Effects of Growth in the Presence of Subinhibitory Concentrations of Dicloxacillin on Staphylococcus epidermidis and Staphylococcus haemolyticus Biofilms

Low concentrations of antibiotics can inhibit microbial adherence to medical device surfaces. However, little is known about the changes that occur in the physiology of bacteria within biofilms formed in the presence of subinhibitory (sub-MIC) concentrations of antibiotics. In this study, the densities and matrix compositions ofbiofilms formed by two coagulase-negative Staphylococcus species in the absence and in the presence of sub-MIC concentrations of dicloxacillin were evaluated. Biofilms formed in the presence of sub-MIC concentrations of dicloxacillin contained less biomass, and there were notable changes in the composition of the biofilm matrix. Changes in the spatial structure were also verified by confocal scanning laser microscopy, indicating that biofilms grown in the presence of sub-MIC concentrations of dicloxicilln had a lower cell density. Physiological alterations in the bacteria within biofilms grown in the presence of subinhibitory concentrations of the antibiotic were also evaluated. The results showed that there were differences in bacterial surface characteristics when cultures were grown in the presence of sub-MIC concentrations of dicloxacillin, including decreased hydrophobicity and decreased expression of the exopolysaccharide poly-N-acetylglucosamine. The elemental composition of the cell surface was also analyzed, and whereas in Staphylococcus epidermidis there were decreases in the oxygen and nitrogen contents, in Staphylococcus haemolyticus there were increases in these two parameters. Additionally, increases in resistance to several antibiotics were observed for the cells within biofilms formed in the presence of dicloxacillin.     

Nse1 RING-like domain supports functions of the Smc5-Smc6 holocomplex in genome stability

The Smc5-Smc6 holocomplex plays essential but largely enigmatic roles in chromosome segregation, and facilitates DNA repair. The Smc5-Smc6 complex contains six conserved non-SMC subunits. One of these, Nse1, contains a RING-like motif that often confers ubiquitin E3 ligase activity. We have functionally characterized the Nse1 RING-like motif, to determine its contribution to the chromosome segregation and DNA repair roles of Smc5-Smc6. Strikingly, whereas a full deletion of nse1 is lethal, the Nse1 RING-like motif is not essential for cellular viability. However, Nse1 RING mutant cells are hypersensitive to a broad spectrum of genotoxic stresses, indicating that the Nse1 RING motif promotes DNA repair functions of Smc5-Smc6. We tested the ability of both human and yeast Nse1 to mediate ubiquitin E3 ligase activity in vitro and found no detectable activity associated with full-length Nse1 or the isolated RING domains. Interestingly, however, the Nse1 RING-like domain is required for normal Nse1-Nse3-Nse4 trimer formation in vitro and for damage-induced recruitment of Nse4 and Smc5 to subnuclear foci in vivo. Thus, we propose that the Nse1 RING-like motif is a protein–protein interaction domain required for Smc5-Smc6 holocomplex integrity and recruitment to, or retention at, DNA lesions.     

The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction

Background  

Amino acids responsible for structure, core function or specificity may be inferred from multiple protein sequence alignments where a limited set of residue types are tolerated. The rise in available protein sequences continues to increase the power of techniques based on this principle.     

Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors

Non-nucleoside inhibitors of HCV NS5b RNA polymerase were discovered by a fragment-based lead discovery approach, beginning with crystallographic fragment screening. The NS5b binding affinity and biochemical activity of fragment hits and inhibitors was determined by surface plasmon resonance (Biacore) and an enzyme inhibition assay, respectively. Crystallographic fragment screening hits with 1–10 mM binding affinity (K_D) were iteratively optimized to give leads with 200 nM biochemical activity and low μM cellular activity in a Replicon assay.     

A SIM-ultaneous role for SUMO and ubiquitin

Ubiquitin and ubiquitin-like proteins (Ubls) share a beta-GRASP fold and have key roles in cellular growth and suppression of genome instability. Despite their common fold, SUMO and ubiquitin are classically portrayed as distinct, and they can have antagonistic roles. Recently, a new family of proteins, the small ubiquitin-related modifier (SUMO)-targeted ubiquitin ligases (STUbLs), which directly connect sumoylation and ubiquitylation, has been discovered. Uniquely, STUbLs use SUMO-interaction motifs (SIMs) to recognize their sumoylated targets. STUbLs are global regulators of protein sumoylation levels, and cells lacking STUbLs display genomic instability and hypersensitivity to genotoxic stress. The human STUbL, RNF4, is implicated in several diseases including cancer, highlighting the importance of characterizing the cellular functions of STUbLs.     

The air spora close to a compost facility in Northeast Oklahoma: Part I—spore trap sampling

A compost facility in northeast Oklahoma is located relatively close to a residential area and is the focus of complaints about smell and concerns about health effects. Several species of Aspergillus have been known to cause health problems, and at least one of these species is dominant in compost. The atmosphere surrounding the compost facility was monitored for 1 year using Burkard spore traps to determine if there was a significant difference in Penicillium/Aspergillus type spores concentration between a test and control site. Samplers were situated 710 m downwind for the test site and 6,085 m upwind at the control site. There was no significant difference in mean concentration of Penicillium/Aspergillus type spores between the two sites (t = 0.576 P > 0.05). The mean concentration of total spores was significantly higher at the upwind control site (t = −7.64, P < 0.01). Wind direction was examined to determine if the compost facility was a possible source for any spikes in concentration. No clear relationship was found between wind direction and mean Penicillium/Aspergillus concentration at the test site, but peak concentrations of Penicillium/Aspergillus seen at the test site were on days when it was downwind from the composting facility. However, these concentrations were no higher than those seen at the control site on other days. If the compost was releasing large amounts of Penicillium/Aspergillus type spores into the atmosphere they were generally diluted to background levels by the time they reached the test site.     

A comparison of SCOP and CATH with respect to domain-domain interactions

The analysis and prediction of protein-protein interaction sites from structural data are restricted by the limited availability of structural complexes that represent the complete protein-protein interaction space. The domain classification schemes CATH and SCOP are normally used independently in the analysis and prediction of protein domain-domain interactions. In this article, the effect of different domain classification schemes on the number and type of domain-domain interactions observed in structural data is systematically evaluated for the SCOP and CATH hierarchies. Although there is a large overlap in domain assignments between SCOP and CATH, 23.6% of CATH interfaces had no SCOP equivalent and 37.3% of SCOP interfaces had no CATH equivalent in a nonredundant set. Therefore, combining both classifications gives an increase of between 23.6 and 37.3% in domain-domain interfaces. It is suggested that if possible, both domain classification schemes should be used together, but if only one is selected, SCOP provides better coverage than CATH. Employing both SCOP and CATH reduces the false negative rate of predictive methods, which employ homology matching to structural data to predict protein-protein interaction by an estimated 6.5%.     

Impacts of Herbicide Application and Mechanical Cleanings on Growth and Mortality of Two Timber Species in Saccharum spontaneum Grasslands of the Panama Canal Watershed

Reforestation has been suggested as a strategy to control Saccharum spontaneum, an invasive grass that impedes regeneration in disturbed areas of the Panama Canal Watershed (PCW). In this study, the effects of different intensities of herbicide application and mechanical cleanings on the growth and mortality of Terminalia amazonia and Tectona grandis saplings were evaluated in S. spontaneum grasslands within the PCW. Both species exhibited greater height, basal diameter, wood volume index, wider crown diameters, deeper live crowns, and lower mortality with increasing intensity of mechanical cleanings and herbicide application. Height and competition of S. spontaneum correlated negatively with intensity of mechanical cleanings and herbicide application. Grass control costs did not differ between tree species but did increase significantly with intensity of mechanical cleanings and herbicide application. We recommend fire suppression, annual herbicide application, and at least four mechanical cleanings per year in Tec. grandis plantations during the first 3 years of plantation establishment. Given the slower initial growth and mortality patterns of Ter. amazonia, aggressive grass control treatments should be continued until individuals are sufficiently large to effectively shade S. spontaneum. Results from this study suggest that reforestation with commercial timber species can rapidly establish and control S. spontaneum growth in the PCW. Reforestation of areas already invaded or at risk of being invaded by S. spontaneum appears to be a viable strategy to reduce its abundance and subsequent negative ecological effects in the PCW.