828 research outputs found
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
Recombinant expression of the fdxD gene of Rhodobacter capsulatus and characterization of its product, a [2Fe-2S] ferredoxin
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 (<sup>14</sup>C), 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.
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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, -pinene and β-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.
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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<sub>x</sub>
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 (RSO<sub>4</sub>H) 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
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