Identification of archaeal proteins that affect the exosome function in vitro

Background  

The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors.     

Modulation of humoral immune response to oral BCG vaccination by Mycobacterium bovis BCG Moreau Rio de Janeiro (RDJ) in healthy adults

We hypothesize that the energy strategy of a cell is a key factor for determining how, or if, the immune system interacts with that cell. Cells have a limited number of metabolic states, in part, depending on the type of fuels the cell consumes. Cellular fuels include glucose (carbohydrates), lipids (fats), and proteins. We propose that the cell's ability to switch to, and efficiently use, fat for fuel confers immune privilege. Additionally, because uncoupling proteins are involved in the fat burning process and reportedly in protection from free radicals, we hypothesize that uncoupling proteins play an important role in immune privilege. Thus, changes in metabolism (caused by oxidative stresses, fuel availability, age, hormones, radiation, or drugs) will dictate and initiate changes in immune recognition and in the nature of the immune response. This has profound implications for controlling the symptoms of autoimmune diseases, for preventing graft rejection, and for targeting tumor cells for destruction.     

High-throughput screening assay for the quantification of Cer d18:1/16:0, d18:1/24:0, d18:1/24:1, d18:1/18:0, d18:1/14:0, d18:1/20:0, and d18:1/22:0 in HepG2 cells using RapidFire mass spectrometry

Ceramides are known to be involved in various biological processes with their physiological levels elevated in various disease conditions such as diabetes, Alzheimer's, atherosclerosis. To facilitate the rapid screening of Cer d18:1/16:0, d18:1/24:0, d18:1/24:1, d18:1/18:0, d18:1/14:0, d18:1/20:0, and d18:1/22:0 inhibition in HepG2 cells, a RapidFire coupled to tandem mass spectrometry (RF–MS/MS) method has been developed. The RF platform provides an automated solid-phase extraction system that gave a throughput of 12.6 s per sample to an MS/MS system using electrospray ionization under the positive ion mode. Chromatographic separation of Cer d18:1/16:0, d18:1/24:0, d18:1/24:1, d18:1/18:0, d18:1/14:0, d18:1/20:0, and d18:1/22:0 was achieved using a ternary gradient on C₈ type E cartridge. The MS/MS ion transitions monitored were 538.2 → 264.2, 650.7 → 264.2, 648.6 → 264.2, 566.4 → 264.2, 510.4 → 264.2, 594.4 → 264.2, 622.5 → 264.2, and 552.3 → 250.2 for Cer d18:1/16:0, d18:1/24:0, d18:1/24:1, d18:1/18:0, d18:1/14:0, d18:1/20:0, d18:1/22:0, and the internal standard (Cer d17:1/18:0), respectively. The RF–MS/MS methodology showed an excellent performance with an average Z′ value of 0.5–0.7. This is the first report of an RF–MS/MS assay for screening of ceramides which is amenable for high-throughput screening.     

Anti-Inflammatory and Anti-Rheumatic Potential of Selective Plant Compounds by Targeting TLR-4/AP-1 Signaling: A Comprehensive Molecular Docking and Simulation Approaches

Plants are an important source of drug development and numerous plant derived molecules have been used in clinical practice for the ailment of various diseases. The Toll-like receptor-4 (TLR-4) signaling pathway plays a crucial role in inflammation including rheumatoid arthritis. The TLR-4 binds with pro-inflammatory ligands such as lipopolysaccharide (LPS) to induce the downstream signaling mechanism such as nuclear factor κappa B (NF-κB) and mitogen activated protein kinases (MAPKs). This signaling activation leads to the onset of various diseases including inflammation. In the present study, 22 natural compounds were studied against TLR-4/AP-1 signaling, which is implicated in the inflammatory process using a computational approach. These compounds belong to various classes such as methylxanthine, sesquiterpene lactone, alkaloid, flavone glycosides, lignan, phenolic acid, etc. The compounds exhibited different binding affinities with the TLR-4, JNK, NF-κB, and AP-1 protein due to the formation of multiple hydrophilic and hydrophobic interactions. With TLR-4, rutin had the highest binding energy (−10.4 kcal/mol), poncirin had the highest binding energy (−9.4 kcal/mol) with NF-κB and JNK (−9.5 kcal/mol), respectively, and icariin had the highest binding affinity (−9.1 kcal/mol) with the AP-1 protein. The root means square deviation (RMSD), root mean square fraction (RMSF), and radius of gyration (RoG) for 150 ns were calculated using molecular dynamic simulation (MD simulation) based on rutin’s greatest binding energy with TLR-4. The RMSD, RMSF, and RoG were all within acceptable limits in the MD simulation, and the complex remained stable for 150 ns. Furthermore, these compounds were assessed for the potential toxic effect on various organs such as the liver, heart, genotoxicity, and oral maximum toxic dose. Moreover, the blood–brain barrier permeability and intestinal absorption were also predicted using SwissADME software (Lausanne, Switzerland). These compounds exhibited promising physico-chemical as well as drug-likeness properties. Consequently, these selected compounds portray promising anti-inflammatory and drug-likeness properties.     

The effect of data scaling on dual prices and sensitivity analysis in linear programs

In many practical situations scaling the data is necessary to solve linear programs. This note explores the relationships in translating the sensitivity analysis between the original and the scaled problems.     

Luminescence switching behavior through redox reaction in Ce3+ co-doped LaPO4:Tb3+ nanorods: re-dispersible and polymer film

Re-dispersible Tb(3+) doped LaPO(4) nanorods have been prepared using ethylene glycol (EG) as a capping agent as well as reaction medium at a relatively low temperature of 150 °C. The X-ray diffraction study reveals that all the doped samples are well crystalline with a monoclinic structure of the LaPO(4) phase. The luminescence intensity of (5)D(4)→(7)F(5) transition at 543 nm (green) is more prominent than that of (5)D(4)→(7)F(6) transition at 487 nm (blue) for all the samples. This is related to the polarizing effect from [PO(4)](3-) to the Tb(3+) site. Concentration dependent luminescence study shows that the luminescence intensity of Tb(3+) increases up to 10 at.% and decreases above this. This is due to the concentration quenching effect arising from cross relaxation among Tb(3+)-Tb(3+) ions. The results show that nanoparticles prepared in EG medium gives an enhanced luminescence compared to that prepared in water. This is attributed to the multiphonon relaxation effect from O-H groups surrounding over nanoparticles as well as the extent of increase of agglomeration among particles for samples prepared in water. Significant enhancement in the emission of Tb(3+) is also observed when Ce(3+) is used as the sensitizer in LaPO(4):Tb(3+)nanorods. The optimum concentration of Ce(3+) for maximum luminescence is found to be 7 at.% in Ce(3+) sensitized LaPO(4):Tb(3+) (5 at.%). Based on the energy transfer process from Ce(3+) to Tb(3+), the luminescence of Tb(3+) can be switched OFF and ON by performing oxidation and reduction of Ce(3+)?Ce(4+) using KMnO(4) and ascorbic acid, respectively. The samples are re-dispersible in water, methanol and can be incorporated into polyvinyl alcohol (PVA) films. They show a dark green emission under ultraviolet radiation.     

Poly(methyl methacrylate) composites with size‐selected silver nanoparticles fabricated using cluster beam technique

An embedment of metal nanoparticles of well‐defined sizes in thin polymer films is of significant interest for a number of practical applications, in particular, for preparing materials with tunable plasmonic properties. In this article, we present a fabrication route for metal–polymer composites based on cluster beam technique allowing the formation of monocrystalline size‐selected silver nanoparticles with a ±5–7% precision of diameter and controllable embedment into poly (methyl methacrylate). It is shown that the soft‐landed silver clusters preserve almost spherical shape with a slight tendency to flattening upon impact. By controlling the polymer hardness (from viscous to soft state) prior the cluster deposition and annealing conditions after the deposition the degree of immersion of the nanoparticles into polymer can be tuned, thus, making it possible to create composites with either particles partly or fully embedded into the film. Good size selection and rather homogeneous dispersion of nanoparticles in the thin polymer film lead to excellent plasmonic properties characterized by the narrow band and high quality factor of localized surface plasmon resonance. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1152–1159     

Modulation of humoral immune response to oral BCG vaccination by Mycobacterium bovis BCG Moreau Rio de Janeiro (RDJ) in healthy adults

Background  

Oral administration of BCG was the route initially used by Calmette and Guérin, but was replaced by intradermal administration in virtually all countries after the Lubeck accident. However, Brazil continued to administer oral BCG Moreau RDJ, which was maintained until the mid-1970s when it was substituted by the intradermal route. Although BCG vaccination has been used in humans since 1921, little is known of the induced immune response. The aim of this study was to analyse immunological responses after oral vaccination with M. bovis BCG Moreau RDJ.