Analysis of the root system architecture of Arabidopsis provides a quantitative readout of crosstalk between nutritional signals

As plant roots forage the soil for food and water, they translate a multifactorial input of environmental stimuli into a multifactorial developmental output that manifests itself as root system architecture (RSA). Our current understanding of the underlying regulatory network is limited because root responses have traditionally been studied separately for individual nutrient deficiencies. In this study, we quantified 13 RSA parameters of Arabidopsis thaliana in 32 binary combinations of N, P, K, S, and light. Analysis of variance showed that each RSA parameter was determined by a typical pattern of environmental signals and their interactions. P caused the most important single-nutrient effects, while N-effects were strongly light dependent. Effects of K and S occurred mostly through nutrient interactions in paired or multiple combinations. Several RSA parameters were selected for further analysis through mutant phenotyping, which revealed combinations of transporters, receptors, and kinases acting as signaling modules in K–N interactions. Furthermore, nutrient response profiles of individual RSA features across NPK combinations could be assigned to transcriptionally coregulated clusters of nutrient-responsive genes in the roots and to ionome patterns in the shoots. The obtained data set provides a quantitative basis for understanding how plants integrate multiple nutritional stimuli into complex developmental programs

Lorentz Violation for Photons and Ultra-High Energy Cosmic Rays

Lorentz symmetry breaking at very high energies may lead to photon dispersion relations of the form omega^2=k^2+xi_n k^2(k/M_Pl)^n with new terms suppressed by a power n of the Planck mass M_Pl. We show that first and second order terms of size xi_1 > 10^(-14) and xi_2 < -10^(-6), respectively, would lead to a photon component in cosmic rays above 10^(19) eV that should already have been detected, if corresponding terms for electrons and positrons are significantly smaller. This suggests that Lorentz invariance breakings suppressed up to second order in the Planck scale are unlikely to be phenomenologically viable for photons.Comment: 4 revtex pages, 3 postscript figures included, version published in PR

ApoFnr binds as a monomer to promoters regulating expression of enterotoxin genes of Bacillus cereus.

International audienceBacillus cereus Fnr is a member of the Crp/Fnr (cAMP-binding protein/fumarate nitrate reduction regulatory protein) family of helix-turn-helix transcriptional regulators. It is essential for the expression of Hbl and Nhe enterotoxin genes independently of the oxygen tension in the environment. We studied aerobic Fnr binding to target sites in promoters regulating the expression of enterotoxin genes. B. cereus Fnr was overexpressed and purified as either a C-terminal His-tagged (FnrHis) fusion protein or an N-terminal fusion protein tagged with the Strep-tag (IBA BioTAGnology) (StrepFnr). Both recombinant Fnr proteins were produced as apoforms (clusterless) and occured as mixtures of monomers and oligomers in solution. However, apoFnrHis was mainly monomeric, while apoStrepFnr was mainly oligomeric, suggesting that the His-tagged C-terminal extremity may interfere with oligomerization. The oligomeric state of apoStrepFnr was dithiothreitol sensitive, underlining the importance of a disulphide bridge for apoFnr oligomerization. Electrophoretic mobility shift assays showed that monomeric apoFnr, but not oligomeric apoFnr, bound to specific sequences located in the promoter regions of the enterotoxin regulators fnr, resDE and plcR and the structural genes hbl and nhe. The question of whether apoFnr binding is regulated in vivo by redox-dependent oligomerization is discussed

Angular Power Spectrum Estimation of Cosmic Ray Anisotropies with Full or Partial Sky Coverage

We study the angular power spectrum estimate in order to search for large scale anisotropies in the arrival directions distribution of the highest-energy cosmic rays. We show that this estimate can be performed even in the case of partial sky coverage and validated over the full sky under the assumption that the observed fluctuations are statistically spatial stationary. If this hypothesis - which can be tested directly on the data - is not satisfied, it would prove, of course, that the cosmic ray sky is non isotropic but also that the power spectrum is not an appropriate tool to represent its anisotropies, whatever the sky coverage available. We apply the method to simulations of the Pierre Auger Observatory, reconstructing an input power spectrum with the Southern site only and with both Northern and Southern ones. Finally, we show the improvement that a full-sky observatory brings to test an isotropic distribution, and we discuss the sensitivity of the Pierre Auger Observatory to large scale anisotropies.Comment: 16 pages, 6 figures, version accepted for publication by JCA

Nutrient recycling facilitates long-term stability of marine microbial phototroph–heterotroph interactions

Biological interactions underpin the functioning of marine ecosystems, be it via competition, predation, mutualism or symbiosis processes. Microbial phototroph–heterotroph interactions propel the engine that results in the biogeochemical cycling of individual elements, and they are critical for understanding and modelling global ocean processes. Unfortunately, studies thus far have focused on exponentially growing cultures in nutrient-rich media, meaning knowledge of such interactions under in situ conditions is rudimentary at best. Here, we have performed long-term phototroph–heterotroph co-culture experiments under nutrient-amended and natural seawater conditions, and show that it is not the concentration of nutrients but rather their circulation that maintains a stable interaction and a dynamic system. Using the Synechococcus–Roseobacter interaction as a model phototroph–heterotroph case study, we show that although Synechococcus is highly specialized for carrying out photosynthesis and carbon fixation, it relies on the heterotroph to remineralize the inevitably leaked organic matter, making nutrients circulate in a mutualistic system. In this sense we challenge the general belief that marine phototrophs and heterotrophs compete for the same scarce nutrients and niche space, and instead suggest that these organisms more probably benefit from each other because of their different levels of specialization and complementarity within long-term stable-state systems

The Pierre Auger Observatory: Results on Ultra-High Energy Cosmic Rays

The focus of this article is on recent results on ultra-high energy cosmic rays obtained with the Pierre Auger Observatory. The world's largest instrument of this type and its performance are described. The observations presented here include the energy spectrum, the primary particle composition, limits on the fluxes of photons and neutrinos and a discussion of the anisotropic distribution of the arrival directions of the most energetic particles. Finally, plans for the construction of a Northern Auger Observatory in Colorado, USA, are discussed.Comment: Proceedings of the International Workshop on Advances in Cosmic Ray Science, Waseda University, Shinjuku, Tokyo, Japan, March 2008; to be published in the Journal of the Physical Society of Japan (JPSJ) supplemen

Insights into the secondary fraction of the organic aerosol in a Mediterranean urban area: Marseille

A comprehensive aerosol characterization was conducted at Marseille during summer, including organic (OC) and elemental carbon (EC), major ionic species, radiocarbon (¹⁴C), water-soluble OC and HULIS (HUmic LIke Substances), elemental composition and primary and secondary organic markers. This paper is the second paper of a two-part series that uses this dataset to investigate the sources of Organic Aerosol (OA). While the first paper investigates the primary sources (El Haddad et al., 2010), this second paper focuses on the secondary fraction of the organic aerosol. <br><br> In the context of overall OC mass balance, primary OC (POC) contributes on average for only 22% and was dominated by vehicular emissions accounting on average for 17% of OC. As a result, 78% of OC mass cannot be attributed to the major primary sources and remains un-apportioned. Radiocarbon measurements suggest that more than 70% of this fraction is of non-fossil origin, assigned predominantly to biogenic secondary organic carbon (BSOC). Therefore, contributions from three traditional BSOC precursors, isoprene, $\alpha$-pinene and &beta;-caryophyllene, were considered. These were estimated using the ambient concentrations of Secondary Organic Aerosol (SOA) markers from each precursor and laboratory-derived marker mass fraction factors. <br><br> Secondary organic markers derived from isoprene photo-oxidation (ie: 2-methylglyceric acid and 2-methyltetrols) do not exhibit the same temporal trends. This variability was assigned to the influence of NO_x concentration on their formation pathways and to their potential decay by further processing in the atmosphere. The influence of changes in isoprene chemistry on assessment of isoprene SOC contribution was evaluated explicitly. The results suggest a 60-fold variation between the different estimates computed using different isoprene SOC markers, implying that the available profiles do not reflect the actual isoprene SOC composition observed in Marseille. <br><br> Using the marker-based approach, the aggregate contribution from traditional BSOC was estimated at only 4.2% of total OC and was dominated by α-pinene SOC accounting on average for 3.4% of OC. As a result, these estimates underpredict the inexplicably high loadings of OC. This underestimation can be associated with (1) uncertainties underlying the marker-based approach, (2) presence of other SOC precursors and (3) further processing of fresh SOC, as indicated by organosulfates (RSO₄H) and HUmic LIke Substances (HULIS) measurements

THUMP from archaeal tRNA:m(2)(2)G10 methyltransferase, a genuine autonomously folding domain

The tRNA:m(2)(2)G10 methyltransferase of Pyrococus abyssi (PAB1283, a member of COG1041) catalyzes the N(2),N(2)-dimethylation of guanosine at position 10 in tRNA. Boundaries of its THUMP (THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases)—containing N-terminal domain [1–152] and C-terminal catalytic domain [157–329] were assessed by trypsin limited proteolysis. An inter-domain flexible region of at least six residues was revealed. The N-terminal domain was then produced as a standalone protein (THUMPα) and further characterized. This autonomously folded unit exhibits very low affinity for tRNA. Using protein fold-recognition (FR) methods, we identified the similarity between THUMPα and a putative RNA-recognition module observed in the crystal structure of another THUMP-containing protein (ThiI thiolase of Bacillus anthracis). A comparative model of THUMPα structure was generated, which fulfills experimentally defined restraints, i.e. chemical modification of surface exposed residues assessed by mass spectrometry, and identification of an intramolecular disulfide bridge. A model of the whole PAB1283 enzyme docked onto its tRNA(Asp) substrate suggests that the THUMP module specifically takes support on the co-axially stacked helices of T-arm and acceptor stem of tRNA and, together with the catalytic domain, screw-clamp structured tRNA. We propose that this mode of interactions may be common to other THUMP-containing enzymes that specifically modify nucleotides in the 3D-core of tRNA

Fossil AGN jets as ultra high energy particle accelerators

Remnants of AGN jets and their surrounding cocoons leave colossal magnetohydrodynamic (MHD) fossil structures storing total energies ~10^{60} erg. The original active galacic nucleus (AGN) may be dead but the fossil will retain its stable configuration resembling the reversed-field pinch (RFP) encountered in laboratory MHD experiments. In an RFP the longitudinal magnetic field changes direction at a critical distance from the axis, leading to magnetic re-connection there, and to slow decay of the large-scale RFP field. We show that this field decay induces large-scale electric fields which can accelerate cosmic rays with an E^{-2} power-law up to ultra-high energies with a cut-off depending on the fossil parameters. The cut-off is expected to be rigidity dependent, implying the observed composition would change from light to heavy close to the cut-off if one or two nearby AGN fossils dominate. Given that several percent of the universe's volume may house such slowly decaying structures, these fossils may even re-energize ultra-high energy cosmic rays from distant/old sources, offsetting the ``GZK-losses'' due to interactions with photons of the cosmic microwave background radiation and giving evidence of otherwise undetectable fossils. In this case the composition would remain light to the highest energies if distant sources or fossils dominated, but otherwise would be mixed. It is hoped the new generation of cosmic ray experiments such as the Pierre Auger Observatory and ultra-high energy neutrino telescopes such as ANITA and lunar Cherenkov experiments will clarify this.Comment: 11 pages, 6 figures, additional references and explanations. Accepted for publication in MNRA