Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea

A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea.     

Evidence that conserved residues Cys-62 and Cys-154 within the Azotobacter vinelandii nitrogenase MoFe protein α-subunit are essential for nitrogenase activity but conserved residues His-83 and Cys-88 are not

Metallocluster extrusion requirements, interspecies MoFe-protein primary sequence comparisons and comparison of the primary sequences of the MoFe-protein subunits with each other have been used to assign potential P-cluster (Fe-S cluster) domains within the MoFe protein. In each alpha-beta unit of the MoFe protein, alpha-subunit domains, which include potential Fe-S cluster ligands Cys-62, His-83, Cys-88 and Cys-154, and beta-subunit domains, which include potential Fe-S cluster ligands Cys-70, His-90, Cys-95 and Cys-153, are proposed to comprise nearly equivalent P-cluster environments located adjacent to each other in the native protein. As an approach to test this model and to probe the functional properties of the P clusters, amino acid residue substitutions were placed at the alpha-subunit Cys-62, His-83, Cys-88 and Cys-154 positions by site-directed mutagenesis of the Azotobacter vinelandii nifD gene. The diazotrophic growth rates, MoFe-protein acetylene-reduction activities, and whole-cell S = 3/2 electron paramagnetic resonance spectra of these mutants were examined. Results of these experiments show that MoFe-protein alpha-subunit residues, Cys-62 and Cys-154, are probably essential for MoFe-protein activity but that His-83 and Cys-88 residues are not. These results indicate either that His-83 and Cys-88 do not provide essential P-cluster ligands or that a new cluster-ligand arrangement is formed in their absence.     

Abortion is incommensurable with fetal alcohol syndrome

A recent article argued for the immorality of abortion regardless of personhood status by comparing the impairment caused by fetal alcohol syndrome to the impairment caused by abortion. I argue that two of the premises in this argument fail and that, as such, one cannot reasonably attribute moral harms to abortion on the basis of the moral harms caused by fetal alcohol syndrome. The impairment argument relies on an inconsistent instantiation, which undermines the claim that personhood is irrelevant, and it does not fulfill its own ceteris paribus clause, which demands that no additional benefit be gained from abortion that would not be gained from causing fetal alcohol syndrome.     

Interaction of soil moisture and elevated CO2 on the above-ground growth rate, root length density and gas exchange of turves from temperate pasture

Interactions between water availability and elevated atmosphericCO₂ concentrations have the potential to be important factorsin determining future forage supply from temperate pastures.Using large turves from an established pasture, the responseof these communities at 350 or 700 l l^–1 CO₂ to a soilmoisture deficit and to recovery from the deficit in comparisonto turves that were well-watered throughout was measured. Priorto this experiment the turves had been exposed to the CO₂ treatmentsfor 324 d. Net CO₂ exchange continued at elevated CO₂ even when the volumetricsoil moisture content was less than 0.10 m³ m^–3 soil;at the same moisture deficit gas exchange at ambient CO₂ waszero. The additional carbon fixed by the elevated CO₂ turveswas primarily allocated below-ground as shown by the maintenanceof root length density at the same level as in well-wateredturves. When the dry turves were rewatered there was compensatorygrowth at ambient CO₂ so that the above-ground growth rate exceededthat of turves that had not experienced a moisture deficit.At the start of this experiment, the turves that were growingat 700 l I^–1 CO₂ had a greater proportion of legume (principallywhite clover, Trifolium repens L.) in the harvested herbage.There was a trend for the legume content at elevated CO₂ tobe reduced under a soil moisture deficit. The results indicate different strategies in response to soilmoisture deficits depending on the CO₂ concentration. At ambientCO₂, growth stopped, but plants were able to respond stronglyon rewatering; while at elevated CO₂ growth continued (particularlybelow-ground), but no additional growth was evident on rewatering.Ecosystem gas exchange measurements taken at the end of theexperiment (after 429 d of exposure to CO₂) showed 33% moreCO₂ was fixed at elevated CO₂ with only a small (12%) and nonsignificantdownward regulation. Key words: Carbon dioxide, climate change, grassland, gas exchange, soil moisture deficit     

Molecular Comparison of Bacterial Communities on Peripheral Intravenous Catheters and Matched Skin Swabs

Skin bacteria at peripheral intravenous catheter (PIVC) insertion sites pose a serious risk of microbial migration and subsequent colonisation of PIVCs, and the development of catheter related bloodstream infections (CRBSIs). Common skin bacteria are often associated with CRBSIs, therefore the bacterial communities at PIVC skin sites are likely to have major implications for PIVC colonisation. This study aimed to determine the bacterial community structures on skin at PIVC insertion sites and to compare the diversity with associated PIVCs. A total of 10 PIVC skin site swabs and matching PIVC tips were collected by a research nurse from 10 hospitalised medical/surgical patients at catheter removal. All swabs and PIVCs underwent traditional culture and high-throughput sequencing. The bacterial communities on PIVC skin swabs and matching PIVCs were diverse and significantly associated (correlation coefficient = 0.7, p<0.001). Methylobacterium spp. was the dominant genus in all PIVC tip samples, but not so for skin swabs. Sixty-one percent of all reads from the PIVC tips and 36% of all reads from the skin swabs belonged to this genus. Staphylococcus spp., (26%), Pseudomonas spp., (10%) and Acinetobacter spp. (10%) were detected from skin swabs but not from PIVC tips. Most skin associated bacteria commonly associated with CRBSIs were observed on skin sites, but not on PIVCs. Diverse bacterial communities were observed at skin sites despite skin decolonization at PIVC insertion. The positive association of skin and PIVC tip communities provides further evidence that skin is a major source of PIVC colonisation via bacterial migration but microbes present may be different to those traditionally identified via culture methods. The results provide new insights into the colonisation of catheters and potential pathogenesis of bacteria associated with CRBSI, and may assist in developing new strategies designed to reduce the risk of CRBSI.     

Distributions of Virus-Like Particles and Prokaryotes within Microenvironments

Microbial interactions are important for ecosystem function, but occur at the microscale and so are difficult to observe. Previous studies in marine systems have shown significant shifts in microbial community abundance and composition over scales of micrometres to centimetres. This study investigates the microscale abundance distributions of virus-like particles (VLPs) and prokaryotes in the lower reaches of a river to determine the extent to which microscale microbial patchiness exists in freshwater systems. Here we report local hotspots surrounded by gradients that reach a maximum 80 and 107 fold change in abundance over 0.9 cm for prokaryotic and VLP subpopulations. Changes in prokaryotic and VLP hotspots were tightly coupled. There were no gradients at tens of centimetres across the boundary layers, which is consistent with strong mixing and turbulence-driven aggregation found in river systems. Quantification of the patchiness shows a marked asymmetry with patches 10 times greater than background common, but depletions being rare or absent in most samples. This consistent asymmetry suggests that coldspots depleted by grazing and lysis are rapidly mixed to background concentrations, while the prevalence of hotspots indicates persistence against disruption. The hotspot to coldspot relative abundance may be useful for understanding microbial river dynamics. The patchiness indicates that the mean- field approach of bulk phase sampling misses the microbially relevant community variation and may underestimate the concentrations of these important microbial groups.