Out-of-frame T cell receptor beta transcripts are eliminated by multiple pathways In Vivo

Non-productive antigen receptor genes with frame shifts generated during the assembly of these genes are found in many mature lymphocytes. Transcripts from these genes have premature termination codons (PTCs) and could encode truncated proteins if they are not either inactivated or destroyed by nonsense-mediated decay (NMD). In mammalian cells, NMD can be activated by pathways that rely on the presence of an intron downstream of the PTC; however, NMD can also be activated by pathways that do not rely on these downstream introns, and pathways independent of NMD can inactivate PTC-containing transcripts. Here, through the generation and analysis of mice with gene-targeted modifications of the endogenous T cell receptor beta (Tcrb) locus, we demonstrate that in T cells in vivo, optimal clearance of PTC-containing Tcrb transcripts depends on the presence of an intron downstream of the PTC

Volcano impacts on climate and biogeochemistry in a coupled carbon–climate model

Volcanic eruptions induce a dynamical response in the climate system characterized by short-term global reductions in both surface temperature and precipitation, as well as a response in biogeochemistry. The available observations of these responses to volcanic eruptions, such as to Pinatubo, provide a valuable method to compare against model simulations. Here, the Community Climate System Model Version 3 (CCSM3) reproduces the physical climate response to volcanic eruptions in a realistic way, as compared to direct observations from the 1991 eruption of Mount Pinatubo. The model's biogeochemical response to eruptions is smaller in magnitude than observed, but because of the lack of observations, it is not clear why or where the modeled carbon response is not strong enough. Comparison to other models suggests that this model response is much weaker over tropical land; however, the precipitation response in other models is not accurate, suggesting that other models could be getting the right response for the wrong reason. The underestimated carbon response in the model compared to observations could also be due to the ash and lava input of biogeochemically important species to the ocean, which are not included in the simulation. A statistically significant reduction in the simulated carbon dioxide growth rate is seen at the 90% level in the average of 12 large eruptions over the period 1870–2000, and the net uptake of carbon is primarily concentrated in the tropics, with large spatial variability. In addition, a method for computing the volcanic response in model output without using a control ensemble is tested against a traditional methodology using two separate ensembles of runs; the method is found to produce similar results in the global average. These results suggest that not only is simulating volcanoes a good test of coupled carbon–climate models, but also that this test can be performed without a control simulation in cases where it is not practical to run separate ensembles with and without volcanic eruptions.NASA Astrobiology Institute (NNGO6G127G)National Science Foundation (U.S.) (Grant 1049033)National Science Foundation (U.S.) (Grant 1021614

How many orthonormal bases are needed to distinguish all pure quantum states?

We collect some recent results that together provide an almost complete answer to the question stated in the title. For the dimension d=2 the answer is three. For the dimensions d=3 and d>4 the answer is four. For the dimension d=4 the answer is either three or four. Curiously, the exact number in d=4 seems to be an open problem

Exploring the sensitivity of interannual basin-scale air-sea CO2 fluxes to variability in atmospheric dust deposition using ocean carbon cycle models and atmospheric CO2 inversions

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 112 (2007): G02012, doi:10.1029/2006JG000236.Estimates of sources/sinks of carbon dioxide (CO2) at the Earth's surface are commonly made using atmospheric CO2 inverse modeling, terrestrial and oceanic biogeochemical modeling, and inventory-based studies. In this study, we compare sea-air CO2 fluxes from the Time-Dependent Inverse (TDI) atmosphere model and the marine Biogeochemical Elemental Cycling (BEC) model to study the processes involved in ocean carbon cycling at subbasin scales. A dust generation and transport model, based on analyzed meteorology and terrestrial vegetation cover, is also used to estimate the interannual variability in dust and iron deposition to different ocean basins. Overall, a fairly good agreement is established between the TDI and BEC model results for the net annual patterns and seasonal cycle of sea-air CO2 exchange. Sensitivity studies with the ocean biogeochemical model using increased or reduced atmospheric iron inputs indicate the relative sensitivity of air-sea CO2 exchange. The simulated responses to changes in iron inputs are not instantaneous (peak response after ∼2−3 years). The TDI model derived seasonal cycles for the Southern Ocean (South Atlantic) are better matched by the BEC model by increasing (decreasing) iron inputs through atmospheric aerosols. Our results suggest that some of the interannual variability in TDI model air-sea CO2 fluxes during the past decade may be explainable by dust variability that relaxes/increases iron limitation in high-nitrate, low-chlorophyll (HNLC) ocean regions.S. C. Doney and N. Mahowald acknowledge support from NASA grant NNG05GG30G. J. K. Moore was funded by NSF grant OCE-0452972

Atmospheric aerosols at the Pierre Auger Observatory and environmental implications

The Pierre Auger Observatory detects the highest energy cosmic rays. Calorimetric measurements of extensive air showers induced by cosmic rays are performed with a fluorescence detector. Thus, one of the main challenges is the atmospheric monitoring, especially for aerosols in suspension in the atmosphere. Several methods are described which have been developed to measure the aerosol optical depth profile and aerosol phase function, using lasers and other light sources as recorded by the fluorescence detector. The origin of atmospheric aerosols traveling through the Auger site is also presented, highlighting the effect of surrounding areas to atmospheric properties. In the aim to extend the Pierre Auger Observatory to an atmospheric research platform, a discussion about a collaborative project is presented.Comment: Regular Article, 16 pages, 12 figure

Radiative forcing of climate: the historical evolution of the radiative forcing concept, the forcing agents and their quantification, and applications

We describe the historical evolution of the conceptualization, formulation, quantification, application and utilization of “radiative forcing (RF, see e.g., IPCC, 1990)” of Earth’s climate. Basic theories of shortwave and long wave radiation were developed through the 19th and 20th centuries, and established the analytical framework for defining and quantifying the perturbations to the Earth’s radiative energy balance by natural and anthropogenic influences. The insight that the Earth’s climate could be radiatively forced by changes in carbon dioxide, first introduced in the 19th century, gained empirical support with sustained observations of the atmospheric concentrations of the gas beginning in 1957. Advances in laboratory and field measurements, theory, instrumentation, computational technology, data and analysis of well-mixed greenhouse gases and the global climate system through the 20th Century enabled the development and formalism of RF; this allowed RF to be related to changes in global-mean surface temperature with the aid of increasingly sophisticated models. This in turn led to RF becoming firmly established as a principal concept in climate science by 1990. The linkage with surface temperature has proven to be the most important application of the RF concept, enabling a simple metric to evaluate the relative climate impacts of different agents. The late 1970s and 1980s saw accelerated developments in quantification including the first assessment of the effect of the forcing due to doubling of carbon dioxide on climate (the “Charney” report, National Research Council, 1979). The concept was subsequently extended to a wide variety of agents beyond well-mixed greenhouse gases (WMGHGs: carbon dioxide, methane, nitrous oxide, and halocarbons) to short-lived species such as ozone. The WMO (1986) and IPCC (1990) international assessments began the important sequence of periodic evaluations and quantifications of the forcings by natural (solar irradiance changes and stratospheric aerosols resulting from volcanic eruptions) and a growing set of anthropogenic agents (WMGHGs, ozone, aerosols, land surface changes, contrails). From 1990s to the present, knowledge and scientific confidence in the radiative agents acting on the climate system has proliferated. The conceptual basis of RF has also evolved as both our understanding of the way radiative forcing drives climate change, and the diversity of the forcing mechanisms, have grown. This has led to the current situation where “Effective Radiative Forcing (ERF, e.g., IPCC, 2013)” is regarded as the preferred practical definition of radiative forcing in order to better capture the link between forcing and global-mean surface temperature change. The use of ERF, however, comes with its own attendant issues, including challenges in its diagnosis from climate models, its applications to small forcings, and blurring of the distinction between rapid climate adjustments (fast responses) and climate feedbacks; this will necessitate further elaboration of its utility in the future. Global climate model simulations of radiative perturbations by various agents have established how the forcings affect other climate variables besides temperature e.g., precipitation. The forcing-response linkage as simulated by models, including the diversity in the spatial distribution of forcings by the different agents, has provided a practical demonstration of the effectiveness of agents in perturbing the radiative energy balance and causing climate changes. The significant advances over the past half-century have established, with very high confidence, that the global-mean ERF due to human activity since preindustrial times is positive (the 2013 IPCC assessment gives a best estimate of 2.3 W m-2, with a range from 1.1 to 3.3 W m-2; 90% confidence interval). Further, except in the immediate aftermath of climatically-significant volcanic eruptions, the net anthropogenic forcing dominates over natural radiative forcing mechanisms. Nevertheless, the substantial remaining uncertainty in the net anthropogenic ERF leads to large uncertainties in estimates of climate sensitivity from observations and in predicting future climate impacts. The uncertainty in the ERF arises principally from the incorporation of the rapid climate adjustments in the formulation, the well-recognized difficulties in characterizing the preindustrial state of the atmosphere, and the incomplete knowledge of the interactions of aerosols with clouds. This uncertainty impairs the quantitative evaluation of climate adaptation and mitigation pathways in the future. A grand challenge in Earth System science lies in continuing to sustain the relatively simple essence of the radiative forcing concept in a form similar to that originally devised, and at the same time improving the quantification of the forcing. This, in turn, demands an accurate, yet increasingly complex and comprehensive, accounting of the relevant processes in the climate system

Importance of different parameterization changes for the updated dust cycle modeling in the Community Atmosphere Model (version 6.1)

The Community Atmosphere Model (CAM6.1), the atmospheric component of the Community Earth System Model (CESM; version 2.1), simulates the life cycle (emission, transport, and deposition) of mineral dust and its interactions with physio-chemical components to quantify the impacts of dust on climate and the Earth system. The accuracy of such quantifications relies on how well dust-related processes are represented in the model. Here we update the parameterizations for the dust module, including those on the dust emission scheme, the aerosol dry deposition scheme, the size distribution of transported dust, and the treatment of dust particle shape. Multiple simulations were undertaken to evaluate the model performance against diverse observations, and to understand how each update alters the modeled dust cycle and the simulated dust direct radiative effect. The model–observation comparisons suggest that substantially improved model representations of the dust cycle are achieved primarily through the new more physically-based dust emission scheme. In comparison, the other modifications induced small changes to the modeled dust cycle and model–observation comparisons, except the size distribution of dust in the coarse mode, which can be even more influential than that of replacing the dust emission scheme. We highlight which changes introduced here are important for which regions, shedding light on further dust model developments required for more accurately estimating interactions between dust and climate.</p

Modeling the global emission, transport and deposition of trace elements associated with mineral dust

Trace element deposition from desert dust has important impacts on ocean primary productivity, the quantification of which could be useful in determining the magnitude and sign of the biogeochemical feedback on radiative forcing. However, the impact of elemental deposition to remote ocean regions is not well understood and is not currently included in global climate models. In this study, emission inventories for eight elements primarily of soil origin, Mg, P, Ca, Mn, Fe, K, Al, and Si are determined based on a global mineral data set and a soil data set. The resulting elemental fractions are used to drive the desert dust model in the Community Earth System Model (CESM) in order to simulate the elemental concentrations of atmospheric dust. Spatial variability of mineral dust elemental fractions is evident on a global scale, particularly for Ca. Simulations of global variations in the Ca / Al ratio, which typically range from around 0.1 to 5.0 in soils, are consistent with observations, suggesting that this ratio is a good signature for dust source regions. The simulated variable fractions of chemical elements are sufficiently different; estimates of deposition should include elemental variations, especially for Ca, Al and Fe. The model results have been evaluated with observations of elemental aerosol concentrations from desert regions and dust events in non-dust regions, providing insights into uncertainties in the modeling approach. The ratios between modeled and observed elemental fractions range from 0.7 to 1.6, except for Mg and Mn (3.4 and 3.5, respectively). Using the soil database improves the correspondence of the spatial heterogeneity in the modeling of several elements (Ca, Al and Fe) compared to observations. Total and soluble dust element fluxes to different ocean basins and ice sheet regions have been estimated, based on the model results. The annual inputs of soluble Mg, P, Ca, Mn, Fe and K associated with dust using the mineral data set are 0.30 Tg, 16.89 Gg, 1.32 Tg, 22.84 Gg, 0.068 Tg, and 0.15 Tg to global oceans and ice sheets

Modeling the global emission, transport and deposition of trace elements associated with mineral dust

Trace element deposition from desert dust has important impacts on ocean primary productivity, the quantification of which could be useful in determining the magnitude and sign of the biogeochemical feedback on radiative forcing. However, the impact of elemental deposition to remote ocean regions is not well understood and is not currently included in global climate models. In this study, emission inventories for eight elements primarily of soil origin, Mg, P, Ca, Mn, Fe, K, Al, and Si are determined based on a global mineral data set and a soil data set. The resulting elemental fractions are used to drive the desert dust model in the Community Earth System Model (CESM) in order to simulate the elemental concentrations of atmospheric dust. Spatial variability of mineral dust elemental fractions is evident on a global scale, particularly for Ca. Simulations of global variations in the Ca / Al ratio, which typically range from around 0.1 to 5.0 in soils, are consistent with observations, suggesting that this ratio is a good signature for dust source regions. The simulated variable fractions of chemical elements are sufficiently different; estimates of deposition should include elemental variations, especially for Ca, Al and Fe. The model results have been evaluated with observations of elemental aerosol concentrations from desert regions and dust events in non-dust regions, providing insights into uncertainties in the modeling approach. The ratios between modeled and observed elemental fractions range from 0.7 to 1.6, except for Mg and Mn (3.4 and 3.5, respectively). Using the soil database improves the correspondence of the spatial heterogeneity in the modeling of several elements (Ca, Al and Fe) compared to observations. Total and soluble dust element fluxes to different ocean basins and ice sheet regions have been estimated, based on the model results. The annual inputs of soluble Mg, P, Ca, Mn, Fe and K associated with dust using the mineral data set are 0.30 Tg, 16.89 Gg, 1.32 Tg, 22.84 Gg, 0.068 Tg, and 0.15 Tg to global oceans and ice sheets