In atmospheric and space environment studies it is key to understand and to quantify the coupling of atmospheric regions and the solar impacts on the whole atmosphere system. There is thus a need for ...a numerical model that encompasses the whole atmosphere and can self‐consistently simulate the dynamic, physical, chemical, radiative, and electrodynamic processes that are important for the Sun‐Earth system. This is the goal for developing the National Center for Atmospheric Research (NCAR) Whole Atmosphere Community Climate Model (WACCM). In this work, we report the development and preliminary validation of the thermospheric extension of WACCM (WACCM‐X), which extends from the Earth's surface to the upper thermosphere. The WACCM‐X uses the finite volume dynamical core from the NCAR Community Atmosphere Model and includes an interactive chemistry module resolving most known neutral chemistry and major ion chemistry in the middle and upper atmosphere, and photolysis and photoionization. Upper atmosphere processes, such as nonlocal thermodynamic equilibrium, radiative transfer, auroral processes, ion drag, and molecular diffusion of major and minor species, have been included in the model. We evaluate the model performance by examining the quantities essential for the climate and weather of the upper atmosphere: the mean compositional, thermal, and wind structures from the troposphere to the upper thermosphere and their variability on interannual, seasonal, and daily scales. These quantities are compared with observational and previous model results.
Byline: N. Butchart (1), A. A. Scaife (2), M. Bourqui (3,4), J. Grandpre (4), S. H. E. Hare (3), J. Kettleborough (5), U. Langematz (6), E. Manzini (7), F. Sassi (8), K. Shibata (9), D. Shindell ...(10), M. Sigmond (11) The effect of climate change on the Brewer--Dobson circulation and, in particular, the large-scale seasonal-mean transport between the troposphere and stratosphere is compared in a number of middle atmosphere general circulation models. All the models reproduce the observed upwelling across the tropical tropopause balanced by downwelling in the extra tropics, though the seasonal cycle in upwelling in some models is more semi-annual than annual. All the models also consistently predict an increase in the mass exchange rate in response to growing greenhouse gas concentrations, irrespective of whether or not the model includes interactive ozone chemistry. The mean trend is 11 kt s.sup.-1 year.sup.-1 or about 2% per decade but varies considerably between models. In all but one of the models the increase in mass exchange occurs throughout the year though, generally, the trend is larger during the boreal winter. On average, more than 60% of the mean mass fluxes can be explained by the EP-flux divergence using the downward control principle. Trends in the annual mean mass fluxes derived from the EP-flux divergence also explain about 60% of the trend in the troposphere-to-stratosphere mass exchange rate when averaged over all the models. Apart from two models the interannual variability in the downward control derived and actual mass fluxes were generally well correlated, for the annual mean. Author Affiliation: (1) Met Office, FitzRoy Road, Exeter, Devon, EX1 3PB, UK (2) Hadley Centre, Met Office, Exeter, UK (3) Department of Meteorology, University of Reading, Reading, UK (4) McGill University, Montreal, Canada (5) Rutherford Laboratory, British Atmospheric Data Centre, Didcot, UK (6) Freie Universitat of Berlin, Berlin, Germany (7) National Institute for Geophysics and Volcanology, Bologna, Italy (8) National Center for Atmospheric Research, Boulder, CO, USA (9) Meteorological Research Institute, Tsukuba, Japan (10) NASA-Goddard Institute for Space Studies, New York, USA (11) University of Toronto, Toronto, Canada Article History: Registration Date: 29/05/2006 Received Date: 15/11/2005 Accepted Date: 20/05/2006 Online Date: 16/08/2006
We compare the two approaches that have been used to measure the lowermost ionosphere, the measurement of the propagation of very low frequency (VLF) radio waves and the in situ sampling by sounding ...rockets. We focus on the altitude, latitude, and zenith angle variation of the electron density profiles inferred from these two observational techniques as compared with a theoretical photochemical model. Our results show that below 68–70 km, the VLF data and the model agree better with each other than with the sounding rocket profile. At the lowest altitudes, near 60 km, both the VLF data and the model show a greater electron density at higher latitudes, consistent with a cosmic ray flux that increases with latitude, whereas the limited rocket data show a maximum at the tropics. Above 68–70 km, the VLF data and the sounding rockets agree better and at tropical latitudes, the model fails to reproduce the observations. Specifically, the calculated electron density is lower than the data by up to a factor of 2. Possible reasons for the model deficit include underestimates of the solar Lyman alpha flux, the solar X‐ray flux and the mesospheric nitric oxide density. Once these three factors are mitigated, the model is in agreement with the observations between 60 and 80 km.
Plain Language Summary
Over the past 50–60 years, there have been two approaches toward measuring the lowermost ionosphere (below 90 km), the D region. One is by modeling the propagation of VLF radio waves; the other is by in situ sampling via rockets. Until now, these techniques have not been rigorously intercompared. By comparing both with each other and with a theoretical photochemical model, we show how they are complementary. The very low frequency data are most accurate below 70 km, while the rocket data are more accurate above 70 km. The photochemical model can be made to agree with these data provided certain assumptions are made about the solar Lyman alpha flux, solar X‐rays, and mesospheric nitric oxide (NO).
Key Points
We compare two independent techniques for measuring the D region ionosphere
Modeling VLF radio waves is most accurate below 70 km, in situ rockets are most accurate above 70 km
Photochemical model can agree with observations, but there are uncertainties concerning neutral atmosphere and solar flux inputs
We have performed simulations using the Naval Research Laboratory's physics‐based model of the ionosphere, Sami3 is A Model of the Ionosphere (SAMI3), to illustrate how neutral wind dynamics is ...responsible for day‐to‐day variability of the ionosphere. We have used neutral winds specified from the extended version of the specified dynamics Whole Atmosphere Community Climate Model (SD‐WACCM‐X), in which meteorology below 92 km is constrained by atmospheric specifications from an operational weather forecast model and reanalysis. To assess the realism of the simulations against observations, we have carried out a case study during January–February 2009, a dynamically disturbed time characterized by a sudden stratospheric warming (SSW) commencing 24 January 2009. Model results are compared with total electron content (TEC) from Jet Propulsion Laboratory global ionospheric maps. We show that SAMI3/SD‐WACCM‐X captures longitudinal variability in the equatorial ionization anomaly associated with nonmigrating tides, with strongest contributions coming from the diurnal eastward wave number 2 (DE2) and DE3. Both migrating and nonmigrating tides contribute to significant day‐to‐day variability, with TEC varying up to 16%. Our simulation during the SSW period reveals that at the Jicamarca longitude (285°E) on 27 January 2009 nonmigrating tides contribute to an enhancement of the electron density in the morning followed by a decrease in the afternoon. An enhancement of the semidiurnal eastward wave number 2 (SE2) and SE3 nonmigrating tides, likely associated with the appearance of the SSW, suggests that these tides increase the longitudinal variability of the SSW impact on the ionosphere. The conclusion is that realistic meteorology propagating upward from the lower atmosphere influences the dynamo region and reproduces aspects of the observed variability in the ionosphere.
Key Points
Lower atmospheric contributions to ionosphere simulated during the 2009 SSW
DE2 and DE3 tides are primary drivers of longitudinal variability during this period
Semidiurnal nonmigrating tides play a role in SSW effects on ionosphere
A global analysis of convective cloud in the tropical tropopause region (12–17 km) is presented. The analysis is based on high‐resolution global imagery of cloud brightness temperatures from ...satellites and from contemporaneous reanalysis temperatures. The coverage by deep convection decreases nearly exponentially with increasing altitude in the tropopause region. Convection is found at temperatures colder than the tropical cold point tropopause over ∼0.5% (±0.25%) of the tropics. Convection rarely penetrates more than 1.5 km above the tropopause. Large‐scale relationships between cold tropopause temperatures and deep convection indicate that where the tropopause is coldest convection penetrates most frequently. Small‐scale relationships show that the coldest diurnal tropopause temperatures occur after the diurnal peak in deep convection at tropopause levels over land. The coverage by deep convection is used to estimate the mass exchange or turnover time due to convection in the tropopause region. This turnover time is of the order of weeks at 12 km but increases to longer than a year at 18 km, with significant uncertainties in the tropopause region.
Basal-like breast cancer is an aggressive subtype of mammary carcinoma. Despite expressing basal markers, typical of mammary stem cells, this tumor has been proposed to originate from luminal ...progenitors, which are downstream of stem cells along the mammary epithelial hierarchy. This suggests that committed luminal progenitors may reacquire basal, stem-like characteristics, but the mechanisms that regulate this transition remain unclear. Using mouse models, we found that luminal progenitors express high levels of the Met receptor for hepatocyte growth factor (HGF), as compared with the other mammary epithelial sub-populations. Constitutive activation of Met led luminal progenitors to attain stem cell properties, including enhanced clonogenic activity in vitro and de novo ability to reconstitute mammary glands in repopulation assays in vivo. Moreover, in response to Met signaling, luminal progenitors gave rise to hyperplastic ductal morphogenesis and preferentially underwent basal lineage commitment at the expense of luminal cell-fate specification. Opposite and symmetric results were produced by systemic pharmacological inhibition of Met. Hence, Met signaling targets luminal progenitors for expansion, impairs their differentiation toward the mature luminal phenotype and enables their commitment toward the basal lineage. These results emphasize a critical role for Met in promoting deregulated proliferation and basal plasticity of normal luminal progenitors in the mammary gland, a complex of events that may be required for sustaining the functional and phenotypic properties of basal-like breast tumors.
A simulation of the middle atmosphere is presented using a general circulation model (GCM) forced with observed sea surface temperature for the period 1950–2000. The GCM extends to the lower ...thermosphere and reproduces realistic dynamical and temperature distributions. The period contains several El Niño and La Niña events, which are identified using the NINO3 index. Composite anomalies of relevant meteorological fields are obtained by stratifying the northern winter season according to the NINO3 index. These anomalies have the structure of vertically propagating planetary waves extending from the troposphere to the mesosphere. Circulation anomalies in the middle atmosphere are accompanied by large temperature anomalies that are of opposite sign in the stratosphere and mesosphere, the former being warmer and the latter colder during El Niño events. Near the summer mesopause, changes in momentum deposition by parameterized gravity waves results in warming during El Niño. Detailed statistical analysis is used to determine the significance of these anomalies. A chemical/transport simulation is carried out using output from the GCM. It shows that when the lower stratosphere is colder (as during La Niña events), some ozone depletion takes place. Conversely, when the lower stratosphere is warmer and more disturbed, as is the case during El Niño events, heterogeneous chemical processes are inhibited.
Abstract
Large-scale Rossby normal modes are studied for the Northern Hemisphere winters of 2005, 2006, 2008, and 2009 using global observational meteorological analyses spanning the 0–92-km altitude ...range. Spectral analysis of geopotential height fields shows pronounced peaks at westward-propagating zonal wavenumber 1 near the theoretical locations of the free Rossby waves at 25, 16, 10, and 5 days that, in some cases, have amplitudes significantly larger than the estimated background spectrum. Evidence is also found for a wavenumber-2 free mode near 4 days. A coherence analysis is used to extract the amplitude and phase of the waves, and to isolate those regions of the latitude/altitude plane where the signals are statistically significant. Although the spectral location, temporal evolution, and vertical structure of several of these waves are suggestive of the presence of Rossby normal modes, this study shows that in the real atmosphere the waves only occasionally have the global properties of classical normal modes. Moreover, no evidence is found that the amplitudes of these modes are enhanced during stratospheric sudden warmings.
Microalgae show great promise as sources of starch, one of the most widely consumed macromolecules. In this study, we evaluated the impact of three starch-inducing factors, namely nitrogen ...deprivation, supra-optimal temperature, and red light, on the physiology and starch accumulation capacity of Chlorella vulgaris. This starch accumulation was monitored by measuring the total carbohydrate content and transmission electron microscopy (TEM) imaging. Nitrogen deprivation and a supra-optimal temperature of 39 °C resulted in carbohydrate contents of 69.7 and 64.3 % of dry weight (DW) respectively. This constituted a 5.3- and 3.3-fold increase in carbohydrate productivity compared to the control, after 4 days of cultivation. During this period, carbohydrates represented over 80 % of the produced material (DW basis). However, nitrogen deprivation and supra-optimal temperature were accompanied by extensive stress, leading to lower cell division rates and damage to the photosynthetic apparatus. Red light illumination resulted in a more moderate production of carbohydrates. After 4 days of cultivation, the carbohydrate content reached 46.8 %, representing a 3.0-fold increase in productivity compared to control. The composition of the starch formed under red light was surprisingly poor in amylose, similar to transitory-type starch rather than storage starch. Most notably, the starch accumulation under red light was sustained over 7 days without affecting the rate of cell division and quantum yield efficiency. To the best of our knowledge, red light is the only factor reported so far to induce a significant starch accumulation without hindering cell division and photosynthesis efficiency, even after long-term exposure (7 days). Furthermore, all three conditions induced a cell wall thickening, albeit without affecting the recovery of accumulated starch by high-pressure homogenization. These results highlight the potential of red light as a starch inducer in Chlorella vulgaris and open up perspectives for the production of starch-based bioplastics from microalgae.
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•Chlorella vulgaris CCALA924 was grown in an incubator with a 16-h light/8-h dark period.•Red light promoted starch accumulation, maintaining cell division and photosynthesis capacity.•Nitrogen deprivation resulted in the highest starch accumulation overall.•A supra-optimal temperature of 39 °C severely impaired microalga growth.•Cell wall thickening occurred for all inducers without hindering cell rupture.
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