Current practice in bicistronic ires reporter use: A systematic review

Bicistronic reporter assays have been instrumental for transgene expression, understanding of internal ribosomal entry site (IRES) translation, and identification of novel cap-independent translational elements (CITE). We observed a large methodological variability in the use of bicistronic reporter assays and data presentation or normalization procedures. Therefore, we systematically searched the literature for bicistronic IRES reporter studies and analyzed methodological details, data visualization, and normalization procedures. Two hundred fifty-seven publications were identified using our search strategy (published 1994–2020). Experimental studies on eukaryotic adherent cell systems and the cell-free translation assay were included for further analysis. We evaluated the following methodological details for 176 full text articles: the bicistronic reporter design, the cell line or type, transfection methods, and time point of analyses post-transfection. For the cell-free translation assay, we focused on methods of in vitro transcription, type of translation lysate, and incubation times and assay temperature. Data can be presented in multiple ways: raw data from individual cistrons, a ratio of the two, or fold changes thereof. In addition, many different control experiments have been suggested when studying IRES-mediated translation. In addition, many different normalization and control experiments have been suggested when studying IRES-mediated translation. Therefore, we also categorized and summarized their use. Our unbiased analyses provide a representative overview of bicistronic IRES reporter use. We identified parameters that were reported inconsistently or incompletely, which could hamper data reproduction and interpretation. On the basis of our analyses, we encourage adhering to a number of practices that should improve transparency of bicistronic reporter data presentation and improve methodological descriptions to facilitate data replication

The electrooxidation of small organic molecules on platinum nanoparticles supported on gold: influence of platinum deposition procedure

The electrocatalytic properties of small platinum nanoparticles were investigated for the oxidation of CO, methanol, and formic acid using voltammetry, chronoamperometry, and surface-enhanced Raman spectroscopy. The particles were generated by galvanostatic deposition of platinum on a polished gold surface from an H2PtCl6 containing electrolyte and ranged between 10 and 20 nm in diameter for low platinum surface concentrations, 10 and 120 nm for medium concentrations, and full Pt monolayers for high concentrations. CO stripping and bulk CO oxidation experiments on the particles up to 120 nm in diameter displayed pronounced structural effects. The CO oxidation current-time transients show a current decay for low platinum coverages and a current maximum for medium and high coverages. These results were also observed in the literature for particles of 2- to 5-nm size and agglomerates of these particles. The similarities between the literature and our results, despite large differences in particle size and morphology, suggest that particle structure and morphology are also very important catalytic parameters. Surface-enhanced Raman spectroscopy data obtained for the oxidation of CO on the Pt-modified Au electrodes corroborate this conclusion. A difference in the ratio between CO adsorbed in linear- and bridge-bonded positions on the Pt nanoparticles of different sizes demonstrates the influence of the surface morphology. The oxidation activity of methanol was found to decrease with the particle size, while the formic acid oxidation rate increases. Again, a structural effect is observed for particles of up to ca. 120 nm in diameter, which is much larger than the particles for which a particle size effect was reported in the literature. The particle shape effect for the methanol oxidation reaction can be explained by a reduction in available "ensemble sites" and a reduction in the mobility of CO formed by decomposition of methanol. As formic acid does not require Pt ensemble sites, decreasing the particle size, and thus, the relative number of defects, increases the reaction rate

High-Stress Shear-Induced Crystallization in Isotactic Polypropylene and Propylene/Ethylene Random Copolymers

Crystallization of an isotactic polypropylene (iPP) homopolymer and two propylene/ethylene random copolymers (RACO), induced by high-stress shear, was studied using in situ synchrotron wide-angle X-ray diffraction (WAXD) at 137 °C. The “depth sectioning” method (Fernandez-Ballester, Journal of Rheology 53:5 (2009), pp. 1229−1254) was applied in order to isolate the contributions of different layers in the stress gradient direction and to relate specific structural evolution to the corresponding local stress. This approach gives quantitative results in terms of the specific length of fibrillar nuclei as a function of the applied stress. As expected, crystallization becomes faster with increasing stress—from the inner to the outer layer—for all three materials. Stress-induced crystallization in a RACO with 7.3 mol % ethylene content was triggered at only 1 °C below its nominal melting temperature. The comparison of iPP and RACO’s with 3.4 and 7.3 mol % ethylene monomer reveals the effect of ethylene defects on high-stress shear induced crystallization at 137 °C. It is found that, for a given applied stress, the specific nuclei length formed by flow increases with ethylene content—which is attributed to a greater high molecular weight tail. However, the linear growth rate is significantly reduced by the presence of ethylene comonomers and it is found that this effect dominates the overall crystallization kinetics. Finally, a time lag is found between development of parent lamellae and the emergence of daughter lamellae, consistent with the concept of daughter lamellae nucleated by homoepitaxy on the lateral faces of existing parent lamellae. Includes supporting information

Synovial fluid from end-stage osteoarthritis induces proliferation and fibrosis of articular chondrocytes via MAPK and RhoGTPase signaling

OBJECTIVES: Alterations in the composition of synovial fluid have been associated with adverse effects on cartilage integrity and function. Here, we examined the phenotypic and proliferative behavior of human articular chondrocytes when cultured in vitro for 13 days with synovial fluid derived from end-stage osteoarthritis patients. MATERIALS AND METHODS: Chondrocyte proliferation and phenotypical changes induced by osteoarthritic synovial fluid were analyzed using DNA staining, RT-qPCR, immunostainings, and immunoblotting. The molecular mechanisms by which osteoarthritic synovial fluid induced fibrosis and proliferation were studied using a phospho-protein antibody array and luciferase-based transcription factor activity assays. Specific pathway inhibitors were used to probe the involvement of pathways in fibrosis and proliferation. RESULTS: Prolonged stimulation with osteoarthritic synovial fluid sustained chondrocyte proliferation and induced profound phenotypic changes, favoring a fibrotic over a chondrogenic or hypertrophic phenotype. A clear loss of chondrogenic markers at both the transcriptional and protein level was observed, while expression of several fibrosis-associated markers were upregulated over time. Phospho-kinase analysis revealed activation of MAPK and RhoGTPase signaling pathways by osteoarthritic synovial fluid, which was confirmed by elevated transcriptional activity of Elk-1 and SRF. Inhibitor studies revealed that ERK played a central role in the loss of chondrocyte phenotype, while EGFR and downstream mediators p38, JNK and Rac/Cdc42 were essential for fibrosis-associated collagen expression. Finally, we identified EGF signaling as a key activator of chondrocyte proliferation. CONCLUSIONS: Osteoarthritic synovial fluid promoted chondrocyte fibrosis and proliferation through EGF receptor activation and downstream MAPK and RhoGTPase signaling