A GFP-based assay for rapid screening of compounds affecting ARE-dependent mRNA turnover

A reporter transcript containing the green fluorescent protein (GFP) gene upstream of the destabilizing 3′-untranslated region (3′-UTR) of the murine IL-3 gene was inserted in mouse PB-3c-15 mast cells. The GFP-IL-3 transcript was inherently unstable due to the presence of an adenosine-uridine (AU)-rich element (ARE) in the 3′-UTR and was subject to rapid decay giving a low baseline of GFP fluorescence. Transcript stabilization with ionomycin resulted in an increase of fluorescence that is quantitated by FACS analysis of responding cells. Using this system we have identified okadaic acid as a novel stabilizing compound, and investigated the upstream signaling pathways leading to stabilization. This reporter system has the advantage of speed and simplicity over standard methods currently in use and in addition to serving as a research tool it can be easily automated to increase throughput for drug discover

Direct identification of differentially expressed genes by cycle sequencing and cycle labelling using the differential display PCR primers

Differential display PCR (DD-PCR) is an mRNA fingerprinting technique to identify differentially expressed genes by comparative display of arbitrarily amplified cDNA subsets. This attractively simple screening method was, however, followed by a labour intensive multistep identification procedure for DD-PCR products. In this report we demonstrate for the mouse mast cell protease 2 (MMCP-2) and the cytotoxic T-lymphocyte associated gene transcript CTLA-1 a streamlined approach by (i) direct cycle sequencing with the upstream differential display (DD) primer, followed by (ii) the PCR based generation of an antisense northern probe with the downstream anchor prime

Roles of AUF1 isoforms, HuR and BRF1 in ARE‐dependent mRNA turnover studied by RNA interference

HT1080 cells stably expressing green fluorescent protein (GFP) linked to a 3′ terminal AU‐rich element (ARE) proved to be a convenient system to study the dynamics of mRNA stability, as changes in mRNA levels are reflected in increased or decreased fluorescence intensity. This study examined whether mRNA stability can be regulated by small interfering RNAs (siRNAs) targeted to AU‐binding proteins (AUBPs), which in turn should reveal their intrinsic role as stabilizers or destabilizers of ARE‐mRNAs. Indeed, siRNAs targeting HuR or BRF1 decreased or increased fluorescence, respectively. This effect was abolished if cells were treated with both siRNAs, thus indicating antagonistic control of ARE‐mRNA stability. Unexpectedly, downregulation of all four AUF1 isoforms by targeting common exons did not affect fluorescence whereas selective downregulation of p40AUF1/p45AUF1 strongly increased fluorescence by stabilizing the GFP-ARE reporter mRNA. This observation was fully confirmed by the finding that only selective reduction of p40AUF1/p45AUF1 induced the production of GM‐CSF, an endogenous target of AUF1. These data suggest that the relative levels of individual isoforms, rather than the absolute amount of AUF1, determine the net mRNA stability of ARE‐containing transcripts, consistent with the differing ARE‐binding capacities of the isoform

Biosensors in Biomedical Research: Development and Applications of Gene Chips

Nucleic-acid hybridisation techniques are a central tool for the genetic analysis of biological systems. Gene chips are complex arrays of recombinant plasmids or oligonucleotides immobilised on a glass chip of only 1 cm2. This technology allows, for the first time, the multiparallel expression-analysis of thousands of genes. Gene chips will be indispensable tools for the upcoming analysis of the human genome, once the entire sequence is known

mTOR dependent transformed human cells have a distinct set of essential genes from bcr-abl transformed cells

Constitutively active intracellular signaling drives and sustains cancer growth. The mTOR kinase integrates multiple inputs sensing nutrient, energy and growth factor levels to promote protein synthesis and anabolic metabolism, and is hyperactivated in a broad range of cancers. The bcr-abl kinase is a fusion protein generated by chromosomal translocation and gives rise to chronic myeloid leukemia and a small sub-set of leukemias. Using an in vitro transformed murine cell model, we performed shRNA knockdown of 25 genes previously shown to be essential for mTOR dependent oncogenic growth and survival. None of the genes were essential in the bcr-abl transformed line. Interrogation of this gene set in human cancer cell lines revealed that many of these genes were essential in cells dependent on mTOR signaling (defined by sensitivity to pharmacological mTOR inhibition). However, none of the genes were essential in bcr-abl transformed K562 cells that are insensitive to mTOR inhibition. Thus there is a clear divide between cells transformed via bcr-abl directed oncogenesis and other modes of transformation where mTOR, due to its central role in regulating cell growth and metabolism, is recruited as part of an oncogenic program. These validated hits represent a set of genes essential for executing critical functions downstream of mTOR and may be novel therapeutic targets for cancer

Individual Particle Characteristics, Optical Properties and Evolution of an Extreme Long‐Range Transported Biomass Burning Event in the European Arctic (Ny‐Ålesund, Svalbard Islands)

This paper reports an exceptional biomass burning (BB) advection event from Alaska registered at Ny‐Ålesund from 10 to 17 July 2015 with particular interest on the influence of the airborne particle characteristics on the optical properties of the aerosol during the event. To this purpose we considered two DEKATI 12‐stage aerosol samples spanning the entire advection and analyzed them by scanning electron microscopy techniques. Aerosol chemical data and microphysical properties were also evaluated in order to correlate any change of individual particle characteristics with the bulk properties of the aerosol. The results of individual particle analysis depict a complex event characterized by a first phase (P1) of massive input of BB carbonaceous particles (i.e., tar balls, popcorn refractory particles, and organic particles), and by a second phase (P2) dominated by inorganic salts. The peculiar feature of this BB event is the exceptionally large grain size of the subspherical organic particles at the beginning of the event with respect to the background. At these conditions a significant increase of the scattering efficiency may occur even for a small increase of the size parameter. Results of the simulation of the complex refractive indices (n‐ik) confirm this evaluation. Aerosol evolution during the event resulted from the combination of three distinct occurrences: (a) progressive rotation of air mass circulation toward non‐BB source areas, (b) development of a thick fog layer in the planetary boundary layer, and (c) sea salt spray direct advection of local/regional provenance

RTE and CTE mRNA export elements synergistically increase expression of unstable, Rev-dependent HIV and SIV mRNAs

Studies of retroviral mRNA export identified two distinct RNA export elements utilizing conserved eukaryotic mRNA export mechanism(s), namely the Constitutive Transport Element (CTE) and the RNA Transport Element (RTE). Although RTE and CTE are potent in nucleocytoplasmic mRNA transport and expression, neither element is as powerful as the Rev-RRE posttranscriptional control. Here, we found that whereas CTE and the up-regulatory mutant RTEm26 alone increase expression from a subgenomic gag and env clones, the combination of these elements led to a several hundred-fold, synergistic increase. The use of the RTEm26-CTE combination is a simple way to increase expression of poorly expressed retroviral genes to levels otherwise only achieved via more cumbersome RNA optimization. The potent RTEm26-CTE element could be useful in lentiviral gene therapy vectors, DNA-based vaccine vectors, and gene transfer studies of other poorly expressed genes

Syrosingopine sensitizes cancer cells to killing by metformin

We report that the anticancer activity of the widely used diabetic drug metformin is strongly potentiated by syrosingopine. Synthetic lethality elicited by combining the two drugs is synergistic and specific to transformed cells. This effect is unrelated to syrosingopine's known role as an inhibitor of the vesicular monoamine transporters. Syrosingopine binds to the glycolytic enzyme α-enolase in vitro, and the expression of the γ-enolase isoform correlates with nonresponsiveness to the drug combination. Syrosingopine sensitized cancer cells to metformin and its more potent derivative phenformin far below the individual toxic threshold of each compound. Thus, combining syrosingopine and codrugs is a promising therapeutic strategy for clinical application for the treatment of cancer

The RNA-Binding Protein KSRP Promotes Decay of β-Catenin mRNA and Is Inactivated by PI3K-AKT Signaling

β-catenin plays an essential role in several biological events including cell fate determination, cell proliferation, and transformation. Here we report that β-catenin is encoded by a labile transcript whose half-life is prolonged by Wnt and phosphatidylinositol 3-kinase–AKT signaling. AKT phosphorylates the mRNA decay-promoting factor KSRP at a unique serine residue, induces its association with the multifunctional protein 14-3-3, and prevents KSRP interaction with the exoribonucleolytic complex exosome. This impairs KSRP's ability to promote rapid mRNA decay. Our results uncover an unanticipated level of control of β-catenin expression pointing to KSRP as a required factor to ensure rapid degradation of β-catenin in unstimulated cells. We propose KSRP phosphorylation as a link between phosphatidylinositol 3-kinase–AKT signaling and β-catenin accumulation

Differential cross section measurements for the production of a W boson in association with jets in proton–proton collisions at √s = 7 TeV

Measurements are reported of differential cross sections for the production of a W boson, which decays into a muon and a neutrino, in association with jets, as a function of several variables, including the transverse momenta (pT) and pseudorapidities of the four leading jets, the scalar sum of jet transverse momenta (HT), and the difference in azimuthal angle between the directions of each jet and the muon. The data sample of pp collisions at a centre-of-mass energy of 7 TeV was collected with the CMS detector at the LHC and corresponds to an integrated luminosity of 5.0 fb[superscript −1]. The measured cross sections are compared to predictions from Monte Carlo generators, MadGraph + pythia and sherpa, and to next-to-leading-order calculations from BlackHat + sherpa. The differential cross sections are found to be in agreement with the predictions, apart from the pT distributions of the leading jets at high pT values, the distributions of the HT at high-HT and low jet multiplicity, and the distribution of the difference in azimuthal angle between the leading jet and the muon at low values.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio