A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy

Due to the mounting evidence that RNA structure plays a critical role in regulating almost any physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid imidazolide (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 shows moderate improvements with respect to the state-of-the-art selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) reagent NAI on naked RNA under in vitro conditions, but it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. When used as a restraint to drive RNA structure prediction, data derived by SHAPE-MaP with 2A3 yields more accurate predictions than NAI-derived data. Due to its extreme efficiency and accuracy, we can anticipate that 2A3 will rapidly take over conventional SHAPE reagents for probing RNA structures both in vitro and in vivo

Methyl 5,6-dimeth­oxy-1H-indole-2-carboxyl­ate

The title compound, C12H13NO4, was prepared as a precursor to an indole derivative with possible anti­mitotic properties. The mol­ecule is very nearly planar; the maximum deviation of any non-H atom from the mean plane of the indole ring is 0.120 (3) Å for each of two meth­oxy C atoms. The pairs of mol­ecules related by the inversion centre at (0,0,) are connected by two symmetry-equivalent N—H⋯O hydrogen bonds, while the pairs of mol­ecules related by the inversion centre at (0,0,0) exhibit a π-stacking inter­action of the indole rings, with an inter­planar separation of 3.39 (3) Å

5-Meth­oxy-1-(3,4,5-trimethoxy­phen­yl)-1H-indole

The title compound, C18H19NO4, was prepared as an indole derivative with possible anti­mitotic properties. The planes of the indole and trimethoxy­phenyl rings make a dihedral angle of 45.35 (5)° with one another. In the crystal, mol­ecules related by a twofold screw axis exhibit arene C—H⋯arene-π inter­actions which are 3.035 (1) Å in length

Bis(2-naphthyl­meth­yl)diphenyl­silane

The title compound, C34H28Si, was prepared as an inter­nal standard for diffusion-ordered NMR spectroscopy. The four ligands are arranged tetra­hedrally around the Si atom. The two naphthalene systems are nearly perpendicular, making an angle of 86.42 (4)° with one another. A naphthalene system and a phenyl ring are also nearly perpendicular, making an angle of 86.18 (6)° with one another. In the crystal, the mol­ecules pack in columns parallel to the a axis, and exhibit arene C—H⋯π(arene) inter­actions both within and between columns

(1-Bromo­naphthalen-2-yl)acetonitrile

The title compound, C12H8BrN, was prepared as a starting material for a Suzuki cross-coupling reaction with a pinacol ester. The torsion angle about the ring–methylene C—C bond is 30.7 (3)°, such that the N atom is displaced by 1.174 (4) Å from the plane of the naphthalene ring system

NuSTAR observations of the powerful radio-galaxy Cygnus A

We present NuSTAR observations of the powerful radio galaxy Cygnus A, focusing on the central absorbed active galactic nucleus (AGN). Cygnus A is embedded in a cool-core galaxy cluster, and hence we also examine archival XMM-Newton data to facilitate the decomposition of the spectrum into the AGN and intracluster medium (ICM) components. NuSTAR gives a source-dominated spectrum of the AGN out to >70keV. In gross terms, the NuSTAR spectrum of the AGN has the form of a power law (Gamma~1.6-1.7) absorbed by a neutral column density of N_H~1.6x10^23 cm^-2. However, we also detect curvature in the hard (>10keV) spectrum resulting from reflection by Compton-thick matter out of our line-of-sight to the X-ray source. Compton reflection, possibly from the outer accretion disk or obscuring torus, is required even permitting a high-energy cutoff in the continuum source; the limit on the cutoff energy is E_cut>111keV (90% confidence). Interestingly, the absorbed power-law plus reflection model leaves residuals suggesting the absorption/emission from a fast (15,000-26,000km/s), high column-density (N_W>3x10^23 cm^-2), highly ionized (xi~2,500 erg cm/s) wind. A second, even faster ionized wind component is also suggested by these data. We show that the ionized wind likely carries a significant mass and momentum flux, and may carry sufficient kinetic energy to exercise feedback on the host galaxy. If confirmed, the simultaneous presence of a strong wind and powerful jets in Cygnus A demonstrates that feedback from radio-jets and sub-relativistic winds are not mutually exclusive phases of AGN activity but can occur simultaneously.Comment: 13 pages; accepted for publication in The Astrophysical Journa

Treatment of pancreatic ductal adenocarcinoma with tumor antigen specific-targeted delivery of paclitaxel loaded PLGA nanoparticles

Abstract Background Pancreatic ductal adenocarcinoma (PDA) remains the most aggressive cancers with a 5-year survival below 10%. Systemic delivery of chemotherapy drugs has severe side effects in patients with PDA and does not significantly improve overall survival rate. It is highly desirable to advance the therapeutic efficacy of chemotherapeutic drugs by targeting their delivery and increasing accumulation at the tumor site. MUC1 is a membrane-tethered glycoprotein that is aberrantly overexpressed in > 80% of PDA thus making it an attractive antigenic target. Methods Poly lactic-co-glycolic acid nanoparticles (PLGA NPs) conjugated to a tumor specific MUC1 antibody, TAB004, was used as a nanocarrier for targeted delivery into human PDA cell lines in vitro and in PDA tumors in vivo. The PLGA NPs were loaded with fluorescent imaging agents, fluorescein diacetate (FDA) and Nile Red (NR) or isocyanine green (ICG) for in vitro and in vivo imaging respectively or with a chemotherapeutic drug, paclitaxel (PTX) for in vitro cytotoxicity assays. Confocal microscopy was used to visualize internalization of the nanocarrier in vitro in PDA cells with high and low MUC1 expression. The in vivo imaging system (IVIS) was used to visualize in vivo tumor targeting of the nanocarrier. MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide) assay was used to determine in vitro cell survival of cells treated with PTX-loaded nanocarrier. One-sided t-test comparing treatment groups at each concentration and two-way ANOVAs comparing internalization of antibody and PLGA nanoparticles. Results In vitro, TAB004-conjugated ICG-nanocarriers were significantly better at internalizing in PDA cells than its non-conjugated counterpart. Similarly, TAB004-conjugated PTX-nanocarriers were significantly more cytotoxic in vitro against PDA cells than its non-conjugated counterpart. In vivo, TAB004-conjugated ICG-nanocarriers showed increased accumulation in the PDA tumor compared to the non-conjugated nanocarrier while sparing normal organs. Conclusions The study provides promising data for future development of a novel MUC1-targeted nanocarrier for direct delivery of imaging agents or drugs into the tumor microenvironment

The corona of the broad-line radio galaxy 3C 390.3

We present the results from a joint Suzaku/NuSTAR broad-band spectral analysis of 3C 390.3. The high quality data enables us to clearly separate the primary continuum from the reprocessed components allowing us to detect a high energy spectral cut-off ($E_\text{cut}=117_{-14}^{+18}$ keV), and to place constraints on the Comptonization parameters of the primary continuum for the first time. The hard over soft compactness is 69$_{-24}^{+124}$ and the optical depth 4.1$_{-3.6}^{+0.5}$, this leads to an electron temperature of $30_{-8}^{+32}$ keV. Expanding our study of the Comptonization spectrum to the optical/UV by studying the simultaneous Swift-UVOT data, we find indications that the compactness of the corona allows only a small fraction of the total UV/optical flux to be Comptonized. Our analysis of the reprocessed emission show that 3C 390.3 only has a small amount of reflection (R~0.3), and of that the vast majority is from distant neutral matter. However we also discover a soft X-ray excess in the source, which can be described by a weak ionized reflection component from the inner parts of the accretion disk. In addition to the backscattered emission, we also detect the highly ionized iron emission lines Fe XXV and Fe XXVI

Implementation of a Distributed Architecture for Managing Collection and Dissemination of Data for Fetal Alcohol Spectrum Disorder

We implemented a distributed system for management of data for an international collaboration studying Fetal Alcohol Spectrum Disorders (FASD). Subject privacy was protected, researchers without dependable Internet access were accommodated, and researchers’ data were shared globally. Data dictionaries codified the nature of the data being integrated, data compliance was assured through multiple consistency checks, and recovery systems provided a secure, robust, persistent repository. The system enabled new types of science to be done, using distributed technologies that are expedient for current needs while taking useful steps towards integrating the system in a future grid-based cyberinfrastructure. The distributed architecture, verification steps, and data dictionaries suggest general strategies for researchers involved in collaborative studies, particularly where data must be de-identified before being shared. The system met both the collaboration’s needs and the NIH Roadmap’s goal of wide access to databases that are robust and adaptable to researchers’ needs

Implementation of a Shared Data Repository and Common Data Dictionary for Fetal Alcohol Spectrum Disorders Research

Many previous attempts by fetal alcohol spectrum disorders researchers to compare data across multiple prospective and retrospective human studies have failed due to both structural differences in the collected data as well as difficulty in coming to agreement on the precise meaning of the terminology used to describe the collected data. Although some groups of researchers have an established track record of successfully integrating data, attempts to integrate data more broadly amongst different groups of researchers have generally faltered. Lack of tools to help researchers share and integrate data has also hampered data analysis. This situation has delayed improving diagnosis, intervention, and treatment before and after birth. We worked with various researchers and research programs in the Collaborative Initiative on Fetal Alcohol Spectrum Disorders (CI-FASD) to develop a set of common data dictionaries to describe the data to be collected, including definitions of terms and specification of allowable values. The resulting data dictionaries were the basis for creating a central data repository (CI-FASD Central Repository) and software tools to input and query data. Data entry restrictions ensure that only data which conform to the data dictionaries reach the CI-FASD Central Repository. The result is an effective system for centralized and unified management of the data collected and analyzed by the initiative, including a secure, long-term data repository. CI-FASD researchers are able to integrate and analyze data of different types, collected using multiple methods, and collected from multiple populations, and data are retained for future reuse in a secure, robust repository