157 research outputs found
Modeling multidimensional effects in the propagation of radiative shocks
Radiative shocks (also called supercritical shocks) are high Mach number shock waves that photoionize the medium ahead of the shock front and give rise to a radiative precursor. They are generated in the laboratory using high-energy or high-power lasers and are frequently present in a wide range of astronomical objects. Their modelisation in one dimension has been the subject of numerous studies, but generalization to three dimensions is not straightforward. We calculate analyticaly the absorption of radiation in a grey uniform cylinder and show how it decreases with , the product of the opacity and of the cylinder radius . Simple formulas, whose validity range increases when diminishes, are derived for the radiation field on the axis of symmetry. Numerical calculations in three dimensions of the radiative energy density, flux and pressure created by a stationary shock wave show how the radiation decreases whith . Finally, the bidimensional structures of both the precursor and the radiation field are calculated with time-dependent radiation hydrodynamics numerical simulations and the influence of two-dimensional effects on the electron density, the temperature, the shock velocity and the shock geometry are exhibited. These simulations show how the radiative precursor shortens, cools and slows down when is decreased
The transcriptional cycle of HIV-1 in real-time and live cells
RNA polymerase II ( RNAPII) is a fundamental enzyme, but few studies have analyzed its activity in living cells. Using human immunodeficiency virus ( HIV) type 1 reporters, we study real- time messenger RNA ( mRNA) biogenesis by photobleaching nascent RNAs and RNAPII at specific transcription sites. Through modeling, the use of mutant polymerases, drugs, and quantitative in situ hybridization, we investigate the kinetics of the HIV- 1 transcription cycle. Initiation appears efficient because most polymerases demonstrate stable gene association. We calculate an elongation rate of approximately 1.9 kb/ min, and, surprisingly, polymerases remain at transcription sites 2.5 min longer than nascent RNAs. With a total polymerase residency time estimated at 333 s, 114 are assigned to elongation, and 63 are assigned to 3'- end processing and/ or transcript release. However, mRNAs were released seconds after polyadenylation onset, and analysis of polymerase density by chromatin immunoprecipitation suggests that they pause or lose processivity after passing the polyA site. The strengths and limitations of this kinetic approach to analyze mRNA biogenesis in living cells are discussed
Gold/Silica biochips: applications to Surface Plasmon Resonance and fluorescence quenching
We report Gold/Silica biochips for low cost biosensor devices. Firstly, the
study of biochemical interactions on silica by means of Surface Plasmon
Resonance (SPR) is presented. Secondly, Gold/Silica biochips are employed to
reduce the strong quenching that occurs when a fluorophore is close to the gold
surface. Furthermore, the control of the Silica-like thickness allows
optimizing the distance between the metallic surface and the fluorophore in
order to enhance the fluorescent signal. These results represent the first
steps towards highly sensitive, specific and low cost biosensors based, for
example, on Surface Plasmon Coupled Emission (SPCE) techniques
Pseudomonas aeruginosa Expresses a Functional Human Natriuretic Peptide Receptor Ortholog: Involvement in Biofilm Formation
This is the final version of the article. Available from the publisher via the DOI in this record.Considerable evidence exists that bacteria detect eukaryotic communication molecules and modify their virulence accordingly. In previous studies, it has been demonstrated that the increasingly antibiotic-resistant pathogen Pseudomonas aeruginosa can detect the human hormones brain natriuretic peptide (BNP) and C-type natriuretic peptide (CNP) at micromolar concentrations. In response, the bacterium modifies its behavior to adapt to the host physiology, increasing its overall virulence. The possibility of identifying the bacterial sensor for these hormones and interfering with this sensing mechanism offers an exciting opportunity to directly affect the infection process. Here, we show that BNP and CNP strongly decrease P. aeruginosa biofilm formation. Isatin, an antagonist of human natriuretic peptide receptors (NPR), prevents this effect. Furthermore, the human NPR-C receptor agonist cANF(4-23) mimics the effects of natriuretic peptides on P. aeruginosa, while sANP, the NPR-A receptor agonist, appears to be weakly active. We show in silico that NPR-C, a preferential CNP receptor, and the P. aeruginosa protein AmiC have similar three-dimensional (3D) structures and that both CNP and isatin bind to AmiC. We demonstrate that CNP acts as an AmiC agonist, enhancing the expression of the ami operon in P. aeruginosa. Binding of CNP and NPR-C agonists to AmiC was confirmed by microscale thermophoresis. Finally, using an amiC mutant strain, we demonstrated that AmiC is essential for CNP effects on biofilm formation. In conclusion, the AmiC bacterial sensor possesses structural and pharmacological profiles similar to those of the human NPR-C receptor and appears to be a bacterial receptor for human hormones that enables P. aeruginosa to modulate biofilm expression. IMPORTANCE: The bacterium Pseudomonas aeruginosa is a highly dangerous opportunist pathogen for immunocompromised hosts, especially cystic fibrosis patients. The sites of P. aeruginosa infection are varied, with predominance in the human lung, in which bacteria are in contact with host molecular messengers such as hormones. The C-type natriuretic peptide (CNP), a hormone produced by lung cells, has been described as a bacterial virulence enhancer. In this study, we showed that the CNP hormone counteracts P. aeruginosa biofilm formation and we identified the bacterial protein AmiC as the sensor involved in the CNP effects. We showed that AmiC could bind specifically CNP. These results show for the first time that a human hormone could be sensed by bacteria through a specific protein, which is an ortholog of the human receptor NPR-C. The bacterium would be able to modify its lifestyle by favoring virulence factor production while reducing biofilm formation.We thank Magalie Barreau and Olivier Maillot for technical assistance.
We thank Christine Farmer for linguistic insight for the manuscript.
T. Rosay is a recipient of a doctoral fellowship from the French Ministry
of Research (MRE). This work was supported by grants from the
Communauté d’Agglomération d’Evreux, the Conseil Général de l’Eure,
European Union (FEDER no. 31970), the French Association “Vaincre la
Mucoviscidose” and the InterReg IVA PeReNE project
Observation of collapsing radiative shocks in laboratory experiments
This article reports the observation of the dense, collapsed layer produced by a radiative shock in a laboratory experiment. The experiment uses laser irradiation to accelerate a thin layer of solid-density material to above 100 km/s100km∕s, the first to probe such high velocities in a radiative shock. The layer in turn drives a shock wave through a cylindrical volume of Xe gas (at ∼ 6 mg/cm3∼6mg∕cm3). Radiation from the shocked Xe removes enough energy that the shocked layer increases in density and collapses spatially. This type of system is relevant to a number of astrophysical contexts, providing the potential to observe phenomena of interest to astrophysics and to test astrophysical computer codes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87760/2/082901_1.pd
Blockchain and Government Transformation
In today’s digital age, transactions are made increasingly in the
virtual universe. Some do all financial transactions online, but some do not even
want to think about this possibility since the consideration is unreliable. To
make online financial transactions more reliable, many technologies have
already been tested. Since passwords, tokens, physical code generation accessories,
there have been many attempts, being the most elaborate, the blockchain.
Governments, especially in developed countries, often find it difficult to
gain the trust of their citizens, especially when it comes to evidence of service
provision and improvement of existing services. In developing countries,
blockchain requests from governments would be useful in eliminating some
important problems, such as corruption, while ensuring more effective deployment
and distribution of resources. The adoption of such technologies can also
help to facilitate better use of resources. In this paper, we will analyze the impact
of the application of blockchain technology on e-government.2020-2
Online Monitoring of the Osiris Reactor with the Nucifer Neutrino Detector
Originally designed as a new nuclear reactor monitoring device, the Nucifer
detector has successfully detected its first neutrinos. We provide the second
shortest baseline measurement of the reactor neutrino flux. The detection of
electron antineutrinos emitted in the decay chains of the fission products,
combined with reactor core simulations, provides an new tool to assess both the
thermal power and the fissile content of the whole nuclear core and could be
used by the Inter- national Agency for Atomic Energy (IAEA) to enhance the
Safeguards of civil nuclear reactors. Deployed at only 7.2m away from the
compact Osiris research reactor core (70MW) operating at the Saclay research
centre of the French Alternative Energies and Atomic Energy Commission (CEA),
the experiment also exhibits a well-suited configuration to search for a new
short baseline oscillation. We report the first results of the Nucifer
experiment, describing the performances of the 0.85m3 detector remotely
operating at a shallow depth equivalent to 12m of water and under intense
background radiation conditions. Based on 145 (106) days of data with reactor
ON (OFF), leading to the detection of an estimated 40760 electron
antineutrinos, the mean number of detected antineutrinos is 281 +- 7(stat) +-
18(syst) electron antineutrinos/day, in agreement with the prediction 277(23)
electron antineutrinos/day. Due the the large background no conclusive results
on the existence of light sterile neutrinos could be derived, however. As a
first societal application we quantify how antineutrinos could be used for the
Plutonium Management and Disposition Agreement.Comment: 22 pages, 16 figures - Version
Evidence for intron length conservation in a set of mammalian genes associated with embryonic development
<p>Abstract</p> <p>Background</p> <p>We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples of genes that showed the most extreme conservation of total intron content in mammals.</p> <p>Results</p> <p>Gene sets annotated as being involved in pattern specification in the early embryo or containing the homeobox DNA-binding domain, were significantly enriched among genes with highly conserved intron content. We used ancestral sequences reconstructed with probabilistic models that account for insertion and deletion mutations to distinguish insertion and deletion events on lineages leading to human and mouse from their last common ancestor. Using a randomization procedure, we show that genes containing the homeobox domain show less change in intron content than expected, given the number of insertion and deletion events within their introns.</p> <p>Conclusions</p> <p>Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.</p
Modelling Reveals Kinetic Advantages of Co-Transcriptional Splicing
Messenger RNA splicing is an essential and complex process for the removal of intron sequences. Whereas the composition of the splicing machinery is mostly known, the kinetics of splicing, the catalytic activity of splicing factors and the interdependency of transcription, splicing and mRNA 3′ end formation are less well understood. We propose a stochastic model of splicing kinetics that explains data obtained from high-resolution kinetic analyses of transcription, splicing and 3′ end formation during induction of an intron-containing reporter gene in budding yeast. Modelling reveals co-transcriptional splicing to be the most probable and most efficient splicing pathway for the reporter transcripts, due in part to a positive feedback mechanism for co-transcriptional second step splicing. Model comparison is used to assess the alternative representations of reactions. Modelling also indicates the functional coupling of transcription and splicing, because both the rate of initiation of transcription and the probability that step one of splicing occurs co-transcriptionally are reduced, when the second step of splicing is abolished in a mutant reporter
The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing
Kinetic analysis shows that RNA polymerase elongation kinetics are not modulated by co-transcriptional splicing and that post-transcriptional splicing can proceed at the site of transcription without the presence of the polymerase
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