Markus Rampp

The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity

BackgroundThe square halophilic archaeon Haloquadratum walsbyi dominates NaCl-saturated and MgCl2 enriched aquatic ecosystems, which imposes a serious desiccation stress, caused by the extremely low water activity. The genome sequence was analyzed and physiological and physical experiments were carried out in order to reveal how H. walsbyi has specialized into its narrow and hostile ecological niche and found ways to cope with the desiccation stress.ResultsA rich repertoire of proteins involved in phosphate metabolism, phototrophic growth and extracellular protective polymers, including the largest archaeal protein (9159 amino acids), a homolog to eukaryotic mucins, are amongst the most outstanding features. A relatively low GC content (47.9%), 15–20% less than in other halophilic archaea, and one of the lowest coding densities (76.5%) known for prokaryotes might be an indication for the specialization in its unique environmentConclusionAlthough no direct genetic indication was found that can explain how this peculiar organism retains its square shape, the genome revealed several unique adaptive traits that allow this organism to thrive in its specific and extreme niche.

Improved models of stellar core collapse and still no explosions: what is missing?

Two-dimensional hydrodynamic simulations of stellar core collapse are presented which for the first time were performed by solving the Boltzmann equation for the neutrino transport including a state-of-the-art description of neutrino interactions. Stellar rotation is also taken into account. Although convection develops below the neutrinosphere and in the neutrino-heated region behind the supernova shock, the models do not explode. This suggests missing physics, possibly with respect to the nuclear equation of state and weak interactions in the subnuclear regime. However, it might also indicate a fundamental problem with the neutrino-driven explosion mechanism.

Radiation hydrodynamics with neutrinos - Variable Eddington factor method for core-collapse supernova simulations

Neutrino transport and neutrino interactions in dense matter play a crucial role in stellar core collapse, supernova explosions and neutron star formation. Here we present a detailed description of a new numerical code for treating the time and energy dependent neutrino transport in hydrodynamical simulations of such events. The code is based on a variable Eddington factor method to deal with the integro-differential character of the Boltzmann equation. The moments of the neutrino distribution function and the energy and lepton number exchange with the stellar medium are determined by iteratively solving the zeroth and first order moment equations in combination with a model Boltzmann equation. The latter is discretized on a grid of tangent rays. The integration of the transport equations and the neutrino source terms is performed in a time-implicit way. In the present version of the program, the transport part is coupled to an explicit hydrodynamics code which follows the evolution of the stellar plasma by a finite-volume method with piecewise parabolic interpolation, using a Riemann solver to calculate the hydrodynamic states. The neutrino source terms are implemented in an operator-split step. Neutrino transport and hydrodynamics can be calculated with different spatial grids and different time steps. The structure of the described code is modular and offers a high degree of flexibility for an application to relativistic and multi-dimensional problems at different levels of refinement and accuracy. We critically evaluate results for a number of test cases, including neutrino transport in rapidly moving stellar media and approximate relativistic core collapse, and suggest a path for generalizing the code to be used in multi-dimensional simulations of convection in neutron stars and supernovae.

Supernova Simulations with Boltzmann Neutrino Transport: A Comparison of Methods

Accurate neutrino transport has been built into spherically symmetric simulations of stellar core collapse and postbounce evolution. The results of such simulations agree that spherically symmetric models with standard microphysical input fail to explode by the delayed, neutrino-driven mechanism. Independent groups implemented fundamentally different numerical methods to tackle the Boltzmann neutrino transport equation. Here we present a direct and detailed comparison of such neutrino radiation-hydrodynamics simulations for two codes, AGILE-BOLTZTRAN of the Oak Ridge-Basel group and VERTEX of the Garching group. The former solves the Boltzmann equation directly by an implicit, general relativistic discrete-angle method on the adaptive grid of a conservative implicit hydrodynamics code with second-order TVD advection. In contrast, the latter couples a variable Eddington factor technique with an explicit, moving-grid, conservative high-order Riemann solver with important relativistic effects treated by an effective gravitational potential. The presented study is meant to test our neutrino radiation-hydrodynamics implementations and to provide a data basis for comparisons and verifications of supernova codes to be developed in the future. Results are discussed for simulations of the core collapse and postbounce evolution of a 13 M☉ star with Newtonian gravity and a 15 M☉ star with relativistic gravity.

Spherically Symmetric Simulation with Boltzmann Neutrino Transport of Core Collapse and Postbounce Evolution of a 15 M☉ Star

We present a spherically symmetric, Newtonian core collapse simulation of a 15 M☉ star with a 1.28 M☉ iron core. The time-, energy-, and angle-dependent transport of electron neutrinos (νe) and antineutrinos (e) was treated with a new code that iteratively solves the Boltzmann equation and the equations for neutrino number, energy, and momentum to order O(v/c) in the velocity v of the stellar medium. The supernova shock expands to a maximum radius of 350 km instead of only ~240 km as in a comparable calculation with multigroup flux-limited diffusion (MGFLD) by Bruenn, Mezzacappa, & Dineva. This may be explained by stronger neutrino heating due to the more accurate transport in our model. Nevertheless, after 180 ms of expansion the shock finally recedes to a radius around 250 km (compared to ~170 km in the MGFLD run). The effect of an accurate neutrino transport is helpful but not large enough to cause an explosion of the considered 15 M☉ star. Therefore, postshock convection and/or an enhancement of the core neutrino luminosity by convection or reduced neutrino opacities in the neutron star seem necessary for neutrino-driven explosions of such stars. We find an electron fraction Ye > 0.5 in the neutrino-heated matter, which suggests that the overproduction problem of neutron-rich nuclei with mass numbers A ≈ 90 in exploding models may be absent when a Boltzmann solver is used for the νe and e transport.

Dnmt2-dependent methylomes lack defined DNA methylation patterns

Several organisms have retained methyltransferase 2 (Dnmt2) as their only candidate DNA methyltransferase gene. However, information about Dnmt2-dependent methylation patterns has been limited to a few isolated loci and the results have been discussed controversially. In addition, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which raised the possibility that Dnmt2-only genomes might be unmethylated. We have now used whole-genome bisulfite sequencing to analyze the methylomes of Dnmt2-only organisms at single-base resolution. Our results show that the genomes of Schistosoma mansoni and Drosophila melanogaster lack detectable DNA methylation patterns. Residual unconverted cytosine residues shared many attributes with bisulfite deamination artifacts and were observed at comparable levels in Dnmt2-deficient flies. Furthermore, genetically modified Dnmt2-only mouse embryonic stem cells lost the DNA methylation patterns found in wild-type cells. Our results thus uncover fundamental differences among animal methylomes and suggest that DNA methylation is dispensable for a considerable number of eukaryotic organisms.

A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T.

The halophilic γ-proteobacterium Halomonas elongata DSM 2581T thrives at high salinity by synthesizing and accumulating the compatible solute ectoine. Ectoine levels are highly regulated according to external salt levels but the overall picture of its metabolism and control is not well understood. Apart from its critical role in cell adaptation to halophilic environments, ectoine can be used as a stabilizer for enzymes and as a cell protectant in skin and health care applications and is thus produced annually on a scale of tons in an industrial process using H. elongata as producer strain. This paper presents the complete genome sequence of H. elongata (4 061 296 bp) and includes experiments and analysis identifying and characterizing the entire ectoine metabolism, including a newly discovered pathway for ectoine degradation and its cyclic connection to ectoine synthesis. The degradation of ectoine (doe) proceeds via hydrolysis of ectoine (DoeA) to Nα-acetyl-l-2,4-diaminobutyric acid, followed by deacetylation to diaminobutyric acid (DoeB). In H. elongata, diaminobutyric acid can either flow off to aspartate or re-enter the ectoine synthesis pathway, forming a cycle of ectoine synthesis and degradation. Genome comparison revealed that the ectoine degradation pathway exists predominantly in non-halophilic bacteria unable to synthesize ectoine. Based on the resulting genetic and biochemical data, a metabolic flux model of ectoine metabolism was derived that can be used to understand the way H. elongata survives under varying salt stresses and that provides a basis for a model-driven improvement of industrial ectoine production.

Electron capture rates on nuclei and implications for stellar core collapse

Supernova simulations to date have assumed that during core collapse electron captures occur dominantly on free protons, while captures on heavy nuclei are Pauli blocked and are ignored. We have calculated rates for electron capture on nuclei with mass numbers A=65-112 for the temperatures and densities appropriate for core collapse. We find that these rates are large enough so that, in contrast to previous assumptions, electron capture on nuclei dominates over capture on free protons. This leads to significant changes in core collapse simulations.

Toward gravitational wave signals from realistic core-collapse supernova models

We have computed the gravitational wave signal from supernova core collapse by using the most realistic input physics available at present. We start from state-of-the-art progenitor models of rotating and nonrotating massive stars and simulate the dynamics of their core collapse by integrating the equations of axisymmetric hydrodynamics, together with the Boltzmann equation for the neutrino transport, including an elaborate description of neutrino interactions, and a realistic equation of state. Using the Einstein quadrupole formula we compute the quadrupole wave amplitudes, the Fourier wave spectra, the amount of energy radiated in the form of gravitational waves, and the signal-to-noise ratios for the Laser Interferometer Gravitational-Wave Observatory (LIGO) I and the tuned Advanced LIGO (LIGO II) interferometers resulting from both nonradial mass motion and anisotropic neutrino emission. The simulations demonstrate that the dominant contribution to the gravitational wave signal is produced by neutrino-driven convection behind the supernova shock. For stellar cores rotating at the extreme of current stellar evolution predictions, the core bounce signal is detectable (S/N 7) with LIGO II for a supernova up to a distance of ~5 kpc, whereas the signal from postshock convection is observable (S/N 7) with LIGO II up to a distance of ~100 kpc and with LIGO I to a distance of ~5 kpc. If the core is nonrotating, its gravitational wave emission can be measured with LIGO II up to a distance of ~15 kpc (S/N 8), while the signal from the Ledoux convection in the deleptonizing nascent neutron star can be detected up to a distance of ~10 kpc (S/N 8). Both kinds of signals are generically produced by convection in any core-collapse supernova.

Haloquadratum walsbyi: Limited Diversity in a Global Pond

Background Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared. Principal Findings Both chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4–20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23T but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23T carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea. Conclusions Deletion-coupled insertions show that Hqr. walsbyi evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.