Modelling the upper atmosphere of the gas giant planets

At Jupiter and Saturn the thermosphere is the region of the neutral atmosphere that coexists with the ionosphere. It is thus the region of the atmosphere that is most strongly coupled to the magnetosphere, and is responsible via the ionosphere for the transfer of planetary angular momentum to the magnetosphere. Both planets also exhibit high thermospheric temperatures that are yet to be explained. We study the coupled thermosphere-ionosphere-magnetosphere systems of Jupiter and Saturn using a thermospheric general circulation model and simple models of the ionosphere and magnetosphere. Our principle result is that meridional winds in the thermosphere are of critical importance to the interaction. Angular momentum extracted from the thermosphere by magnetospheric drag is found to be replaced largely by meridional advection, not, as commonly supposed, by vertical viscous transfer. These same meridional winds are also able to couple together regions of the magnetosphere that otherwise would not interact. We find it very hard to reproduce the observed thermospheric temperatures with our model. Under a limited range of circumstances it is shown that redistribution of thermal energy from high- to low-latitudes by winds can explain the available observations. However, the inclusion of ion drag generates a circulation in the polar regions that acts as a heat pump and efficiently cools the thermosphere, significantly reducing the efficiency of the redistributive winds

Axial symmetry breaking of Saturn's thermosphere

The source of the various planetary-period signals in Saturn’s magnetosphere is at present unknown. We investigate the possibility that the source of these signals is an axially asymmetric wind system in the thermosphere. We describe a feedback mechanism that has the potential to drive such axially asymmetric wind systems. The proposed mechanism relates thermospheric winds to heating from particle precipitation, via the generation of horizontal and field-aligned currents. The relevant physical processes are investigated using a highly simplified general circulation model of Saturn’s thermosphere and ionosphere. Our principal result is that the feedback mechanism is effective in permanently breaking the axial symmetry of the thermosphere, generating a drifting vortex-like structure at high latitudes. However, the precipitating electron energies required to power this structure are of the order of 5 MeV, 2–3 orders of magnitude greater than the observed auroral electron energies, and the highly axially asymmetric distribution of precipitation required across the polar regions of the planet is also inconsistent with observations. Despite these flaws, the model qualitatively explains several features of the observed variation in the pulsing of SKR emissions; in particular, the seasonal variation and the faster rotation rate in the winter hemisphere. We cannot reproduce the apparent 7 month lag in the response of the Saturn Kilometric Radiation (SKR) rotation rate to seasonal variation, but instead suggest the possibility that this effect may have its origin in long chemical time-scales in the upper atmosphere. We also predict the possible existence of secondary periodic features in the SKR emissions with periods of ∼15 planetary rotations, driven by complex wave behaviour in the thermosphere

Upper atmospheres and ionospheres of planets and satellites

The upper atmospheres of the planets and their satellites are more directly exposed to sunlight and solar wind particles than the surface or the deeper atmospheric layers. At the altitudes where the associated energy is deposited, the atmospheres may become ionized and are referred to as ionospheres. The details of the photon and particle interactions with the upper atmosphere depend strongly on whether the object has anintrinsic magnetic field that may channel the precipitating particles into the atmosphere or drive the atmospheric gas out to space. Important implications of these interactions include atmospheric loss over diverse timescales, photochemistry and the formation of aerosols, which affect the evolution, composition and remote sensing of the planets (satellites). The upper atmosphere connects the planet (satellite) bulk composition to the near-planet (-satellite) environment. Understanding the relevant physics and chemistry provides insight to the past and future conditions of these objects, which is critical for understanding their evolution. This chapter introduces the basic concepts of upper atmospheres and ionospheres in our solar system, and discusses aspects of their neutral and ion composition, wind dynamics and energy budget. This knowledge is key to putting in context the observations of upper atmospheres and haze on exoplanets, and to devise a theory that explains exoplanet demographics.Comment: Invited Revie

Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines

BACKGROUND: Aberrant epigenetic modifications, including DNA methylation, are key regulators of gene activity in tumorigenesis. Breast cancer is a heterogeneous disease, and large-scale analyses indicate that tumor from normal and benign tissues, as well as molecular subtypes of breast cancer, can be distinguished based on their distinct genomic, transcriptomic, and epigenomic profiles. In this study, we used affinity-based methylation sequencing data in 30 breast cancer cell lines representing functionally distinct cancer subtypes to investigate methylation and mutation patterns at the whole genome level. RESULTS: Our analysis revealed significant differences in CpG island (CpGI) shore methylation and mutation patterns among breast cancer subtypes. In particular, the basal-like B type, a highly aggressive form of the disease, displayed distinct CpGI shore hypomethylation patterns that were significantly associated with downstream gene regulation. We determined that mutation rates at CpG sites were highly correlated with DNA methylation status and observed distinct mutation rates among the breast cancer subtypes. These findings were validated by using targeted bisulfite sequencing of differentially expressed genes (n=85) among the cell lines. CONCLUSIONS: Our results suggest that alterations in DNA methylation play critical roles in gene regulatory process as well as cytosine substitution rates at CpG sites in molecular subtypes of breast cancer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12918-016-0356-2) contains supplementary material, which is available to authorized users

Why is the H3+ hot spot above Jupiter's Great Red Spot so hot?

Recent observations of Jupiter's Great Red Spot indicate that the thermosphere above the storm is hotter than its surroundings by more than 700 K. Possible suggested sources for this heating have thus far included atmospheric gravity waves and lightning-driven acoustic waves. Here, we propose that Joule heating, driven by Great Red Spot vorticity penetrating up into the lower stratosphere and coupling to the thermosphere, may contribute to the large observed temperatures. The strength of Joule heating will depend on the local inclination angle of the magnetic field and thus the observed emissions and inferred temperatures should vary with planetary longitude as the Great Red Spot tracks across the planet. This article is part of a discussion meeting issue 'Advances in hydrogen molecular ions: H3+, H5+ and beyond'