Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I

Virus-responsive signaling pathways that induce alpha/beta interferon production and engage intracellular immune defenses influence the outcome of many viral infections. The processes that trigger these defenses and their effect upon host permissiveness for specific viral pathogens are not well understood. We show that structured hepatitis C virus (HCV) genomic RNA activates interferon regulatory factor 3 (IRF3), thereby inducing interferon in cultured cells. This response is absent in cells selected for permissiveness for HCV RNA replication. Studies including genetic complementation revealed that permissiveness is due to mutational inactivation of RIG-I, an interferon-inducible cellular DExD/H box RNA helicase. Its helicase domain binds HCV RNA and transduces the activation signal for IRF3 by its caspase recruiting domain homolog. RIG-I is thus a pathogen receptor that regulates cellular permissiveness to HCV replication and, as an interferon-responsive gene, may play a key role in interferon-based therapies for the treatment of HCV infection.     

Increases in summer temperatures decrease the survival of an invasive forest insect

Higher temperatures projected under current climate change models are generally predicted to exert an overall positive effect on the success of invasive insects through increased survivability, developmental rates and fecundity, and by facilitating geographic range expansion. However, these effects have primarily focused on the shifts in winter temperatures with limited attention to the role that summer heat may play in shaping species ranges or fitness. We examined the thermal ecology of an ecologically important invasive forest insect, the hemlock woolly adelgid (Adelges tsugae), by determining survival during its summer dormancy phase under increasing temperature regimens. From laboratory and field experiments, we documented a positive association between increased temperatures and duration of exposure, and A. tsugae mortality. Adelges tsugae mortality was minimal (<20%) when exposed to summer temperatures characteristic to its native range (<25 °C), but markedly increased (up to 100%) when exposed to temperatures that occur occasionally or rarely in natural settings (>30 °C). At the warmest, southernmost edge of their range, field mortality of A. tsugae ranged from 8.5 to 81.9% and was strongly correlated with site temperature regimens. Further, we found no significant differences in A. tsugae survival between populations collected from Maine and Georgia, and over a 3-year period within Georgia, indicating that A. tsugae may not be acclimating to heat. These results highlight the importance of including summer temperatures in studies regarding increased temperatures on insect dynamics, and may alter historical predictions of climate change impacts on invasive insects and the conservation of forest ecosystems.     

Physical Mapping of Human 7q and 14q Subtelomeric DNA Sequences in the Great Apes

Phylogenetic divergence of the members of the Pongidae familyhas been based on genetic evidence. The terminal repeat array(T₂AG₃) has lately been considered as an additional basis toanalyze genomes of highly related species. The recent isolationof subtelomeric DNA probes specific for human (HSA) chromosomes7q and 14q has prompted us to cross-hybridize them to the chromosomesof the chimpanzee (PTR), gorilla (GGO) and orangutan (PPY) tosearch for its equivalent locations in the great ape species.Both probes hybridized to the equivalent telomeric sites ofthe long (q) arms of all three great ape species. Hybridizationsignals to the 7q subtelomeric DNA sequence probe were observedat the telomeres of HSA 7q, PTR 6q, GGO 6q and PPY 10q, whilehybridization signals to the 14q subtelomeric DNA sequence probewere observed at the telomeres of HSA 14q, PTR 15q, GGO 18qand PPY 15q. No hybridization signals to the chromosome 7-specificalpha satellite DNA probe on the centromeric regions of theape chromosomes were observed. Our observations demonstratesequence homology of the subtelomeric repeat families D7S427and D14S308 in the ape chromosomes. An analogous number of subtelomericrepeat units exists in these chromosomes and has been preservedthrough the course of differentiation of the hominoid species.Our investigation also suggests a difference in the number ofalpha satellite DNA repeat units in the equivalent ape chromosomes,possibly derived from interchromosomal transfers and subsequentamplification of ancestral alpha satellite sequences.     

The peptidyltransferase centre of the Escherichia coli ribosome. The histidine of protein L16 affects the reconstitution and control of the active centre but is not essential for release-factor-mediated peptidyl-tRNA hydrolysis and peptide bond formation

Modification of the Escherichia coli 50S ribosomal subunit with histidine-specific diethyl pyrocarbonate affects peptide bond formation and release-factor-dependent peptidyl-tRNA hydrolysis. Unmodified L16 can restore activity to a split protein fraction from the altered subunit but other proteins of the core also contain histidine residues important for the activity of the peptidyltransferase centre. When isolated and purified by centrifugation, particles reconstituted with unmodified proteins and modified L16 do not retain the altered L16. The modified protein does mediate the partial restoration of peptide bond formation and release-factor-2 activities to these particles. It must be exerting its effect during the assembly of the peptidyltransferase centre in the reconstituted particle. A particle could be reconstituted which lacks L16 and has significant activity in peptide bond formation and peptidyl-tRNA hydrolysis. L16 stimulates these activities. A tighter ribosomal binding of the release factor 2, dependent upon the absence of protein L11, can in part compensate for the loss of activity of the peptidyltransferase centre when it is assembled with either modified L16 or in the absence of L16. The protein and its histidine residue seem important, therefore, for the peptidyltransferase centre to be formed in the correct conformation but not essential for activity once the centre is assembled.     

The ribosomal binding domain of the Escherichia coli release factors. Modification of tyrosine in the N-terminal domain of ribosomal protein L11 affects release factors 1 and 2 differentially

Ribosomal protein L11 is one of only two ribosomal proteins significantly iodinated when Escherichia coli 50 S subunits are modified by immobilized lactoperoxidase, and the major target has been shown previously to be tyrosine at position 7 in the N-terminal domain. This modification reduces in vitro termination activity with release factor (RF)-1 by 70-90%, but RF-2 activity is less affected (30-50%). The loss of activity parallels incorporation of iodine into the subunit. The 50 S subunits from L11-lacking strains of bacteria have highly elevated activity with RF-2 and low activity with RF-1. The iodination does not affect RF-2 activity but reduces the RF-1 activity further. Ribosomal proteins, L2, L6, and L25, are significantly labeled in L11-lacking ribosomes in contrast to the control 50 S subunits. L11 has been modified in isolation and incorporated back efficiently into L11-lacking ribosomes. This L11, iodinated also predominantly at Tyr 7, is unable to restore RF-1 activity to L11-lacking ribosomes in contrast to mock-iodinated protein. These results suggest the involvement of the N terminus of L11 in the binding domain of the bacterial release factors and indicate that there are subtle differences in how the two factors interact with the ribosome.     

Bayesian Dynamical Systems Modelling in the Social Sciences

Data arising from social systems is often highly complex, involving non-linear relationships between the macro-level variables that characterize these systems. We present a method for analyzing this type of longitudinal or panel data using differential equations. We identify the best non-linear functions that capture interactions between variables, employing Bayes factor to decide how many interaction terms should be included in the model. This method punishes overly complicated models and identifies models with the most explanatory power. We illustrate our approach on the classic example of relating democracy and economic growth, identifying non-linear relationships between these two variables. We show how multiple variables and variable lags can be accounted for and provide a toolbox in R to implement our approach.     

Comparison of microbial communities involved in souring and corrosion in offshore and onshore oil production facilities in Nigeria

Samples were obtained from the Obigbo field, located onshore in the Niger delta, Nigeria, from which oil is produced by injection of low-sulfate groundwater, as well as from the offshore Bonga field from which oil is produced by injection of high-sulfate (2,200 ppm) seawater, amended with 45 ppm of calcium nitrate to limit reservoir souring. Despite low concentrations of sulfate (0–7 ppm) and nitrate (0 ppm), sulfate-reducing bacteria (SRB) and heterotrophic nitrate-reducing bacteria (NRB) were present in samples from the Obigbo field. Biologically active deposits (BADs), scraped from corrosion-failed sections of a water- and of an oil-transporting pipeline (both Obigbo), had high counts of SRB and high sulfate and ferrous iron concentrations. Analysis of microbial community composition by pyrosequencing indicated anaerobic, methanogenic hydrocarbon degradation to be a dominant process in all samples from the Obigbo field, including the BADs. Samples from the Bonga field also had significant activity of SRB, as well as of heterotrophic and of sulfide-oxidizing NRB. Microbial community analysis indicated high proportions of potentially thermophilic NRB and near-absence of microbes active in methanogenic hydrocarbon degradation. Anaerobic incubation of Bonga samples with steel coupons gave moderate general corrosion rates of 0.045–0.049 mm/year, whereas near-zero general corrosion rates (0.001–0.002 mm/year) were observed with Obigbo water samples. Hence, methanogens may contribute to corrosion at Obigbo, but the low general corrosion rates cannot explain the reasons for pipeline failures in the Niger delta. A focus of future work should be on understanding the role of BADs in enhancing under-deposit pitting corrosion.