TRAP binding to the Bacillus subtilis trp leader region RNA causes efficient transcription termination at a weak intrinsic terminator

The Bacillus subtilis trpEDCFBA operon is regulated by a transcription attenuation mechanism controlled by the trp RNA-binding attenuation protein (TRAP). TRAP binds to 11 (G/U)AG repeats in the trp leader transcript and prevents formation of an antiterminator, which allows formation of an intrinsic terminator (attenuator). Previously, formation of the attenuator RNA structure was believed to be solely responsible for signaling RNA polymerase (RNAP) to halt transcription. However, base substitutions that prevent formation of the antiterminator, and thus allow the attenuator structure to form constitutively, do not result in efficient transcription termination. The observation that the attenuator requires the presence of TRAP bound to the nascent RNA to cause efficient transcription termination suggests TRAP has an additional role in causing termination at the attenuator. We show that the trp attenuator is a weak intrinsic terminator due to low GC content of the hairpin stem and interruptions in the U-stretch following the hairpin. We also provide evidence that termination at the trp attenuator requires forward translocation of RNA polymerase and that TRAP binding to the nascent transcript can induce this activity

Different modes and potencies of translational repression by sequence-specific RNA–protein interaction at the 5′-UTR

To determine whether sequence-specific RNA–protein interaction at the 5′-untranslated region (5′-UTR) can potently repress translation in mammalian cells, a bicistronic translational repression assay was developed to permit direct assessment of RNA–protein interaction and translational repression in transiently transfected living mammalian cells. Changes in cap-dependent yellow fluorescent protein (YFP) and internal ribosome entry sequence (IRES)-dependent cyan fluorescent protein (CFP) translation were monitored by fluorescence microscopy. Selective repression of YFP or coordinate repression of both YFP and CFP translation occurred, indicating two distinct modes by which RNA-binding proteins repress translation through the 5′-UTR. Interestingly, a single-stranded RNA-binding protein from Bacillus subtilis, tryptophan RNA-binding attenuation protein (TRAP), showed potent translational repression, dependent on the level of TRAP expression and position of its cognate binding site within the bicistronic reporter transcript. As the first of its class to be examined in mammalian cells, its potency in repression of translation through the 5′-UTR may be a general feature for this class of single-stranded RNA-binding proteins. Finally, a one-hybrid screen based on translational repression through the 5′-UTR identified linkers supporting full-translational repression as well as a range of partial repression by TRAP within the context of a fusion protein

IntegratedMRF: random forest-based framework for integrating prediction from different data types

Abstract Summary IntegratedMRF is an open-source R implementation for integrating drug response predictions from various genomic characterizations using univariate or multivariate random forests that includes various options for error estimation techniques. The integrated framework was developed following superior performance of random forest based methods in NCI-DREAM drug sensitivity prediction challenge. The computational framework can be applied to estimate mean and confidence interval of drug response prediction errors based on ensemble approaches with various combinations of genetic and epigenetic characterizations as inputs. The multivariate random forest implementation included in the package incorporates the correlations between output responses in the modeling and has been shown to perform better than existing approaches when the drug responses are correlated. Detailed analysis of the provided features is included in the Supplementary Material. Availability and Implementation The framework has been implemented as a R package IntegratedMRF, which can be downloaded from https://cran.r-project.org/web/packages/IntegratedMRF/index.html, where further explanation of the package is available. Supplementary information Supplementary data are available at Bioinformatics online. </jats:sec

Thalidomide and Dexamethasone in Newly Diagnosed Multiple Myeloma.

Abstract PURPOSE: Thalidomide and dexamethasone has been shown to have excellent antimyeloma activity in both relapsed and newly diagnosed patients. This combination offers a potential oral, less toxic alternative to standard regimens. This retrospective study evaluates the activity of the combination of thalidomide and dexamethasone in patients with newly diagnosed multiple myeloma. METHODS: Thirty-two patients with newly diagnosed multiple myeloma were treated with thalidomide and dexamethasone. The median age of the patients was 69yrs (range 46 to 83). The median serum paraprotein level was 38g/l (range 2 to 76g/l). The median bone marrow plasma cell percentage was 50% (range 10% to 99%) The first sixteen patients were commenced on thalidomide at 200mg od with the dose increased by 200mg every two weeks if tolerated to a maximum of 800mg od. The most recent sixteen patients were commenced on thalidomide at 100mg od with the dose increased to a maximum of 200mg if tolerated. All patients received dexamethasone 10mg qds 4-days-on/4-days-off for the first four weeks and for a four day pulse every four weeks subsequently. RESULTS: Twenty-two of the thirty-two patients (69%) showed a greater than 50% reduction in serum paraprotein and/or urinary Bence Jones protein (BJP) from baseline. From the lower thalidomide dose group thirteen out of sixteen patients(81%) showed a greater than 50% reduction in serum paraprotein and/or urinary BJP from baseline compared with nine out of sixteen (56%) in the higher thalidomide dose group. Thirteen patients (40%) showed a reduction in serum paraprotein and/or urinary BJP of greater than 90%, eight from the lower thalidomide dose group and five from the higher thalidomide dose group. Six of the patients failed to complete one month of treatment due to toxicities. They were all from the higher thalidomide dose group. Toxicities included drowsiness (eleven patients), constipation (six patients), rash (four patients) and peripheral neuropathy (four patients). None of the patients have suffered a venous thromboembolic event. Fewer toxicities were noted in the lower dose thalidomide group. CONCLUSION: The combination of thalidomide and dexamethasone is safe and effective in the treatment of newly diagnosed multiple myeloma. There is less toxicity and no loss of efficacy with lower doses of thalidomide.</jats:p