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

Implementing neural architectures using analog VLSI circuits

Analog very large-scale integrated (VLSI) technology can be used not only to study and simulate biological systems, but also to emulate them in designing artificial sensory systems. A methodology for building these systems in CMOS VLSI technology has been developed using analog micropower circuit elements that can be hierarchically combined. Using this methodology, experimental VLSI chips of visual and motor subsystems have been designed and fabricated. These chips exhibit behavior similar to that of biological systems, and perform computations useful for artificial sensory systems

Links between topography, wind, deflation, lakes and dust: The case of the Bodélé Depression, Chad

The Bodélé Depression, Chad is the planet's largest single source of dust. Deflation from the Bodélé could be seen as a simple coincidence of two key prerequisites: strong surface winds and a large source of suitable sediment. But here we hypothesise that long term links between topography, winds, deflation and dust ensure the maintenance of the dust source such that these two apparently coincidental key ingredients are connected by land-atmosphere processes with topography acting as the overall controlling agent. We use a variety of observational and numerical techniques, including a regional climate model, to show that: 1) contemporary deflation from the Bodélé is delineated by topography and a surface wind stress maximum; 2) the Tibesti and Ennedi mountains play a key role in the generation of the erosive winds in the form of the Bodélé Low Level Jet (LLJ); 3) enhanced deflation from a stronger Bodélé LLJ during drier phases, for example, the Last Glacial Maximum, was probably sufficient to create the shallow lake in which diatoms lived during wetter phases, such as the Holocene pluvial. Winds may therefore have helped to create the depression in which erodible diatom material accumulated. Instead of a simple coincidence of nature, dust from the world's largest source may result from the operation of long term processes on paleo timescales which have led to ideal conditions for dust generation in the world's largest dust source. Similar processes plausibly operate in other dust hotspots in topographic depressions

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

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

Global environmental implications of atmospheric methane removal through chlorine-mediated chemistry-climate interactions

Atmospheric methane is both a potent greenhouse gas and photochemically active, with approximately equal anthropogenic and natural sources. The addition of chlorine to the atmosphere has been proposed to mitigate global warming through methane reduction by increasing its chemical loss. However, the potential environmental impacts of such climate mitigation remain unexplored. Here, sensitivity studies are conducted to evaluate the possible effects of increasing reactive chlorine emissions on the methane budget, atmospheric composition and radiative forcing. Because of non-linear chemistry, in order to achieve a reduction in methane burden (instead of an increase), the chlorine atom burden needs to be a minimum of three times the estimated present-day burden. If the methane removal target is set to 20%, 45%, or 70% less global methane by 2050 compared to the levels in the Representative Concentration Pathway 8.5 scenario (RCP8.5), our modeling results suggest that additional chlorine fluxes of 630, 1250, and 1880 Tg Cl/year, respectively, are needed. The results show that increasing chlorine emissions also induces significant changes in other important climate forcers. Remarkably, the tropospheric ozone decrease is large enough that the magnitude of radiative forcing decrease is similar to that of methane. Adding 630, 1250, and 1880 Tg Cl/year to the RCP8.5 scenario, chosen to have the most consistent current-day trends of methane, will decrease the surface temperature by 0.2, 0.4, and 0.6 °C by 2050, respectively. The quantity and method in which the chlorine is added, its interactions with climate pathways, and the potential environmental impacts on air quality and ocean acidity, must be carefully considered before any action is taken

Twelve thousand years of dust: The Holocene global dust cycle constrained by natural archives

Mineral dust plays an important role in the climate system by interacting with radiation, clouds, and biogeochemical cycles. In addition, natural archives show that the dust cycle experienced variability in the past in response to global and local climate change. The compilation of the DIRTMAP paleodust datasets in the last two decades provided a target for paleoclimate models that include the dust cycle, following a time slice approach. We propose an innovative framework to organize a paleodust dataset that moves on from the positive experience of DIRTMAP and takes into account new scientific challenges, by providing a concise and accessible dataset of temporally resolved records of dust mass accumulation rates and particle grain-size distributions. We consider data from ice cores, marine sediments, loess/paleosol sequences, lake sediments, and peat bogs for this compilation, with a temporal focus on the Holocene period. This global compilation allows investigation of the potential, uncertainties and confidence level of dust mass accumulation rates reconstructions, and highlights the importance of dust particle size information for accurate and quantitative reconstructions of the dust cycle. After applying criteria that help to establish that the data considered represent changes in dust deposition, 43 paleodust records have been identified, with the highest density of dust deposition data occurring in the North Atlantic region. Although the temporal evolution of dust in the North Atlantic appears consistent across several cores and suggest that minimum dust fluxes are likely observed during the Early to mid-Holocene period (6000–8000 years ago), the magnitude of dust fluxes in these observations is not fully consistent, suggesting that more work needs to be done to synthesize datasets for the Holocene. Based on the data compilation, we used the Community Earth System Model to estimate the mass balance and variability of the global dust cycle during the Holocene, with dust load ranging from 17.1 to 20.5 Tg between 2000 and 10 000 years ago, and a minimum in the Early to Mid-Holocene (6000–8000 years ago)

Nitrogen fixation in the South Atlantic Gyre and the Benguela Upwelling System

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 38 (2011): L16608, doi:10.1029/2011GL048315.Dinitrogen (N2) fixation is recognized as an important input of new nitrogen (N) to the open ocean gyres, contributing to the export of organic matter from surface waters. However, very little N2-fixation research has focused on the South Atlantic Gyre, where dust deposition of iron (Fe), an important micronutrient for diazotrophs, is seasonally low. Recent modeling efforts suggest that N2-fixation may in fact be closely coupled to, and greatest in, areas of denitrification, as opposed to the oceanic gyres. One of these areas, the Benguela Upwelling System, lies to the east of the South Atlantic Gyre. In this study we show that N2-fixation in surface waters across the South Atlantic Gyre was low overall (<1.5 nmol N l−1 d−1) with highest rates seen in or near the Benguela Upwelling System (up to ∼8 nmol N l−1 d−1). Surface water dissolved Fe (dFe) concentrations were very low in the gyre (∼0.3 nM or lower), while soluble reactive phosphorus (SRP) concentrations were relatively high (∼0.15 μM). N2-fixation rates across the entire sampling area were significantly positively correlated to dFe, but also to SRP and NO3−. Thus, high NO3− concentrations did not exclude N2-fixation in the upwelling region, which provides evidence that N2-fixation may be occurring in previously unrecognized waters, specifically near denitrification zones. However the gene encoding for a nitrogenase component (nifH) was not detected from known diazotrophs at some stations in or near the upwelling where N2-fixation was greatest, suggesting the presence of unknown diazotrophs in these waters.Funding for this research was provided by NSF grants OCE‐0452883 (to E.A.W. and M.A.S.), OCE‐0825922 (to E.A.W.), and The Gordon and Betty Moore Foundation (JPZ)