Developments in the MPI-M Earth System Model version 1.2 (MPI-ESM1.2) and Its Response to Increasing CO2.

A new release of the Max Planck Institute for Meteorology Earth System Model version 1.2 (MPI-ESM1.2) is presented. The development focused on correcting errors in and improving the physical processes representation, as well as improving the computational performance, versatility, and overall user friendliness. In addition to new radiation and aerosol parameterizations of the atmosphere, several relatively large, but partly compensating, coding errors in the model's cloud, convection, and turbulence parameterizations were corrected. The representation of land processes was refined by introducing a multilayer soil hydrology scheme, extending the land biogeochemistry to include the nitrogen cycle, replacing the soil and litter decomposition model and improving the representation of wildfires. The ocean biogeochemistry now represents cyanobacteria prognostically in order to capture the response of nitrogen fixation to changing climate conditions and further includes improved detritus settling and numerous other refinements. As something new, in addition to limiting drift and minimizing certain biases, the instrumental record warming was explicitly taken into account during the tuning process. To this end, a very high climate sensitivity of around 7 K caused by low-level clouds in the tropics as found in an intermediate model version was addressed, as it was not deemed possible to match observed warming otherwise. As a result, the model has a climate sensitivity to a doubling of CO2 over preindustrial conditions of 2.77 K, maintaining the previously identified highly nonlinear global mean response to increasing CO2 forcing, which nonetheless can be represented by a simple two-layer model.

Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8.

BACKGROUND: The Mongolian gerbils are a good model to mimic the Helicobacter pylori-associated pathogenesis of the human stomach. In the current study the gerbil-adapted strain B8 was completely sequenced, annotated and compared to previous genomes, including the 73 supercontigs of the parental strain B128. RESULTS: The complete genome of H. pylori B8 was manually curated gene by gene, to assign as much function as possible. It consists of a circular chromosome of 1,673,997 bp and of a small plasmid of 6,032 bp carrying nine putative genes. The chromosome contains 1,711 coding sequences, 293 of which are strain-specific, coding mainly for hypothetical proteins, and a large plasticity zone containing a putative type-IV-secretion system and coding sequences with unknown function. The cag-pathogenicity island is rearranged such that the cagA-gene is located 13,730 bp downstream of the inverted gene cluster cagB-cag1. Directly adjacent to the cagA-gene, there are four hypothetical genes and one variable gene with a different codon usage compared to the rest of the H. pylori B8-genome. This indicates that these coding sequences might be acquired via horizontal gene transfer.The genome comparison of strain B8 to its parental strain B128 delivers 425 unique B8-proteins. Due to the fact that strain B128 was not fully sequenced and only automatically annotated, only 12 of these proteins are definitive singletons that might have been acquired during the gerbil-adaptation process of strain B128. CONCLUSION: Our sequence data and its analysis provide new insight into the high genetic diversity of H. pylori-strains. We have shown that the gerbil-adapted strain B8 has the potential to build, possibly by a high rate of mutation and recombination, a dynamic pool of genetic variants (e.g. fragmented genes and repetitive regions) required for the adaptation-processes. We hypothesize that these variants are essential for the colonization and persistence of strain B8 in the gerbil stomach during in ammation.

Analysis of 5' junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5'-end attachment requiring microhomology-mediated end-joining.

Insertion of the human non-LTR retrotransposon LINE-1 (L1) into chromosomal DNA is thought to be initiated by a mechanism called target-primed reverse transcription (TPRT). This mechanism readily accounts for the attachment of the 3'-end of an L1 copy to the genomic target, but the subsequent integration steps leading to the attachment of the 5'-end to the chromosomal DNA are still cause for speculation. By applying bioinformatics to analyze the 5' junctions of recent L1 insertions in the human genome, we provide evidence that L1 uses at least two distinct mechanisms to link the 5'-end of the nascent L1 copy to its genomic target. While 5'-truncated L1 elements show a statistically significant preference for short patches of overlapping nucleotides between their target site and the point of truncation, full-length insertions display no distinct bias for such microhomologies at their 5'-ends. In a second genome-wide approach, we analyzed Alu elements to examine whether these nonautonomous retrotransposons, which are thought to be mobilized through L1 proteins, show similar characteristics. We found that Alu elements appear to be predominantly integrated via a pathway not involving overlapping nucleotides. The results indicate that a cellular nonhomologous DNA end-joining pathway may resolve intermediates from incomplete L1 retrotransposition events and thus lead to 5' truncations.

Antimicrobial activity of the essential oil and some isolated sulfur-rich compounds from Scorodophloeus zenkeri.

The essential oil and several pure sulfur compounds isolated from Scorodophloeus zenkeri were tested for their antibacterial and antifungal activity using a paper disc method, the poisoned food technique, a microatmosphere method and the measurement of cellular ATP content. The essential oil completely inhibited the growth of all fungi tested including yeasts, with the exception of Aspergillus flavus, and was active against the Gram-positive bacteria studied, but not the Gram-negative organisms. 2,4,5,7-Tetrathiaoctane, 2,4,5,6,8-pentathianonane, 2,3,4,6,8-pentathianonane, 2,3,5,6,8,10-hexathiaundecane, 2,3,5-trithiahexane 5-oxide, 2,4,5,7-tetrathiaoctane 2-oxide, 2,3,5,7-tetrathiaoctane 3,3-dioxide and 2,3,5-trithiahexane 3,3-dioxide differed in their effects on the strains studied with respect to both growth and synthesis of cellular ATP. 2,3,5-Trithiahexane, 2,3,4,6-tetrathiaheptane, methyl methanethiosulfonate and bis-methyl-sulfonylmethane exhibited no antimicrobial activity.

Isolation of a novel, phosphate-activated glutaminase from Bacillus pasteurii.

In Bacillus pasteurii glutamine is being taken up efficiently by a sodium-dependent uptake system and subsequently hydrolysed to ammonium and glutamate. Concerning the latter process, a catabolic L-glutamine amidohydrolase (glutaminase) was isolated from the cytoplasm of this alkaliphilic bacterium and purified to homogeneity using liquid chromatography. Biochemical and physical parameters of the pure enzyme were examined in detail. Interestingly, analysis of the glutaminase revealed a marked increase in catalytic activity in the presence of phosphate, a property yet restricted to animal glutaminases. This is the first report on the presence of a phosphate-activated glutaminase in bacteria.

Prochlorococcus marinus strain PCC 9511, a picoplanktonic cyanobacterium, synthesizes the smallest urease.

The urease from the picoplanktonic oceanic Prochlorococcus marinus sp. strain PCC 9511 was purified 900-fold to a specific activity of 94.6 micromol urea min(-1) (mg protein)(-1) by heat treatment and liquid chromatography methods. The enzyme, with a molecular mass of 168 kDa as determined by gel filtration, is the smallest urease known to date. Three different subunits with apparent molecular masses of 11 kDa (gamma or UreA; predicted molecular mass 11 kDa), 13 kDa (ss or UreB; predicted molecular mass 12 kDa) and 63 kDa (alpha or UreC; predicted molecular mass 62 kDa) were detected in the native enzyme, suggesting a quaternary structure of (alphassgamma)(2). The K:(m) of the purified enzyme was determined as being 0.23 mM urea. The urease activity was inhibited by HgCl(2), acetohydroxamic acid and EDTA but neither by boric acid nor by L-methionine-DL-sulfoximine. Degenerate primers were designed to amplify a conserved region of the ureC gene. The amplification product was then used as a probe to clone a 5.7 kbp fragment of the P. marinus sp. strain PCC 9511 genome. The nucleotide sequence of this DNA fragment revealed two divergently orientated gene clusters, ureDABC and ureEFG, encoding the urease subunits, UreA, UreB and UreC, and the urease accessory molecules UreD, UreE, UreF and UreG. A putative NtcA-binding site was found upstream from ureEFG, indicating that this gene cluster might be under nitrogen control.