tRNA

Uridine at the wobble position of tRNA is usually modified, and modification is required for accurate and efficient protein translation. In eukaryotes, wobble uridines are modified into 5-methoxycarbonylmethyluridine (mcm5U), 5-carbamoylmethyluridine (ncm5U) or derivatives thereof. Here, we demonstrate, both by in vitro and in vivo studies, that the Arabidopsis thaliana methyltransferase AT1G31600, denoted by us AtTRM9, is responsible for the final step in mcm5U formation, thus representing a functional homologue of the Saccharomyces cerevisiae Trm9 protein. We also show that the enzymatic activity of AtTRM9 depends on either one of two closely related proteins, AtTRM112a and AtTRM112b. Moreover, we demonstrate that AT1G36310, denoted AtALKBH8, is required for hydroxylation of mcm5U to (S)-mchm5U in tRNAGlyUCC, and has a function similar to the mammalian dioxygenase ALKBH8. Interestingly, atalkbh8 mutant plants displayed strongly increased levels of mcm5U, and also of mcm5Um, its 2′-O-ribose methylated derivative. This suggests that accumulated mcm5U is prone to further ribose methylation by a non-specialized mechanism, and may challenge the notion that the existence of mcm5U- and mcm5Um-containing forms of the selenocysteine-specific tRNASec in mammals reflects an important regulatory process. The present study reveals a role in for several hitherto uncharacterized Arabidopsis proteins in the formation of modified wobble uridines

ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA

Mammals have nine different homologues (ALKBH1–9) of the Escherichia coli DNA repair demethylase AlkB. ALKBH2 is a genuine DNA repair enzyme, but the in vivo function of the other ALKBH proteins has remained elusive. It was recently shown that ALKBH8 contains an additional transfer RNA (tRNA) methyltransferase domain, which generates the wobble nucleoside 5-methoxycarbonylmethyluridine (mcm5U) from its precursor 5-carboxymethyluridine (cm5U). In this study, we report that (R)- and (S)-5-methoxycarbonylhydroxymethyluridine (mchm5U), hydroxylated forms of mcm5U, are present in mammalian , and , respectively, representing the first example of a diastereomeric pair of modified RNA nucleosides. Through in vitro and in vivo studies, we show that both diastereomers of mchm5U are generated from mcm5U, and that the AlkB domain of ALKBH8 specifically hydroxylates mcm5U into (S)-mchm5U in . These findings expand the function of the ALKBH oxygenases beyond nucleic acid repair and increase the current knowledge on mammalian wobble uridine modifications and their biogenesis

Low-frequency measurement of the tunneling amplitude in a flux qubit

We have observed signatures of resonant tunneling in an Al three-junction qubit, inductively coupled to a Nb LC tank circuit. The resonant properties of the tank oscillator are sensitive to the effective susceptibility (or inductance) of the qubit, which changes drastically as its flux states pass through degeneracy. The tunneling amplitude is estimated from the data. We find good agreement with the theoretical predictions in the regime of their validity.Comment: REVTeX4, 3pp., 3 EPS figures. v2: new sample, textual clarifications. v3: minor polishing; final, to appear in PRB Rapid

The role of confined placental mosaicism in fetal growth restriction:A retrospective cohort study

Objective: To evaluate which cytogenetic characteristics of confined placental mosaicism (CPM) detected in the first trimester chorionic villi and/or placentas in terms of chromosome aberration, cell lineage involved and trisomy origin will lead to fetal growth restriction and low birthweight. Methods: Cohort study using routinely collected perinatal data and cytogenetic data of non-invasive prenatal testing, the first trimester chorionic villi sampling and postnatal placentas. Results: 215 CPM cases were found. Fetal growth restriction (FGR) and low birthweight below the 10 th percentile (BW &lt; p10) were seen in 34.0% and 23.1%, respectively. Excluding cases of trisomy 16, 29.1% showed FGR and 17.9% had a BW &lt; p10. The highest rate of FGR and BW &lt; p10 was found in CPM type 3, but differences with type 1 and 2 were not significant. FGR and BW &lt; p10 were significantly more often observed in cases with meiotic trisomies. Conclusion: There is an association between CPM and FGR and BW &lt; p10. This association is not restricted to trisomy 16, neither to CPM type 3, nor to CPM involving a meiotic trisomy. Pregnancies with all CPM types and origins should be considered to be at increased risk of FGR and low BW &lt; p10. A close prenatal fetal monitoring is indicated in all cases of CPM.</p

Molecular Analysis and Genetic Mapping of the Rhodopsin Gene in Families with Autosomal Dominant Retinitis Pigmentosa

Eighty-eight patients/families with autosomal dominant retinitis pigmentosa (RP) were screened for rhodopsin mutations. Direct sequencing revealed 13 different mutations in a total of 14 (i.e., 16%) unrelated patients. Five of these mutations (T4K, Q28H, R135G, F220C, and C222R) have not been reported so far. In addition, multipoint linkage analysis was performed on two large families with autosomal dominant RP due to rhodopsin mutations by using five DNA probes from 3q21-q24. No tight linkage was found between the rhodopsin locus (RHO) and D3S47 (θmax = 0.08). By six-point analysis, RHO was localized in the region between D3S21 and D3S47, with a maximum lod score of 13.447 directly at D3S20