Hydroxymethylated Cytosines Are Associated with Elevated C to G Transversion Rates

It has long been known that methylated cytosines deaminate at higher rates than unmodified cytosines and constitute mutational hotspots in mammalian genomes. The repertoire of naturally occurring cytosine modifications, however, extends beyond 5-methylcytosine to include its oxidation derivatives, notably 5-hydroxymethylcytosine. The effects of these modifications on sequence evolution are unknown. Here, we combine base-resolution maps of methyl- and hydroxymethylcytosine in human and mouse with population genomic, divergence and somatic mutation data to show that hydroxymethylated and methylated cytosines show distinct patterns of variation and evolution. Surprisingly, hydroxymethylated sites are consistently associated with elevated C to G transversion rates at the level of segregating polymorphisms, fixed substitutions, and somatic mutations in tumors. Controlling for multiple potential confounders, we find derived C to G SNPs to be 1.43-fold (1.22-fold) more common at hydroxymethylated sites compared to methylated sites in human (mouse). Increased C to G rates are evident across diverse functional and sequence contexts and, in cancer genomes, correlate with the expression of Tet enzymes and specific components of the mismatch repair pathway (MSH2, MSH6, and MBD4). Based on these and other observations we suggest that hydroxymethylation is associated with a distinct mutational burden and that the mismatch repair pathway is implicated in causing elevated transversion rates at hydroxymethylated cytosines

Abundance of actinobacteria and production of geosmin and 2-methylisoborneol in Danish streams and fish ponds

Occurrence of the odours geosmin and 2-methylisoborneol (MIB) in freshwater environments indicates that odour-producing organisms are commonly occurring. In the present study, we assumed actinomycetes to be a major source of the odours. Seasonal concentrations of odours and abundance of Actinobacteria, which includes actinomycetes and other G+ and high GC bacteria, were determined in one oligotrophic and two eutrophic freshwater streams, as well as in aquacultures connected to these streams, in Denmark. Concentrations of geosmin and MIB ranged from 2 to 9 ng l−1 and were lowest in the winter. Passage of stream water in the aquacultures increased the amount of geosmin and MIB by up to 55% and 110%, respectively. Densities of actinobacteria were determined by fluorescence in situ hybridization with catalyzed reporter deposition (CARD-FISH) technique and were found to make up from 4 to 38 × 107 cells l−1, corresponding to 3–9% of the total bacterial populations. The lowest densities of actinobacteria occurred in the winter. Filamentous bacteria targeted by the FISH probe made up about 2.7–38% (average was 22%) of the actinobacteria and were expected to be actinomycetes. Combined microautoradiography and CARD-FISH demonstrated that 10–38% (incorporation of 3H-thymidine) and 41–65% (incorporation of 3H-leucine) of the actinobacteria were metabolically active. The proportion of active actinobacteria increased up to 2-fold during passage of stream water in the aquacultures, and up to 98% of the cells became active. Sequencing of 16S rRNA genes in 8 bacterial isolates with typical actinomycete morphology from the streams and ponds demonstrated that most of them belonged to the genus Streptomyces. The isolated actinomycetes produced geosmin at rates from 0.1 to 35 ag geosmin bacterium−1 h−1. MIB was produced at similar rates in 5 isolates, whereas no MIB was produced by three of the isolates. Addition of the odours to stream water demonstrated that indigenous stream bacteria were capable of reducing the odours, and that enrichment with LB medium stimulated the degradation. Our study shows that bacterial communities in freshwater include geosmin- and MIB-producing actinobacteria. However, the mechanisms controlling production as well as degradation of the odours in natural waters appear complex and require further research

Solidification of small para-H2 clusters at zero temperature

We have determined the ground-state energies of para-H$_2$ clusters at zero temperature using the diffusion Monte Carlo method. The liquid or solid character of each cluster is investigated by restricting the phase through the use of proper importance sampling. Our results show inhomogeneous crystallization of clusters, with alternating behavior between liquid and solid phases up to N=55. From there on, all clusters are solid. The ground-state energies in the range N=13--75 are established and the stable phase of each cluster is determined. In spite of the small differences observed between the energy of liquid and solid clusters, the corresponding density profiles are significantly different, feature that can help to solve ambiguities in the determination of the specific phase of H$_2$ clusters.Comment: 17 pages, accepted for publication in J. Phys. Chem.

Turbulent dynamo with advective magnetic helicity flux

Many astrophysical bodies harbor magnetic fields that are thought to be sustained by a dynamo process. However, it has been argued that the production of large-scale magnetic fields by mean-field dynamo action is strongly suppressed at large magnetic Reynolds numbers owing to the conservation of magnetic helicity. This phenomenon is known as {\it catastrophic quenching}. Advection of magnetic fields by stellar and galactic winds toward the outer boundaries and away from the dynamo is expected to alleviate such quenching. Here we explore the relative roles played by advective and turbulent--diffusive fluxes of magnetic helicity in the dynamo. In particular, we study how the dynamo is affected by advection. We do this by performing direct numerical simulations of a turbulent dynamo of $\alpha^2$ type driven by forced turbulence in a Cartesian domain in the presence of a flow away from the equator where helicity changes sign. Our results indicate that in the presence of advection, the dynamo, otherwise stationary, becomes oscillatory. We confirm an earlier result for turbulent--diffusive magnetic helicity fluxes that for small magnetic Reynolds numbers (\Rm\lesssim 100...200, based on the wavenumber of the energy-carrying eddies) the magnetic helicity flux scales less strongly with magnetic Reynolds number (\Rm^{-1/2}) than the term describing magnetic helicity destruction by resistivity (\Rm^{-1}). Our new results now suggest that for larger \Rm the former becomes approximately independent of \Rm, while the latter falls off more slowly. We show for the first time that both for weak and stronger winds, the magnetic helicity flux term becomes comparable to the resistive term for \Rm\gtrsim 1000, which is necessary for alleviating catastrophic quenching.Comment: 9 pages, 9 figures, accepted for publication in MNRA

Torpor in marsupials: Recent advances

We report new findings about torpor in marsupials with regard to three energy demanding processes: (i) development and growth, (ii) reproduction, and (iii) rewarming. Young marsupials use torpor extensively after they develop endothermy, and torpor is generally deeper and longer than in the same individuals when they reach adult size. Adult marsupials also employ torpor during pregnancy and/or lactation to reduce energy expenditure and perhaps to store fat for later use. Moreover, to enhance the energy-conserving potential of torpor, desert marsupials bask during arousal to minimize energy costs of rewarming. We show that the functions of torpor extend beyond merely reducing energy expenditure during food shortages and that torpor can save substantial amounts of energy even during the rewarming process

Can hibernators sense and evade fires? Olfactory acuity and locomotor performance during deep torpor.

Increased habitat fragmentation, global warming and other human activities have caused a rise in the frequency of wildfires worldwide. To reduce the risks of uncontrollable fires, prescribed burns are generally conducted during the colder months of the year, a time when in many mammals torpor is expressed regularly. Torpor is crucial for energy conservation, but the low body temperatures (T b) are associated with a decreased responsiveness and torpid animals might therefore face an increased mortality risk during fires. We tested whether hibernators in deep torpor (a) can respond to the smell of smoke and (b) can climb to avoid fires at T bs below normothermic levels. Our data show that torpid eastern pygmy-possums (Cercartetus nanus) are able to detect smoke and also can climb. All males aroused from torpor when the smoke stimulus was presented at an ambient temperature (T a) of 15 °C (T b ∼18 °C), whereas females only raised their heads. The responses were less pronounced at T a 10 °C. The first coordinated movement of possums along a branch was observed at a mean T b of 15.6 °C, and animals were even able to climb their prehensile tail when they reached a mean T b of 24.4 °C. Our study shows that hibernators can sense smoke and move at low T b. However, our data also illustrate that at T b ≤13 °C, C. nanus show decreased responsiveness and locomotor performance and highlight that prescribed burns during winter should be avoided on very cold days to allow torpid animals enough time to respond

Acute perioperative-stress-induced increase of atherosclerotic plaque volume and vulnerability to rupture in apolipoprotein-E-deficient mice is amenable to statin treatment and IL-6 inhibition

Myocardial infarction and stroke are frequent after surgical procedures and consume a considerable amount of benefit of surgical therapy. Perioperative stress, induced by surgery, is composed of hemodynamic and inflammatory reactions. The effects of perioperative stress on atherosclerotic plaques are ill-defined. Murine models to investigate the influence of perioperative stress on plaque stability and rupture are not available. We developed a model to investigate the influence of perioperative stress on plaque growth and stability by exposing apolipoprotein-E-deficient mice, fed a high cholesterol diet for 7 weeks, to a double hit consisting of 30 min of laparotomy combined with a substantial blood loss (approximately 20% of total blood volume; 400 µl). The innominate artery was harvested 72 h after the intervention. Control groups were sham and baseline controls. Interleukin-6 (IL-6) and serum amyloid A (SAA) plasma levels were determined. Plaque load, vascular smooth muscle cell (VSMC) and macrophage content were quantified. Plaque stability was assessed using the Stary score and frequency of signs of plaque rupture were assessed. High-dose atorvastatin (80 mg/kg body weight/day) was administered for 6 days starting 3 days prior to the double hit. A single dose of an IL-6-neutralizing antibody or the fusion protein gp130-Fc selectively targeting IL-6 trans-signaling was subcutaneously injected. IL-6 plasma levels increased, peaking at 6 h after the intervention. SAA levels peaked at 24 h (n=4, P<0.01). Plaque volume increased significantly with the double hit compared to sham (n=8, P<0.01). More plaques were scored as complex or bearing signs of rupture after the double hit compared to sham (n=5-8, P<0.05). Relative VSMC and macrophage content remained unchanged. IL-6-inhibition or atorvastatin, but not blocking of IL-6 trans-signaling, significantly decreased plaque volume and complexity (n=8, P<0.01). Using this model, researchers will be able to further investigate the pathophysiology of perioperative plaque stability, which can result in myocardial infarction, and, additionally, to test potential protective strategies