Methylation damage to RNA induced in vivo in Escherichia coli is repaired by endogenous AlkB as part of the adaptive response

Cytotoxic 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) lesions induced in DNA and RNA in vitro and in pre-damaged DNA and RNA bacteriophages in vivo are repaired by the Escherichia coli (E. coli) protein AlkB and a human homolog, ALKBH3. However, it is not known whether endogenous RNA is repaired in vivo by repair proteins present at physiological concentrations. The concept of RNA repair as a biologically relevant process has therefore remained elusive. Here, we demonstrate AlkB-mediated repair of endogenous RNA in vivo by measuring differences in lesion-accumulation in two independent AlkB-proficient and deficient E. coli strains during exposure to methyl methanesulfonate (MMS). Repair was observed both in AlkB-overproducing strains and in the wild-type strains after AlkB induction. RNA repair appeared to be highest in RNA species below 200 nucleotides in size, mainly comprising tRNAs. Strikingly, at least 10-fold more lesions were repaired in RNA than in DNA. This may be a consequence of some 30-fold higher levels of aberrant methylation in RNA than in DNA after exposure to MMS. A high primary kinetic isotope effect (>10) was measured using a deuterated methylated RNA substrate, D₃-1me(rA), demonstrating that it is the catalytic step, and not the search step that is rate-limiting. Our results demonstrate that RNA repair by AlkB takes place in endogenous RNA as part of an adaptive response in wild-type E. coli cells.     

Genotypical and multiple phenotypical traits discriminate Salix × rubens Schrank clearly from its parent species

Most studies on Salix hybrids concerning the diversity in a hybrid complex included typical morphological characteristics of leaves, buds, twigs and flowers for comparison with genotypic traits. Our analyses are based on a set of phenotypical traits of 19 clones of the S. alba/S. fragilis-aggregate which includes characteristics as phenology, growth, and composition of secondary leaf compounds, for the first time additional to morphological traits. Three clearly distinct groups (S. alba L., S. fragilis L., and S. × rubens Schrank) could be identified based on phenotypical traits and ITS1 and 5.8S nrDNA sequences. S. × rubens revealed additivities at variable ITS1 and 5.8S positions as well as intermediate morphology and secondary compound pattern, but was characterised by significant earlier foliation start. This property leads to a better utilization of the vegetation period and may explain the detected better growth compared to the parent species and therefore also may have contributed to the widespread occurrence of S. × rubens in Central Europe.     

Deposition,resuspension, and decomposition of particulate organic matter in the sediments of Lake Itasca,Minnesota, USA

Sediment traps were used to investigate the settling, resuspension, and decomposition of particulate organic matter in Lake Itasca, MN (USA). Traps were deployed in the epilimnion and hypolimnion of the deepest basin during June, 1988, sampled twice during stratified conditions (August, September) and once after the lake had mixed (October). The downward flux of particulate material increased from summer to fall. The net sedimentation of organic matter ranged from 0.6 to 2.3 g m^–2 d^–1 at 4 m and increased to 2.1 to 3.2 g m^–2 d^–1 two meters above the bottom sediment indicating that resuspended sediment was at least 33% of the settling mass during all periods. The C:N ratios of captured particles (6.8–9.5) were between the ratios of plankton (5.8 to 6.8) and the sediments (9.9 to 10.2) but smaller than the ratios of terrestrial organic materials (13.5 to 222). The monosaccharide compositions of the entrapped particles were similar to plankton samples and different from the distinct composition of the sediments. Capture of rebound particles similar to the primary flux and not decomposition may have been responsible for this similarity. Total monosaccharide concentrations were lower in the sediments than in entrapped particles. Individual sugars exhibited different patterns of accumulation in the sediments. Glucose was lowest in sediments when the relative concentrations were compared to those in source materials and entrapped particles. In contrast, sediments had the highest rhamnose and fucose concentrations. Bacterial biomass could only account for small portions of these sugars in the sediment. The distinct monosaccharide composition of resuspended sediments was not strongly recorded in materials captured by the sediment traps even after the lake had mixed.     

Distinguishing the roles of dispersal in diversity maintenance and in diversity limitation

Considerable recent research effort has gone into studying how dispersal might affect the diversity of local communities. While this general topic has received attention from theoretical and empirical ecologists alike, the research focus has differed between the two groups; theoretical ecologists have explored the role of dispersal in the maintenance of diversity within local communities, whereas empirical ecologists have sought to quantify the role of dispersal in limiting local diversity. We argue that there is no necessary relationship between these two components of diversity and we therefore need to develop empirical approaches to quantify the dispersal-maintained component of diversity, as well as the dispersal-limited component. We develop one such approach in this paper, based on a quantitative partitioning of the natural regeneration within intact communities onto different sources of recruits (local communityvs. dispersal across different spatial or temporal scales).     

Subcellular localization of hexadecanedioic acid activation in human liver

The activation of hexadecanedioic acid has been studied in subcellular fractions of human liver. The activation capacity in a total homogenate of human liver was found to be 0.5 micro mole/min/g wet wt of tissue, about 10% of that for palmitic acid. Hexadecanedioic acid was activated by the mitochondrial and microsomal fractions. The mitochondrial enzyme is probably localized outside the inner mitochondrial compartment. The subcellular distribution of the hexadecanedioic acid activation was almost identical with the distribution of palmitic acid activation. Hexadecanedioic and palmitic acids seemed to compete for the same enzyme.     

Refractive index of phytoplankton derived from its metabolite composition

The refractive index of phytoplankton is calculated from itsmetabolite composition. The mean index of the algal dry mass,relative to the index of water, seems to vary from 1.146 forgreen algae to 1.167 for coccolithophonds. This difference of0.021 reduces to 0.007 and 0.003 when the partial water volumesof the algae are 0.6 and 0.8, respectively. The most importantfactor for the variation of the refractive index is the algalwater content. If a reasonable average range of the partialwater volume is 0.6 ± 0.2, the corresponding range ofthe refractive index relative to sea water becomes 1.06 ±0.04. This result is in excellent agreement with estimates basedon optical measurements of pure algal cultures. The normal dispersionof the refractive index is negligible, but anomalous dispersionin the vicinity of strong absorption bands may be of importancefor the light scattering properties of small phytoplankton.