Distribution and diversity of autotrophic bacteria in groundwater systems based on the analysis of RubisCO genotypes

A molecular approach, based on the detection of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large subunit genes, was applied to investigate the distribution and diversity of autotrophic bacteria in groundwater systems. DNA extracts from 48 sampling stations, including a variety of pristine and polluted, shallow and deep-subsurface groundwater samples obtained from Germany and Austria, served as a template for the PCR amplification of form I (cbbL) and form II (cbbM) large subunit RubisCO genes. The majority of the samples (>80%) contained two different forms of RubisCO. In 17 samples, all three forms of RubisCO were identified. PCR products from four selected groundwater habitats containing all three forms of RubisCO were used to construct clone libraries. Based on restriction fragment length polymorphism (RFLP) analysis, 109 RubisCO-clone-inserts were subjected to sequencing and phylogenetic analysis. With the exception of a form IA RubisCO sequence cluster obtained from deep subsurface samples, which was identical to the RubisCO genes described for Ralstonia metallidurans CH34, most sequences were distantly related to a variety of RubisCO species in chemolithoautotrophic Proteobacteria. Several sequences occurred in isolated lineages. These findings suggest that autotrophic bacteria with the capability to assimilate CO₂ via the Calvin Cycle pathway are widespread inhabitants of groundwater systems.     

Protein Kinase Activity in Hepatitis B Virus

Protein kinase activity was found in hepatitis B virions (Dane particles) purified from the plasma of hepatitis B virus-infected patients, in virion cores, and in hepatitis B core antigen particles purified from hepatitis B virus-infected hepatic tissue and was not found in purified hepatitis B surface antigen particle preparations free of Dane particles. Only a fraction of the major polypeptide (apparent size, 19,700 daltons) in Dane particle cores and hepatitis B core antigen particles from infected liver appeared to be phosphorylated, and phosphorylation changed the electrophoretic mobility in sodium dodecyl sulfate-polyacrylamide gels to that expected for a polypeptide of 20,600 daltons. Five minor polypeptides with apparent sizes between 38,000 and 63,000 daltons were phosphorylated in Dane particles and Dane particle core preparations but were not detected in hepatitis B core antigen particles from infected liver. None of these had electrophoretic mobilities corresponding to those of known hepatitis B surface antigen polypeptides. Prolonged storage of purified hepatitis B core antigen particles or incubation with human immunoglobulin G preparations containing antibody to the hepatitis B core antigen with or without antibody to the hepatitis B e antigen resulted in the conversion of the polypeptide with an apparent size of 20,600 daltons to ones with apparent sizes of 14,700 and approximately 6,000 daltons, suggesting proteolytic cleavage of the 20,600-dalton polypeptide under these conditions.     

Effects and fate of phenol in simulated landfill sites

Phenol was administered to landfill waste in concentrations from 150 to 1,000 ppm via the feed-liquor of lysimeter systems over an 18-week incubation period. Biotic contributions to phenol removal in the landfill waste were of greater significance than abiotic removal. The addition of phenol did not cause the isolation of thermophilic phenol degraders. Plates inoculated from the test lysimeter receiving phenol were eventually predominated by mesophilic phenol-degradingMicrococcus, Nocardia, andArthrobacter spp.; plates inoculated from the control lysimeter, receiving water, were predominated by species incapable of utilizing phenol.     

siRNA screening reveals JNK2 as an evolutionary conserved regulator of triglyceride homeostasis

Lipid homeostasis is essential for proper function of cells and organisms. To unravel new regulators of this system, we developed a screening procedure, combining RNA interference in HeLa cells and TLC, which enabled us to monitor modifications of lipid composition resulting from short, interfering RNA knock-downs. We applied this technique to the analysis of 600 human kinases. Despite the occurrence of off-target effects, we identified JNK2 as a new player in triglyceride (TG) homeostasis and lipid droplet metabolism and, more specifically, in the regulation of lipolysis. Similar control of the level of TGs and lipid droplets was observed for its Schizosaccharomyces pombe homolog, Sty1, suggesting an evolutionary conserved function of mitogen-activated protein kinases in the regulation of lipid storage in eukaryotic cells.     

Amyotrophic lateral sclerosis-associated copper/zinc superoxide dismutase mutations preferentially reduce the repulsive charge of the proteins

We provide bioinformatical evidence that protein charge plays a key role in the disease mechanism of amyotrophic lateral sclerosis (ALS). Analysis of 100 ALS-associated mutations in copper/zinc superoxide dismutase (SOD1) shows that these are site-selective with a preference to decrease the proteins' net repulsive charge. For each SOD1 monomer this charge is normally -6. Because biomolecules as a rule maintain net negative charge to assure solubility in the cellular interior, the result lends support to the hypothesis of protein aggregation as an initiating event in the ALS pathogenesis. The strength of the preferential reduction of repulsive charge is higher in SOD1-associated ALS than in other inherited protein disorders.     

Analyzing the Effects of Growing Season Length on the Net Ecosystem Production of an Alpine Grassland Using Model–Data Fusion

Alpine ecosystems are, similar to arctic ecosystems, characterized by a very long snow season. Previous studies investigating arctic or alpine ecosystems have shown that winter CO₂ effluxes can dominate the annual balance and that the timing and duration of the snow cover plays a crucial role for plant growth and phenology and might also influence the growing season ecosystem CO₂ strength and dynamics. The objective of this study was to analyze seasonal and annual CO₂ balances of a grassland site at an elevation of 2440 m a.s.l in the Swiss central Alps. We continuously measured the NEP using the eddy covariance method from June 2013 to October 2014, covering two growing seasons and one winter. We analyzed the influence of snow melt date on the CO₂ exchange dynamics at this site, because snow melt differed about 24 days between the 2 years. To this end, we employed a process-based ecosystem carbon cycling model to disentangle the co-occurring effects of growing season length, environmental conditions during the growing season, and physiological/structural properties of the canopy on the ecosystem carbon balance. During the measurement period, the site was a net sink for CO₂ although winter efflux contributed significantly to the total balance. The cumulative growing season NEP as well as mean and maximum daily CO₂ uptake rates was lower during the year with the later snow melt, and the results indicated that the differences were mainly due to differing growing season lengths.