Persistence and photochemical decay of springtime total ozone anomalies in the Canadian Middle Atmosphere Model

The persistence and decay of springtime total ozone anomalies over the entire extratropics (midlatitudes plus polar regions) is analysed using results from the Canadian Middle Atmosphere Model (CMAM), a comprehensive chemistry-climate model. As in the observations, interannual anomalies established through winter and spring persist with very high correlation coefficients (above 0.8) through summer until early autumn, while decaying in amplitude as a result of photochemical relaxation in the quiescent summertime stratosphere. The persistence and decay of the ozone anomalies in CMAM agrees extremely well with observations, even in the southern hemisphere when the model is run without heterogeneous chemistry (in which case there is no ozone hole and the seasonal cycle of ozone is quite different from observations). However in a version of CMAM with strong vertical diffusion, the northern hemisphere anomalies decay far too rapidly compared to observations. This shows that ozone anomaly persistence and decay does not depend on how the springtime anomalies are created or on their magnitude, but reflects the transport and photochemical decay in the model. The seasonality of the long-term trends over the entire extratropics is found to be explained by the persistence of the interannual anomalies, as in the observations, demonstrating that summertime ozone trends reflect winter/spring trends rather than any change in summertime ozone chemistry. However this mechanism fails in the northern hemisphere midlatitudes because of the relatively large impact, compared to observations, of the CMAM polar anomalies. As in the southern hemisphere, the influence of polar ozone loss in CMAM increases the midlatitude summertime loss, leading to a relatively weak seasonal dependence of ozone loss in the Northern Hemisphere compared to the observations.

Carpenter Syndrome: Extended RAB23 Mutation Spectrum and Analysis of Nonsense-mediated mRNA Decay

Carpenter syndrome, a rare autosomal recessive disorder characterized by a combination of craniosynostosis, polysyndactyly, obesity, and other congenital malformations, is caused by mutations in RAB23, encoding a member of the Rab-family of small GTPases. In 15 out of 16 families previously reported, the disease was caused by homozygosity for truncating mutations, and currently only a single missense mutation has been identified in a compound heterozygote. Here, we describe a further 8 independent families comprising 10 affected individuals with Carpenter syndrome, who were positive for mutations in RAB23. We report the first homozygous missense mutation and in-frame deletion, highlighting key residues for RAB23 function, as well as the first splice-site mutation. Multi-suture craniosynostosis and polysyndactyly have been present in all patients described to date, and abnormal external genitalia have been universal in boys. High birth weight was not evident in the current group of patients, but further evidence for laterality defects is reported. No genotype-phenotype correlations are apparent. We provide experimental evidence that transcripts encoding truncating mutations are subject to nonsense-mediated decay, and that this plays an important role in the pathogenesis of many RAB23 mutations. These observations refine the phenotypic spectrum of Carpenter syndrome and offer new insights into molecular pathogenesis. (C) 2011 Wiley-Liss, Inc.

Instant preheating mechanism and ultrahigh energy cosmic rays

Top-down models assume that the still unexplained ultrahigh energy cosmic rays (UHECR's) are the decay products of superheavy particles. Such particles may have been produced by one of the post-inflationary reheating mechanisms and may account for a fraction of the cold dark matter. In this paper, we assess the phenomenological applicability of the simplest instant preheating framework not to describe a reheating process, but as a mechanism to generate relic supermassive particles as possible sources of UHECR's. We use cosmic ray flux and cold dark matter observational data to constrain the parameters of the model.

Stickiness in a bouncer model: A slowing mechanism for Fermi acceleration

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Mechanism of the Yb-Er energy transfer in fluorozirconate glass

The mechanism of the Yb(3+)-->Er(3+) energy transfer as a function of the donor and the acceptor concentration was investigated in Yb(3+)-Er(3+) codoped fluorozirconate glass. The luminescence decay curves were measured and analyzed by monitoring the Er(3+)((4)I(11/2)) fluorescence induced by the Yb(3+)((2)F(5/2)) excitation. The energy transfer microparameters were determined and used to estimate the Yb-Er transfer rate of an energy transfer process assisted by excitation migration among donors state (diffusion model). The experimental transfer rates were determined from the best fitting of the acceptor luminescence decay obtained using a theoretical approach analog to that one used in the Inokuti-Hirayama model for the donor luminescence decay. The obtained values of transfer parameter gamma [gamma(exp)] were always higher than that predicted by the Inokuti-Hirayama model. Also, the experimental transfer rate, gamma(2)(exp), was observed to be higher than the transfer rate predicted by the migration model. Assuming a random distribution among excited donors at the initial time (t=0) and that a fast excitation migration, which occurs in a very short time (t

Relativistic three-body model for final state interaction in D+ → K-π+π+ decay

A challenge in mesonic three-body decays of heavy mesons is to quantify the contribution of re-scattering between the final mesons. D decays have the unique feature that make them a key to light meson spectroscopy, in particular to access the Kn S-wave phase-shifts. We built a relativis-tic three-body model for the final state interaction in D+ → K -π+π+ decay based on the ladder approximation of the Bethe-Salpeter equation projected on the light-front. The decay amplitude is separated in a smooth term, given by the direct partonic decay amplitude, and a three-body fully interacting contribution, that is factorized in the standard two-meson resonant amplitude times a reduced complex amplitude that carries the effect of the three-body rescattering mechanism. The off-shell reduced amplitude is a solution of an inhomogeneous Faddeev type three-dimensional integral equation, that includes only isospin 1/2 K -π+ interaction in the S-wave channel. The elastic K-π+ scattering amplitude is parameterized according to the LASS data[1]. The integral equation is solved numerically and preliminary results are presented and compared to the experimental data from the E791 Collaboration[2, 3] and FOCUS Collaboration[4, 5].

Decay of photo-induced conductivity in Sb-doped SnO2 thin films, using monochromatic light of about bandgap energy

Doping tin dioxide (SnO2) with pentavalent Sb5+ ions leads to an enhancement in the electrical conductivity of this material, because Sb5+ substitutes Sn4+ in the matrix, promoting an electronic density increase in the conduction band, due to the donor-like nature of the doping atom. Results of computational simulation, based on the Density Functional Theory (DFT), of SnO2:4%Sb and SnO2:8%Sb show that the bandgap magnitude is strongly affected by the doping concentration, because the energy value found for 4 at%Sb and 8 at%Sb was 3.27 eV and 3.13 eV, respectively, whereas the well known value for undoped SnO2 is about 3.6 eV. Sb-doped SnO2 thin films were obtained by the sol-gel-dip-coating technique. The samples were submitted to excitation with below theoretical bandgap light (450 nm), as well as above bandgap light (266 nm) at low temperature, and a temperature-dependent increase in the conductivity is observed. Besides, an unusual temperature and time dependent decay when the illumination is removed is also observed, where the decay time is slower for higher temperatures. This decay is modeled by considering thermally activated cross section of trapping centers, and the hypothesis of grain boundary scattering as the dominant mechanism for electronic mobility. © 2012 Elsevier B.V. All rights reserved.

Separation of particles leading either to decay or unlimited growth of energy in a driven stadium-like billiard

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Medium effects in the pion-pole mechanism [gamma gamma ->pi(0)->nu(R)(nu)over-bar(L)(nu(L)(nu)over-bar(R))] of neutron star cooling

Nuclear medium effects in the neutrino cooling of neutron stars through the reaction channel γγ→π0 →ν Rν̄L(νLν̄R) are incorporated. Throughout the paper we discuss different possibilities of right-handed neutrinos, massive left-handed neutrinos, and standard massless left-handed neutrinos (reaction is then allowed only with medium modified vertices). It is demonstrated that multiparticle effects suppress the rate of this reaction channel in the dense hadron matter by 6-7 orders of magnitude that does not allow to decrease existing experimental upper limit on the corresponding π0νν̄ coupling. Other possibilities of the manifestation of the given reaction channel in different physical situations, e.g., in the quark color superconducting cores of the most massive neutron stars, are also discussed. We demonstrate that in the color-flavor-locked superconducting phase for temperatures T≲ 0.1-10 MeV (depending on the effective pion mass and the decay width) the process is feasibly the most efficient neutrino cooling process, although the absolute value of the reaction rate is rather small.

Stickiness in a bouncer model: A slowing mechanism for Fermi acceleration

Some phase space transport properties for a conservative bouncer model are studied. The dynamics of the model is described by using a two-dimensional measure preserving mapping for the variables' velocity and time. The system is characterized by a control parameter epsilon and experiences a transition from integrable (epsilon = 0) to nonintegrable (epsilon not equal 0). For small values of epsilon, the phase space shows a mixed structure where periodic islands, chaotic seas, and invariant tori coexist. As the parameter epsilon increases and reaches a critical value epsilon(c), all invariant tori are destroyed and the chaotic sea spreads over the phase space, leading the particle to diffuse in velocity and experience Fermi acceleration (unlimited energy growth). During the dynamics the particle can be temporarily trapped near periodic and stable regions. We use the finite time Lyapunov exponent to visualize this effect. The survival probability was used to obtain some of the transport properties in the phase space. For large epsilon, the survival probability decays exponentially when it turns into a slower decay as the control parameter epsilon is reduced. The slower decay is related to trapping dynamics, slowing the Fermi Acceleration, i.e., unbounded growth of the velocity.

Ago-TNRC6 triggers microRNA-mediated decay by promoting two deadenylation steps.

MicroRNAs (miRNAs) silence the expression of their mRNA targets mainly by promoting mRNA decay. The mechanism, kinetics and participating enzymes for miRNA-mediated decay in mammalian cells remain largely unclear. Combining the approaches of transcriptional pulsing, RNA tethering, overexpression of dominant-negative mutants, and siRNA-mediated gene knockdown, we show that let-7 miRNA-induced silencing complexes (miRISCs), which contain the proteins Argonaute (Ago) and TNRC6 (also known as GW182), trigger very rapid mRNA decay by inducing accelerated biphasic deadenylation mediated by Pan2-Pan3 and Ccr4-Caf1 deadenylase complexes followed by Dcp1-Dcp2 complex-directed decapping in mammalian cells. When tethered to mRNAs, all four human Ago proteins and TNRC6C are each able to recapitulate the two deadenylation steps. Two conserved human Ago2 phenylalanines (Phe470 and Phe505) are critical for recruiting TNRC6 to promote deadenylation. These findings indicate that promotion of biphasic deadenylation to trigger mRNA decay is an intrinsic property of miRISCs.

Mechanistic aspects of mRNA targeting for nonsense-mediated mRNA decay in human cells

The nonsense-mediated mRNA decay (NMD) pathway is best known as a translation-coupled quality control system that recognizes and degrades aberrant mRNAs with ORF-truncating premature termination codons (PTCs), but a more general role of NMD in posttranscriptional regulation of gene expression is indicated by transcriptome-wide mRNA profilings that identified a plethora of physiological mRNAs as NMD substrates. We try to decipher the mechanism of mRNA targeting to the NMD pathway in human cells. Recruitment of the conserved RNA-binding helicase UPF1 to target mRNAs has been reported to occur through interaction with release factors at terminating ribosomes, but evidence for translation-independent interaction of UPF1 with the 3’ untranslated region (UTR) of mRNAs has also been reported. We have transcriptome-wide determined the UPF1 binding sites by individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) in human cells, untreated or after inhibiting translation. We detected a strongly enriched association of UPF1 with 3’ UTRs in undisturbed, translationally active cells. After translation inhibition, a significant increase in UPF1 binding to coding sequence (CDS) was observed, indicating that UPF1 binds RNA before translation and gets displaced from the CDS by translating ribosomes. This suggests that the decision to trigger NMD occurs after association of UPF1 with mRNA, presumably through activation of RNA-bound UPF1 by aberrant translation termination. In a second recent study, we re-visited the reported restriction of NMD in mammals to the ‘pioneer round of translation’, i.e. to cap-binding complex (CBC)-bound mRNAs. The limitation of mammalian NMD to early rounds of translation would indicate a – from an evolutionary perspective – unexpected mechanistic difference to NMD in yeast and plants, where PTC-containing mRNAs seem to be available to NMD at each round of translation. In contrast to previous reports, our comparison of decay kinetics of two NMD reporter genes in mRNA fractions bound to either CBC or the eukaryotic initiation factor 4E (eIF4E) in human cells revealed that NMD destabilizes eIF4E-bound transcripts as efficiently as those associated with CBC. These results corroborate an emerging unified model for NMD substrate recognition, according to which NMD can ensue at every aberrant translation termination event.

eIF4E-bound mRNPs are substrates for nonsense-mediated mRNA decay in mammalian cells

Eukaryotic mRNAs with premature translation-termination codons (PTCs) are recognized and degraded by a process referred to as nonsense-mediated mRNA decay (NMD). The evolutionary conservation of the core NMD factors UPF1, UPF2 and UPF3 would imply a similar basic mechanism of PTC recognition in all eukaryotes. However, unlike NMD in yeast, which targets PTC-containing mRNAs irrespectively of whether their 5' cap is bound by the cap-binding complex (CBC) or by the eukaryotic initiation factor 4E (eIF4E), mammalian NMD has been claimed to be restricted to CBC-bound mRNAs during the pioneer round of translation. In our recent study we compared decay kinetics of two NMD reporter systems in mRNA fractions bound to either CBC or eIF4E in human cells. Our findings reveal that NMD destabilizes eIF4E bound transcripts as efficiently as those associated with CBC. These results corroborate an emerging unified model for NMD substrate recognition, according to which NMD can ensue at every aberrant translation termination event. Additionally, our results indicate that the closed loop structure of mRNA forms only after the replacement of CBC with eIF4E at the 5' cap.

eIF4E‐bound mRNPs are substrates for nonsense‐mediated mRNA decay in mammalian cells

Eukaryotic mRNAs with premature translation-termination codons (PTCs) are recognized and degraded by a process referred to as nonsense-mediated mRNA decay (NMD). The evolutionary conservation of the core NMD factors UPF1, UPF2 and UPF3 would imply a similar basic mechanism of PTC recognition in all eukaryotes. However, unlike NMD in yeast, which targets PTC-containing mRNAs irrespectively of whether their 5' cap is bound by the cap-binding complex (CBC) or by the eukaryotic initiation factor 4E (eIF4E), mammalian NMD has been claimed to be restricted to CBC-bound mRNAs during the pioneer round of translation. In our recent study we compared decay kinetics of two NMD reporter systems in mRNA fractions bound to either CBC or eIF4E in human cells. Our findings reveal that NMD destabilizes eIF4E bound transcripts as efficiently as those associated with CBC. These results corroborate an emerging unified model for NMD substrate recognition, according to which NMD can ensue at every aberrant translation termination event. Additionally, our results indicate that the closed loop structure of mRNA forms only after the replacement of CBC with eIF4E at the 5' cap.

eIF4E-bound mRNPs are substrates for nonsense-mediated mRNA decay in mammalian cells

Eukaryotic mRNAs with premature translation-termination codons (PTCs) are recognized and degraded by a process referred to as nonsense-mediated mRNA decay (NMD). The evolutionary conservation of the core NMD factors UPF1, UPF2 and UPF3 would imply a similar basic mechanism of PTC recognition in all eukaryotes. However, unlike NMD in yeast, which targets PTC-containing mRNAs irrespectively of whether their 5' cap is bound by the cap-binding complex (CBC) or by the eukaryotic initiation factor 4E (eIF4E), mammalian NMD has been claimed to be restricted to CBC-bound mRNAs during the pioneer round of translation. In our recent study we compared decay kinetics of two NMD reporter systems in mRNA fractions bound to either CBC or eIF4E in human cells. Our findings reveal that NMD destabilizes eIF4E bound transcripts as efficiently as those associated with CBC. These results corroborate an emerging unified model for NMD substrate recognition, according to which NMD can ensue at every aberrant translation termination event. Additionally, our results indicate that the closed loop structure of mRNA forms only after the replacement of CBC with eIF4E at the 5' cap.