A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest

Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-angstrom-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation

Simultaneous X-ray spectroscopy of YY Gem with Chandra and XMM-Newton

We report on a detailed study of the X-ray spectrum of the nearby eclipsing spectroscopic binary YY Gem. Observations were obtained simultaneously with both large X-ray observatories, XMM-Newton and Chandra. We compare the high-resolution spectra acquired with the Reflection Grating Spectrometer onboard XMM-Newton and with the Low Energy Transmission Grating Spectrometer onboard Chandra, and evidence in direct comparison the good performance of both instruments in terms of wavelength and flux calibration. The strongest lines in the X-ray spectrum of YY Gem are from oxygen. Oxygen line ratios indicate the presence of a low-temperature component (1-4 MK) with density n_e < 2 10^{10} cm^-3. The X-ray lightcurve reveals two flares and a dip corresponding to the secondary eclipse. An increase of the density during phases of high activity is suggested from time-resolved spectroscopy. Time-resolved global fitting of the European Photon Imaging Camera CCD spectrum traces the evolution of temperature and emission measure during the flares. These medium-resolution spectra show that temperatures > 10^7 K are relevant in the corona of YY Gem although not as dominant as the lower temperatures represented by the strongest lines in the high-resolution spectrum. Magnetic loops with length on the order of 10^9 cm, i.e., about 5 % of the radius of each star, are inferred from a comparison with a one-dimensional hydrodynamic model. This suggests that the flares did not erupt in the (presumably more extended) inter-binary magnetosphere but are related to one of the components of the binary.Comment: 15 pages, accepted for publication in A&

Coronal Temperature Diagnostic Capability of the Hinode/X-Ray Telescope Based on Self-Consistent Calibration

The X-Ray Telescope (XRT) onboard the Hinode satellite is an X-ray imager that observes the solar corona with unprecedentedly high angular resolution (consistent with its 1" pixel size). XRT has nine X-ray analysis filters with different temperature responses. One of the most significant scientific features of this telescope is its capability of diagnosing coronal temperatures from less than 1 MK to more than 10 MK, which has never been accomplished before. To make full use of this capability, accurate calibration of the coronal temperature response of XRT is indispensable and is presented in this article. The effect of on-orbit contamination is also taken into account in the calibration. On the basis of our calibration results, we review the coronal-temperature-diagnostic capability of XRT

High antiplasmodial activity of novel plasmepsins I and II inhibitors

The aim of this study was to develop new antiplasmodial compounds acting through distinct mechanisms during both the liver and the blood stages of the parasite life cycle. Compounds were designed on the basis of the "double-drug" approach: primaquine, which has been linked to statine-based inhibitors of plasmepsins (PLMs), the plasmodial aspartic proteases involved in degradation of hemeoglobin. The compounds were tested in vitro for anti-PLM I/PLM II activities and against chloroquine-sensitive (D10) and chloroquine-resistant (W2) strains of P. falciparum. An antiplasmodial activity (IC50) as low as 0.1 M was obtained, an excellent improvement in comparison with inhibitors previously reported (IC50 = 2-20 M). The killing activity was equally directed against both P. falciparum strains and was correlated to lipophilicity (calculated as ALogP), for all compounds but one (9). All compounds inhibited PLM I and PLM II in the nanomolar range (Ki = 1-700 nM). The most promising compounds (2, 6, 10) were not cytotoxic against human fibroblasts at 100 M and were highly selective for PLMs vs human cathepsin

Investigating ChaMPlane X-ray sources in the Galactic Bulge with Magellan LDSS2 spectra

We have carried out optical and X-ray spectral analyses on a sample of 136 candidate optical counterparts of X-ray sources found in five Galactic-bulge fields included in our Chandra Multi-wavelength Plane Survey. We use a combination of optical spectral fitting and quantile X-ray analysis to obtain the hydrogen column density towards each object, and a three-dimensional dust model of the Galaxy to estimate the most probable distance in each case. We present the discovery of a population of stellar coronal emission sources, likely consisting of pre-main sequence, young main sequence and main sequence stars, as well as a component of active binaries of RS CVn or BY Dra type. We identify one candidate quiescent low-mass X-ray binary with a sub-giant companion; we note that this object may also be an RS CVn system. We report the discovery of three new X-ray detected cataclysmic variables (CVs) in the direction of the Galactic Center (at distances ~2kpc). This number is in excess of predictions made with a simple CV model based on a local CV space density of <~ 10^-5 pc^-3, and a scale height ~200pc. We discuss several possible reasons for this observed excess.Comment: 41 pages, 11 figures. Accepted for publication in Astrophysical Journal, September 10 editio

Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site

Paromomycin is an aminoglycosidic antibiotic that targets the RNA of the bacterial small ribosomal subunit. It binds in the A-site, which is one of the three tRNA binding sites, and affects translational fidelity by stabilizing two adenines (A1492 and A1493) in the flipped-out state. Experiments have shown that various mutations in the A-site result in bacterial resistance to aminoglycosides. In this study, we performed multiple molecular dynamics simulations of the mutated A-site RNA fragment in explicit solvent to analyze changes in the physicochemical features of the A-site that were introduced by substitutions of specific bases. The simulations were conducted for free RNA and in complex with paromomycin. We found that the specific mutations affect the shape and dynamics of the binding cleft as well as significantly alter its electrostatic properties. The most pronounced changes were observed in the U1406C∶U1495A mutant, where important hydrogen bonds between the RNA and paromomycin were disrupted. The present study aims to clarify the underlying physicochemical mechanisms of bacterial resistance to aminoglycosides due to target mutations

Antimicrobial and cell-penetrating peptides induce lipid vesicle fusion by folding and aggregation

According to their distinct biological functions, membrane-active peptides are generally classified as antimicrobial (AMP), cell-penetrating (CPP), or fusion peptides (FP). The former two classes are known to have some structural and physicochemical similarities, but fusogenic peptides tend to have rather different features and sequences. Nevertheless, we found that many CPPs and some AMPs exhibit a pronounced fusogenic activity, as measured by a lipid mixing assay with vesicles composed of typical eukaryotic lipids. Compared to the HIV fusion peptide (FP23) as a representative standard, all designer-made peptides showed much higher lipid-mixing activities (MSI-103, MAP, transportan, penetratin, Pep1). Native sequences, on the other hand, were less fusogenic (magainin 2, PGLa, gramicidin S), and pre-aggregated ones were inactive (alamethicin, SAP). The peptide structures were characterized by circular dichroism before and after interacting with the lipid vesicles. A striking correlation between the extent of conformational change and the respective fusion activities was found for the series of peptides investigated here. At the same time, the CD data show that lipid mixing can be triggered by any type of conformation acquired upon binding, whether α-helical, β-stranded, or other. These observations suggest that lipid vesicle fusion can simply be driven by the energy released upon membrane binding, peptide folding, and possibly further aggregation. This comparative study of AMPs, CPPs, and FPs emphasizes the multifunctional aspects of membrane-active peptides, and it suggests that the origin of a peptide (native sequence or designer-made) may be more relevant to define its functional range than any given name

Solar soft X-rays and solar activity

Soft solar X-rays (8 ⩽ gl ⩽ 12 Å) were observed from OSO-III. An analysis of the X-ray enhancements associated with 165 solar flares revealed that there is a tendency for a weak soft X-ray enhancement to precede the cm- λ burst and H α flare. The peak soft X-ray flux follows the cm- λ peak by about 4 min, on the average. Additionally, it was found that flare-rich active centers tend to produce flares which are stronger X-ray and cm- λ emitters than are flares which take place in flare-poor active centers.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43754/1/11207_2004_Article_BF00155382.pd

Colorectal Cancer Stage at Diagnosis Before vs During the COVID-19 Pandemic in Italy

IMPORTANCE Delays in screening programs and the reluctance of patients to seek medical attention because of the outbreak of SARS-CoV-2 could be associated with the risk of more advanced colorectal cancers at diagnosis. OBJECTIVE To evaluate whether the SARS-CoV-2 pandemic was associated with more advanced oncologic stage and change in clinical presentation for patients with colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS This retrospective, multicenter cohort study included all 17 938 adult patients who underwent surgery for colorectal cancer from March 1, 2020, to December 31, 2021 (pandemic period), and from January 1, 2018, to February 29, 2020 (prepandemic period), in 81 participating centers in Italy, including tertiary centers and community hospitals. Follow-up was 30 days from surgery. EXPOSURES Any type of surgical procedure for colorectal cancer, including explorative surgery, palliative procedures, and atypical or segmental resections. MAIN OUTCOMES AND MEASURES The primary outcome was advanced stage of colorectal cancer at diagnosis. Secondary outcomes were distant metastasis, T4 stage, aggressive biology (defined as cancer with at least 1 of the following characteristics: signet ring cells, mucinous tumor, budding, lymphovascular invasion, perineural invasion, and lymphangitis), stenotic lesion, emergency surgery, and palliative surgery. The independent association between the pandemic period and the outcomes was assessed using multivariate random-effects logistic regression, with hospital as the cluster variable. RESULTS A total of 17 938 patients (10 007 men [55.8%]; mean [SD] age, 70.6 [12.2] years) underwent surgery for colorectal cancer: 7796 (43.5%) during the pandemic period and 10 142 (56.5%) during the prepandemic period. Logistic regression indicated that the pandemic period was significantly associated with an increased rate of advanced-stage colorectal cancer (odds ratio [OR], 1.07; 95%CI, 1.01-1.13; P = .03), aggressive biology (OR, 1.32; 95%CI, 1.15-1.53; P &lt; .001), and stenotic lesions (OR, 1.15; 95%CI, 1.01-1.31; P = .03). CONCLUSIONS AND RELEVANCE This cohort study suggests a significant association between the SARS-CoV-2 pandemic and the risk of a more advanced oncologic stage at diagnosis among patients undergoing surgery for colorectal cancer and might indicate a potential reduction of survival for these patients