Search

Background: The Polio Eradication and Endgame Strategic Plan (PEESP) established a target that at least 50% of the time of personnel receiving funding from the Global Polio Eradication Initiative (GPEI) for polio eradication activities (hereafter, "GPEI-funded personnel") should be dedicated to the strengthening of immunization systems. This article describes the self-reported profile of how GPEI-funded personnel allocate their time toward immunization goals and activities beyond those associated with polio, the training they have received to conduct tasks to strengthen routine immunization systems, and the type of tasks they have conducted., Methods: A survey of approximately 1000 field managers of frontline GPEI-funded personnel was conducted by Boston Consulting Group in the 10 focus countries of the PEESP during 2 phases, in 2013 and 2014, to determine time allocation among frontline staff. Country-specific reports on the training of GPEI-funded personnel were reviewed, and an analysis of the types of tasks that were reported was conducted., Results: A total of 467 managers responded to the survey. Forty-seven percent of the time (range, 23%-61%) of GPEI-funded personnel was dedicated to tasks related to strengthening immunization programs, other than polio eradication. Less time was spent on polio-associated activities in countries that had already interrupted wild poliovirus (WPV) transmission, compared with findings for WPV-endemic countries. All countries conducted periodic trainings of the GPEI-funded personnel. The types of non-polio-related tasks performed by GPEI-funded personnel varied among countries and included surveillance, microplanning, newborn registration and defaulter tracing, monitoring of routine immunization activities, and support of district immunization task teams, as well as promotion of health behaviors, such as clean-water use and good hygiene and sanitation practices., Conclusion: In all countries, GPEI-funded personnel perform critical tasks in the strengthening of routine immunization programs and the control of measles and rubella. In certain countries with very weak immunization systems, GPEI-funded personnel provide critical support for the immunization programs, and sudden discontinuation of their employment would potentially disrupt the immunization programs in their countries and create a setback in capacity and effectiveness that would put children at higher risk for vaccine-preventable diseases., (© The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.)

In 1983, in the face of mounting evidence of excess leukemia among workers at Shell Oil's Wood River (IL) and Deer Park (TX) petroleum refineries, Shell initiated the Benzene Historical Exposure Study (BHES). Shell's prior research had implicated occupational exposure to benzene as the source of the excess leukemia. The BHES report submission, which ultimately found no link between exposure and the excess morbidity, coincided with OSHA's planned hearings over a new regulatory standard for benzene. Over the next two decades, Shell published several papers based on or expanding the BHES data, all of which concluded that the excess of leukemia was unrelated to benzene. A review of the raw data on which Shell and its consultants relied reveals that Shell manipulated and omitted data in order to reach conclusions that exculpated it from liability and helped delay stricter benzene regulation.

Ribonuclease P (RNaseP) catalyses the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5' terminus. The prokaryotic RNaseP holoenzyme consists of a catalytic RNA component and a protein subunit (RNaseP protein), which plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. We determined the three-dimensional high-resolution structure of the RNaseP protein from Staphylococcus aureus (117 amino acid residues) by nuclear magnetic resonance (NMR) spectroscopy in solution. The protein has an alphabeta-fold, similar to the ribonucleoprotein domain. We used small nucleic acid molecules as a model for the 5'-leader sequence to probe the propensity for generic single-stranded RNA binding on the protein surface. The NMR results reveal a contiguous interaction site, which is identical with the previously identified leader sequence binding site in RNaseP holoenzyme. The conserved arginine-rich motif does not bind single-stranded RNA. It is likely that this peptide segment binds selectively to double-stranded sections of P RNA, which are conformationally more rigid. Given the essentiality of RNaseP for the viability of the organism, knowledge of the S. aureus protein structure and insight into its interaction with RNA will help us to develop RNaseP and RNaseP protein as targets for novel antibiotics against this pathogen., (Copyright 2000 Academic Press.)

Background: Hairpin ribozymes (RNA enzymes) catalyze the same chemical reaction as ribonuclease A and yet RNAs do not usually have functional groups analogous to the catalytically essential histidine and lysine sidechains of protein ribonucleases. Some RNA enzymes appear to recruit metal ions to act as Lewis acids in charge stabilization and metal-bound hydroxide for general base catalysis, but it has been reported that the hairpin ribozyme functions in the presence of metal ion chelators. This led us to investigate whether the hairpin ribozyme exploits a metal-ion-independent catalytic strategy., Results: Substitution of sulfur for nonbridging oxygens of the reactive phosphate of the hairpin ribozyme has small, stereospecific and metal-ion-independent effects on cleavage and ligation mediated by this ribozyme. Cobalt hexammine, an exchange-inert metal complex, supports full hairpin ribozyme activity, and the ribozyme's catalytic rate constants display only a shallow dependence on pH., Conclusions: Direct metal ion coordination to phosphate oxygens is not essential for hairpin ribozyme catalysis and metal-bound hydroxide does not serve as the general base in this catalysis. Several models might account for the unusual pH and metal ion independence: hairpin cleavage and ligation might be limited by a slow conformational change; a pH-independent or metal-cation-independent chemical step, such as breaking the 5' oxygen-phosphorus bond, might be rate determining; or finally, functional groups within the ribozyme might participate directly in catalytic chemistry. Whichever the case, the hairpin ribozyme appears to employ a unique strategy for RNA catalysis.

Recognition of tRNA and tRNA-like substrates by the enzyme ATP/CTP:tRNA nucleotidyltransferase requires chemically intact nucleotides within the T-loop, especially at positions 57 and 58, which are invariant purines among naturally occurring tRNAs. To test the effects of base substitutions at these positions, which are distant from the site of catalysis, we synthesized mutant tRNA(Glu) molecules. These in vitro-synthesized RNAs also contained an extra 33 bases at the 5' end and lacked post-transcriptionally modified bases. The precursor tRNAs were used as substrates for nucleotidyltransferases from Escherichia coli and yeast. Substitution of cytidines at either position 57 or 58 had dramatic inhibitory effects on recognition by both enzymes, including raising the apparent Km and lowering the apparent Vmax.; substitution of an adenosine at position 57 or a uridine at position 58 inhibited the reaction only slightly by comparison. Our results demonstrate that the identities of nucleotides at positions 57 and 58 are relevant to recognition by nucleotidyltransferase, and that a purine is required at position 57. The extra bases at the 5' end and the lack of post-transcriptionally modified bases did not substantially inhibit interaction with the enzyme, as judged by the wild-type precursor tRNA(Glu) acting as an effective substrate for both enzymes in the presence of equal concentrations of appropriate tRNA substrates isolated from E. coli.

The hairpin ribozyme, derived from the negative strand of the satellite RNA of tobacco ringspot virus, belongs to the class of small catalytic RNAs that cleave RNA to generate 2',3'-cyclic phosphate and 5'hydroxyl termini and ligate these termini in the reverse reaction to form 3',5'-phosphodiesters. Rate and equilibrium constants for binding, dissociation, cleavage, and ligation steps in the kinetic mechanism were determined using a series of hairpin ribozyme/substrate pairs that differed in the sequence and length of the intermolecular base-paired helices. All hairpin variants cleaved with rate constants of approximately 0.3 min-1 at pH 7.5 in 10 nM MgCl2 at 25 degrees C, regardless of the length or sequence of the intermolecular helices. A rate constant of approximately 3 min-1 was determined for an intermolecular ligation reaction in which both cleavage products were supplied to the ribozyme in trans. Thus, the hairpin favored ligation over cleavage by 10-fold when the ribozyme was saturated with cleavage products. Binding rate constants for cleavage substrates and products were comparable to values reported for other catalytic RNAs but were somewhat slower than binding rates typical of small RNA helices. Substrate dissociation rate constants were much slower than cleavage rate constants for all substrates. Because virtually every substrate that was bound was cleaved before it could dissociate, KMS values were not the same as KdS values. Instead, KMS reflected the ratio of cleavage and substrate binding rate constants and had the same value of approximately 30 nM for all substrates. Calculations based on empirically determined free energy parameters for simple RNA helices indicated that complexes between ribozymes and 5'-cleavage products were slightly less stable than simple helices with the same sequences. In contrast, affinities between ribozymes and cleavage substrates and between ribozymes and 3'-cleavage products were stronger than expected for simple duplexes by about -2.5 kcal/mol, evidence of stabilizing interactions in addition to those contributed by helical base pairs. This kinetic and thermodynamic study demonstrates that the kinetic mechanism of the hairpin ribozyme is distinct from the kinetic mechanisms of other well-characterized ribozymes and provides a foundation for further exploration of the hairpin structure and catalytic mechanism.

Individual species of tRNA from Escherichia coli were treated with hydrazine/3 M NaCl to modify cytidine residues. The chemically modified tRNAs were used as substrate for ATP/CTP: tRNA nucleotidyltransferases from E. coli and yeast, with [alpha-32P]ATP as cosubstrate. tRNAs that were labeled were analyzed for their content of modified cytidines. Cytidines at positions 74 and 75 were found to be required chemically intact for interaction with both enzymes. C56 was also required intact by the E. coli enzyme in all tRNAs, and by the yeast enzyme in several instances. C61 was found to be important in seven of 14 tRNAs with the E. coli enzyme but only in four of 13 tRNAs with that from yeast. Our results support a model in which nucleotidyltransferase extends from the 3' end of its tRNA substrate across the top of the stacked array of bases in the accepter- and psi-stems to the corner of the molecule where the D- and psi-loops are juxtaposed.

The 3'-terminal tRNA-like structure of the tobacco mosaic virus RNA interacts with ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli or yeast in much the same manner as do tRNAs. Primary sites of interaction cluster near the 3' end and in the loop proposed to be analogous to the psi-loop of a tRNA. Some modified bases in the tRNA-like structure inhibit interaction with nucleotidyltransferase, yet the analogous bases in a tRNA do not. The location of some of these nucleotides within the analog to the psi-loop suggests that this structure differs slightly from its counterpart in a tRNA. The location of other such bases in the helical stem near the 3' end can be explained if the pseudoknot is disrupted by these modified bases or if the tertiary structure of the RNA is altered in the enzyme-RNA complex. A partially denatured secondary structure that persists on denaturing gels is proposed.

Fifteen individual species of tRNA were treated with the chemical modifiers diethylpyrocarbonate, 50% aqueous hydrazine or hydrazine/3 M NaCl. Following purification of the chemically modified material on polyacrylamide gels containing 8 M urea, variant minor bands, in addition to the expected main band, were observed for 12 of the 15 tRNAs. Characterization of the content of chemically altered bases in material recovered from such bands indicated that tRNAs containing modified nucleotides in base-paired stems were excluded from the main band and present, often in enhanced amounts, in the minor variant bands. The persistence of residual secondary structure on 8 M urea gels run at 45 degrees C and the ability of chemically modified bases to alter electrophoretic mobilities warrant caution in designing and interpreting experiments in which chemically modified RNA is isolated on gels prior to further analysis. tRNA(Val) (VAC) was unique in that modified bases in non base-paired regions, according to the cloverleaf model of secondary structure, caused exclusion from the main band. Consequently, we propose a secondary structure for partially denatured tRNA(Val) (VAC), in which these bases are located in double stranded regions of the molecule.