1,838 research outputs found

    In Vitro Studies of the Prp9·Prp11·Prp21 Complex Indicate a Pathway for U2 Small Nuclear Ribonucleoprotein Activation

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    Pre-mRNA splicing takes place on a large ribonucleoprotein particle, the spliceosome which contains the five small nuclear ribonucleoproteins (snRNPs), U1, U2, U4, U5, and U6. In Saccharomyces cerevisiae the mRNA splicing factors, Prp9, Prp11, and Prp21, are necessary for addition of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly. This paper describes a study of interactions between these proteins and their role in spliceosome assembly. The proteins were expressed in Escherichia coli. Prp9 and Prp11 were purified by metal affinity chromatography. Prp21 was purified using a solubilization/renaturation protocol. We have combined these separately purified proteins and present direct evidence of a Prp9·Prp11·Prp21 protein complex that is functional in in vitro splicing assays. Characteristics of this Prp9·Prp11·Prp21 complex were further investigated using proteins synthesized in vitro. In addition, we found that Prp9, Prp11, and Prp21 influence the structure of the U2 snRNP in a manner that alters the accessibility of the branch point pairing region of the U2 snRNA to oligonucleotide-directed RNaseH cleavage. We present a model, based on the data presented here and in the accompanying paper, for a combined role of Prp9, Prp11, Prp21, and Prp5 in activating the U2 snRNP for assembly into the pre-spliceosome

    Natural attenuation of arsenic by sediment sorption and oxidation

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    Arsenic sorption onto aquifer sediments was investigated in anaerobic laboratory batch and column uptake experiments and characterized by As, Fe, and Mn X-ray absorption spectroscopy (XAS) to estimate the extent and mechanism of abiotic sorption and oxidation of As(III). Batch experiments at pH 6 showed that the amount of As(III) or As(V) sorption from synthetic background porewater to sediments was similar as a function of total As concentration, but slightly more As(V) was sorbed than As(III) with increasing As concentrations. Column experiments with As(III) solutions in the absence and presence of dissolved Fe^2+ showed more As uptake in the presence of Fe but also more Fe desorption during flushout with As-free solutions such that net As uptake was similar to, or less than that of, the Fe-free experiment. Fits to bulk Fe X-ray absorption near-edge spectroscopy (XANES) spectra showed no change between unreacted and reacted sediments. Manganese XANES revealed small increases in absorption in the spectral region associated with Mn(II) after reaction, indicating sediment Mn reduction. However, XANES spectra showed that Mn is not present as Mn^(IV)O_2(s) but is probably substituted into other sediment minerals as a mixture of Mn(II,III). Quantitative analyses of As XANES spectra, which indicated mixtures of As(III) and As(V) after reaction with As(III) solutions, were used to estimate a fraction of As(V) in excess of native As(V) in the sediment (0.2 mmol kg^−1) that corresponds to sorbed As(III) oxidized to As(V). The spectroscopic and solution data indicate that the aquifer sediments have a limited abiotic capacity to oxidize As(III), which did not exceed 30% of the total amount of As sorbed and was estimated in the range of 0.025−0.4 mmol kg^−1 sediment. In the presence of dissolved Fe^2+, the precipitation of Fe(III) hydrous oxide phases will be an effective mechanism for As scavenging only if there exists sufficient dissolved oxygen in groundwater to oxidize Fe. Once the aqueous oxidative capacity is exhausted, dissolved Fe^2+ may compete with As(III) for the limited abiotic oxidation supplied by sediment Mn-bearing phases

    A Gel Probe Equilibrium Sampler for Measuring Arsenic Porewater Profiles and Sorption Gradients in Sediments: I. Laboratory Development

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    A gel probe equilibrium sampler has been developed to study arsenic (As) geochemistry and sorption behavior in sediment porewater. The gels consist of a hydrated polyacrylamide polymer, which has a 92% water content. Two types of gels were used in this study. Undoped (clear) gels were used to measure concentrations of As and other elements in sediment porewater. The polyacrylamide gel was also doped with hydrous ferric oxide (HFO), an amorphous iron (Fe) oxyhydroxide. When deployed in the field, HFO-doped gels introduce a fresh sorbent into the subsurface thus allowing assessment of in situ sorption. In this study, clear and HFO-doped gels were tested under laboratory conditions to constrain the gel behavior prior to field deployment. Both types of gels were allowed to equilibrate with solutions of varying composition and re-equilibrated in acid for analysis. Clear gels accurately measured solution concentrations (±1%), and As was completely recovered from HFO-doped gels (±4%). Arsenic speciation was determined in clear gels through chromatographic separation of the re-equilibrated solution. For comparison to speciation in solution, mixtures of As(III) and As(V) adsorbed on HFO embedded in gel were measured in situ using X-ray absorption spectroscopy (XAS). Sorption densities for As(III) and As(V) on HFO embedded in gel were obtained from sorption isotherms at pH 7.1. When As and phosphate were simultaneously equilibrated (in up to 50-fold excess of As) with HFO-doped gels, phosphate inhibited As sorption by up to 85% and had a stronger inhibitory effect on As(V) than As(III). Natural organic matter (>200 ppm) decreased As adsorption by up to 50%, and had similar effects on As(V) and As(III). The laboratory results provide a basis for interpreting results obtained by deploying the gel probe in the field and elucidating the mechanisms controlling As partitioning between solid and dissolved phases in the environment

    Animations Are Dynamic, Effective Tools For Science Teaching: If You Just Follow The Rules!

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    Textbook companies are increasingly including larger numbers of animations as complementary resources for students and teachers. Are all animations useful as teaching tools? The answer is no. Animations can be useful for communicating dynamic events and processes but only when specific rules are followed. The authors review the important components of effective animations and their extensive, original research on the value of animations in learning and long-term memory retention. When the rules are applied, students can learn complex material more easily and retain more of what they have learned in short and long term memory than they can by viewing static textbook figures. Our results also indicate that learning from animations and graphics differs between males and females. Insight gained from student feedback is highlighted with some final comments on future research

    Omnidirectional Electric Fish

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    An Enzymatic Palimpsest

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