Towards modeling climate effects of energetic particle precipitation

Energetic particles enter Earth’s atmosphere at the poles. The charged particles are either from solar or magnetospheric origin and alter the chemistry of the middle and upper atmosphere. Most importantly, they enhance the production of nitrogen oxides (NOx) and hydrogen oxides (HOx) in the winter mesosphere and lower thermosphere. Both components are powerful ozone destroyers. The impact of HOx on ozone is limited to the mesosphere, because HOx has a short chemical lifetime (up to hours). In contrast, NOx can persist up to several months in the winter polar middle atmosphere and can be transported downward to the stratosphere. Models covering the middle and upper atmosphere underestimate this downward transport. This may lead to an underestimation of potential climate effects from energetic particle precipitation. This thesis investigates the polar winter transport from the lower thermosphere to the stratosphere. Several observational studies confirmed the downward transport (e.g., Randall et al. 2009; Semeniuk et al. 2005). However, it remains unclear which processes cause the transport from the lower thermosphere to the mesosphere. This thesis quantifies, for the first time, the contribution of advection, eddy diffusion and molecular diffusion for the transport through the mesopause. Advection and molecular diffusion dominate the transport through the mesopause. Eddy diffusion has a negligible impact on the transport. However, if eddy diffusion is enhanced as suggested by observations, it can significantly contribute to the transport. This leaves advection being responsible for the underestimation of the downward transport. Gravity waves are the key driver for the advective downwelling in the polar winter mesosphere. This thesis shows that weakening gravity waves enhances the mesospheric transport bringing it close to satellite observations. The altitude of the mesospheric momentum deposition is identified to be key for the polar downwelling. In addition to the analysis of the winter polar downward transport, climate effects of energetic particles are studied. Energetic particle precipitation reduces significantly ozone in the mesosphere and stratosphere. An ozone loss potentially influences the atmospheric temperature and the strength of the polar vortex. It has been shown that large variations in the polar vortex strength can propagate from the stratosphere down to the surface and force the surface temperature (Baldwin and Dunkerton 2001). This thesis presents the climate impact of a mesospheric and of a stratospheric ozone loss. No statistically significant changes in atmospheric winds are found neither for a mesospheric ozone loss nor for a stratospheric ozone loss. Hence, the influence of energetic particles is too weak to force significantly changes in the surface temperature. In summary, this thesis advances the understanding of energetic particle precipitation. Processes relevant for the winter polar downward transport from the lower thermosphere to the stratosphere are identified. Two novel findings are the importance of advection in the thermosphere and the impact of weaker gravity waves on the dynamics of the middle and upper atmosphere. Based on this thesis, large climate effects of energetic particles seem unlikely

Transport of Nitrogen Oxides through the winter mesopause in HAMMONIA

We analyze the importance of individual transport processes for the winter polar downward transport of nitrogen oxides (NOx) from the thermosphere to the mesosphere. The downward transport of NOx produced by energetic particle precipitation induces chemical alterations in the middle atmosphere and influences ozone chemistry. However, it remains unclear how much each transport process contributes to the downward transport. We use simulations of the atmospheric general circulation and chemistry model HAMMONIA (Hamburg Model of Neutral and Ionized Atmosphere) for the extended winter 2008/2009 with a passive tracer. The model enables us to separate the contributions of advection, eddy and molecular diffusion on the total transport by switching off processes. The results show that molecular diffusion and resolved vertical mixing due to advection effectively transport NOx to the mesosphere. While the impact of molecular diffusion on the transport rapidly decreases below 0.001 hPa, the impact of advection increases. Around the central date of the sudden stratospheric warming in January 2009, advection is strongly enhanced in the thermosphere and mesosphere and the downward transport through the mesopause region is almost entirely driven by advection. Eddy diffusion has limited impact on the transport in the upper mesosphere and negligible impact on the transport in the thermosphere. If eddy diffusion is enhanced as suggested by observations, it can potentially have a larger impact on transport through the mesopause than was previously assumed

Operation of a planar-electrode ion-trap array with adjustable RF electrodes

One path to realizing systems of trapped atomic ions suitable for large-scale quantum computing and simulation is to create a two-dimensional (2D) array of ion traps. Interactions between nearest-neighbouring ions could then be turned on and off by tuning the ions’ relative positions and frequencies. We demonstrate and characterize the operation of a planar-electrode ion-trap array. By driving the trap with a network of phase-locked radio-frequency resonators which provide independently variable voltage amplitudes we vary the position and motional frequency of a Ca ion in two-dimensions within the trap array. Work on fabricating a miniaturised form of this 2D trap array is also described, which could ultimately provide a viable architecture for large-scale quantum simulations.published_or_final_versio

Cell cycle-dependent acetylation of Rb2/p130 in NIH3T3 cells

The retinoblastoma protein (pRb) and the pRb-related proteins, p130 and p107, form the ‘pocket protein' family of cell cycle regulatory factors. A well characterized function of these proteins is the cell cycle-dependent regulation of E2F-responsive genes. The biological activity of pocket proteins is regulated by phosphorylation and for the founding member pRb it has been shown that acetylation also has an important role in modulating its function during the cell cycle. Here, we show that hyperphosphorylated retinoblastoma 2 (Rb2)/p130 also exists in an acetylated form in NIH3T3 cells. Acetylated p130 is present in the nucleus but not in the cytoplasm. Acetylation is cell cycle dependent, starting in S-phase and persisting until late G2-period. Using recombinant p130 and truncated forms for in vitro acetylation by the acetyltransferase p300, we could identify K1079 in the C-terminal part as the major acetylation site by mass spectrometry. Minor acetylation sites were pinpointed to K1068 and K1111 in the C-terminus, and K128 and K130 in the N-terminus. The human papilloma virus 16 protein-E7 preferentially binds to acetylated p130 and significantly increases in vitro p130 acetylation by p300

Postglacial recolonizations, watershed crossings and human translocations shape the distribution of chub lineages around the Swiss Alps

Background: Distributions of European fish species were shaped by glaciations and the geological history of river networks until human activities partially abrogated the restrictions of biogeographical regions. The nearby origins of the Rhine, Rhone, Danube and Po rivers in the Swiss Alps allow the examination of historical and human-influenced patterns in fish genetic structure over a small geographic scale. We investigated these patterns in the widespread European chub (Squalius cephalus) from the Rhone, Rhine and Danube catchments and its proposed southern sister species Italian chub (Squalius squalus) from the Po catchment. Results: A phylogenetic tree constructed from mitochondrial Cytochrome b and COI sequences was consistent with earlier work in that it showed a separation of European chub and Italian chub, which was also reflected in microsatellite allele frequencies, morphological traits and shape differences quantified by geometric morphometrics. A new finding was that the predominant mitochondrial haplotype of European chub from the Rhine and Rhone catchments was also discovered in some individuals from Swiss populations of the Italian chub, presumably as a result of human translocation. Consistent with postglacial recolonizations from multiple refugia along the major rivers, the nuclear genetic structure of the European chub largely reflected drainage structure, but it was modified by watershed crossings between Rhine and Rhone near Lake Geneva as well as between Danube and Rhine near Lake Constance. Conclusion: Our study adds new insights into the cyprinid colonization history of central Europe by showing that multiple processes shaped the distribution of different chub lineages around the Swiss Alps. Interestingly, we find evidence that cross-catchment migration has been mediated by unusual geological events such as drainage captures or watershed crossings facilitated by retreating glaciers, as well as evidence that human transport has interfered with the historical distribution of these fish (European chub haplotypes present in the Italian chub). The desirable preservation of evolutionarily distinct lineages will thus require the prevention of further translocations

The Effect of Recurrent Floods on Genetic Composition of Marble Trout Populations

A changing global climate can threaten the diversity of species and ecosystems. We explore the consequences of catastrophic disturbances in determining the evolutionary and demographic histories of secluded marble trout populations in Slovenian streams subjected to weather extremes, in particular recurrent flash floods and debris flows causing massive mortalities. Using microsatellite data, a pattern of extreme genetic differentiation was found among populations (global FST of 0.716), which exceeds the highest values reported in freshwater fish. All locations showed low levels of genetic diversity as evidenced by low heterozygosities and a mean of only 2 alleles per locus, with few or no rare alleles. Many loci showed a discontinuous allele distribution, with missing alleles across the allele size range, suggestive of a population contraction. Accordingly, bottleneck episodes were inferred for all samples with a reduction in population size of 3–4 orders of magnitude. The reduced level of genetic diversity observed in all populations implies a strong impact of genetic drift, and suggests that along with limited gene flow, genetic differentiation might have been exacerbated by recurrent mortalities likely caused by flash flood and debris flows. Due to its low evolutionary potential the species might fail to cope with an intensification and altered frequency of flash flood events predicted to occur with climate change

1A6/DRIM, a Novel t-UTP, Activates RNA Polymerase I Transcription and Promotes Cell Proliferation

BACKGROUND: Ribosome biogenesis is required for protein synthesis and cell proliferation. Ribosome subunits are assembled in the nucleolus following transcription of a 47S ribosome RNA precursor by RNA polymerase I and rRNA processing to produce mature 18S, 28S and 5.8S rRNAs. The 18S rRNA is incorporated into the ribosomal small subunit, whereas the 28S and 5.8S rRNAs are incorporated into the ribosomal large subunit. Pol I transcription and rRNA processing are coordinated processes and this coordination has been demonstrated to be mediated by a subset of U3 proteins known as t-UTPs. Up to date, five t-UTPs have been identified in humans but the mechanism(s) that function in the t-UTP(s) activation of Pol I remain unknown. In this study we have identified 1A6/DRIM, which was identified as UTP20 in our previous study, as a t-UTP. In the present study, we investigated the function and mechanism of 1A6/DRIM in Pol I transcription. METHODOLOGY/PRINCIPAL FINDINGS: Knockdown of 1A6/DRIM by siRNA resulted in a decreased 47S pre-rRNA level as determined by Northern blotting. Ectopic expression of 1A6/DRIM activated and knockdown of 1A6/DRIM inhibited the human rDNA promoter as evaluated with luciferase reporter. Chromatin immunoprecipitation (ChIP) experiments showed that 1A6/DRIM bound UBF and the rDNA promoter. Re-ChIP assay showed that 1A6/DRIM interacts with UBF at the rDNA promoter. Immunoprecipitation confirmed the interaction between 1A6/DRIM and the nucleolar acetyl-transferase hALP. It is of note that knockdown of 1A6/DRIM dramatically inhibited UBF acetylation. A finding of significance was that 1A6/DRIM depletion, as a kind of nucleolar stress, caused an increase in p53 level and inhibited cell proliferation by arresting cells at G1. CONCLUSIONS: We identify 1A6/DRIM as a novel t-UTP. Our results suggest that 1A6/DRIM activates Pol I transcription most likely by associating with both hALP and UBF and thereby affecting the acetylation of UBF

The climate of a retrograde rotating Earth

To enhance understanding of Earth's climate, numerical experiments are performed contrasting a retrograde and prograde rotating Earth using the Max Planck Institute Earth system model. The experiments show that the sense of rotation has relatively little impact on the globally and zonally averaged energy budgets but leads to large shifts in continental climates, patterns of precipitation, and regions of deep water formation.Changes in the zonal asymmetries of the continental climates are expected given ideas developed more than a hundred years ago. Unexpected was, however, the switch in the character of the European–African climate with that of the Americas, with a drying of the former and a greening of the latter. Also unexpected was a shift in the storm track activity from the oceans to the land in the Northern Hemisphere. The different patterns of storms and changes in the direction of the trades influence fresh water transport, which may underpin the change of the role of the North Atlantic and the Pacific in terms of deep water formation, overturning and northward oceanic heat transport. These changes greatly influence northern hemispheric climate and atmospheric heat transport by eddies in ways that appear energetically consistent with a southward shift of the zonally and annually averaged tropical rain bands. Differences between the zonally averaged energy budget and the rain band shifts leave the door open, however, for an important role for stationary eddies in determining the position of tropical rains. Changes in ocean biogeochemistry largely follow shifts in ocean circulation, but the emergence of a super oxygen minimum zone in the Indian Ocean is not expected. The upwelling of phosphate-enriched and nitrate-depleted water provokes a dominance of cyanobacteria over bulk phytoplankton over vast areas – a phenomenon not observed in the prograde model.What would the climate of Earth look like if it would rotate in the reversed (retrograde) direction? Which of the characteristic climate patterns in the ocean, atmosphere, or land that are observed in a present-day climate are the result of the direction of Earth's rotation? Is, for example, the structure of the oceanic meridional overturning circulation (MOC) a consequence of the interplay of basin location and rotation direction? In experiments with the Max Planck Institute Earth system model (MPI-ESM), we investigate the effects of a retrograde rotation in all aspects of the climate system.The expected consequences of a retrograde rotation are reversals of the zonal wind and ocean circulation patterns. These changes are associated with major shifts in the temperature and precipitation patterns. For example, the temperature gradient between Europe and eastern Siberia is reversed, and the Sahara greens, while large parts of the Americas become deserts. Interestingly, the Intertropical Convergence Zone (ITCZ) shifts southward and the modeled double ITCZ in the Pacific changes to a single ITCZ, a result of zonal asymmetries in the structure of the tropical circulation.One of the most prominent non-trivial effects of a retrograde rotation is a collapse of the Atlantic MOC, while a strong overturning cell emerges in the Pacific. This clearly shows that the position of the MOC is not controlled by the sizes of the basins or by mountain chains splitting the continents in unequal runoff basins but by the location of the basins relative to the dominant wind directions. As a consequence of the changes in the ocean circulation, a super oxygen minimum zone develops in the Indian Ocean leading to upwelling of phosphate-enriched and nitrate-depleted water. These conditions provoke a dominance of cyanobacteria over bulk phytoplankton over vast areas, a phenomenon not observed in the prograde model.</p

Small global-mean cooling due to volcanic radiative forcing

In both the observational record and atmosphere-ocean general circulation model (AOGCM) simulations of the last ∼∼ 150 years, short-lived negative radiative forcing due to volcanic aerosol, following explosive eruptions, causes sudden global-mean cooling of up to ∼∼ 0.3 K. This is about five times smaller than expected from the transient climate response parameter (TCRP, K of global-mean surface air temperature change per W m−2 of radiative forcing increase) evaluated under atmospheric CO2 concentration increasing at 1 % yr−1. Using the step model (Good et al. in Geophys Res Lett 38:L01703, 2011. doi:10.​1029/​2010GL045208), we confirm the previous finding (Held et al. in J Clim 23:2418–2427, 2010. doi:10.​1175/​2009JCLI3466.​1) that the main reason for the discrepancy is the damping of the response to short-lived forcing by the thermal inertia of the upper ocean. Although the step model includes this effect, it still overestimates the volcanic cooling simulated by AOGCMs by about 60 %. We show that this remaining discrepancy can be explained by the magnitude of the volcanic forcing, which may be smaller in AOGCMs (by 30 % for the HadCM3 AOGCM) than in off-line calculations that do not account for rapid cloud adjustment, and the climate sensitivity parameter, which may be smaller than for increasing CO2 (40 % smaller than for 4 × CO2 in HadCM3)