261 research outputs found
Regulated tissue-specific expression of antagonistic pre-mRNA splicing factors
The SR proteins are essential metazoan pre-mRNA splicing factors that can also influence the selection of alternative 5' splice sites in a concentration-dependent manner. Their activity in alternative splicing in vitro is antagonized by members of the hnRNP A/B family of proteins. The opposite effects of members of these two families of antagonistic splicing factors in vitro and upon overexpression in vivo suggest that changes in their relative levels may be a natural mechanism for the regulation of alternative splicing in vivo. One prediction of this model is that the ratios of these antagonists should vary in different cell types and in other situations in which cellular or viral transcripts are differentially spliced. We raised monoclonal antibodies specific for SFS/ASF and used them to measure the abundance of SFS/ASF protein and its isoforms, its phosphorylation state in vivo and during splicing in vitro, and its association with the spliceosome. SF2/ASF exists predominantly or exclusively in a highly phosphorylated state in vivo in all cell types examined, and unphosphorylated protein was not detectable. Unphosphorylated recombinant SFS/ASF becomes rapidly phosphorylated under splicing conditions in HeLa cell extracts and associates stably with one or more exons of beta-globin pre-mRNA. This interaction appears to persist through the splicing reaction and SF2/ASF remains bound to spliced mRNA. We compared the distribution of SFS/ASF to that of its antagonist, hnRNP Al, in different rat tissues and in immortal and transformed cell lines. We found that the protein levels of these antagonistic splicing factors vary naturally over a very wide range, supporting the notion that changes in the ratio of these proteins can affect alternative splicing of a variety of pre-mRNAs in vivo
Reduction of the model noise in non-linear reconstruction via an efficient calculation of the incident field: application to a 434 MHz Scanner
Microwave tomography has been drastically boosted by the development of efficient reconstruction algorithms based on an iterative solution of the corresponding non-linear inverse problem. The accuracy of the electric field radiated by the antennas of a microwave scanner, inside the target area, has been shown to play a significant role on the overall image quality. Taking into account the antenna environment is of prime importance, especially when operating at low frequency. For instance, the wall of a 60 cm diameter whole-body microwave scanner cannot be neglected at 434 MHz, even when using the immersion technique consisting of putting the target in water. Indeed, at such a frequency, the attenuation introduced by water is not sufficient to avoid multiple reflections on the scanner boundary walls. Consequently, the method of calculating the incident field constitutes a key factor in iteratively solving non-linear inverse problems. The selected technique must accommodate high accuracy while maintaining acceptable calculation complexity. In this paper, three distinct techniques are analysed. They are based on the use of i) free-space and ii) non free-space Green's function, and iii) a FDTD approach. All these techniques have been firstly investigated for their 2D version, being used in 2D reconstruction algorithms. However, the scattered field data are collected in a 3D scanner. For assessing the validity of the previous 2D techniques, their results have been compared to both experimentally and 3D-FDTD results.Peer ReviewedPostprint (published version
Interaction of the v-rel protein with an NF-kappa B DNA binding site
The avian reticuloendotheliosis virus T contains within its genome the oncogene rel. The expression of this gene is responsible for the induction of lymphoid tumors in birds. Recently, the rel gene was shown to be related to the p50 DNA binding subunit of the transcription factor complex NF-kappa B. Binding sites for the NF-kappa B complex are found in the enhancer regions of a number of genes, including the immunoglobulin kappa gene and the human immunodeficiency virus long terminal repeat. In this communication we identify an activity from avian reticuloendotheliosis virus T-transformed avian lymphoid cells that binds in an electrophoretic-mobility-shift assay to an NF-kappa B binding site from the kappa enhancer. This activity contains proteins immunologically related to rel, as detected by polyclonal and monoclonal antibodies directed against v-rel. In a DNA affinity precipitation assay using the NF-kappa B site from the human immunodeficiency virus long terminal repeat, v-rel and several other proteins were identified. These data suggest that oncogenic transformation by v-rel is the result of an altered pattern of gene expression
Systems Codes Rapporteur Part II. MIRA: a Multiphysics Approach to Designing a Fusion Power Plant
Investigation of soil-pile-structure interaction induced by vertical loads and tunnelling
The response of pile groups and piled structures to vertical and tunnelling-induced loads is studied. A two-stage model is adopted that can efficiently consider external actions, greenfield tunnelling movements, superstructure stiffness, ultimate pile shaft and base stresses, pile-soil interactions in uniform or layered soils, and local soil behaviour (as either linear elastic, elastic perfectly-plastic, or nonlinear). Several scenarios are analysed: namely, piles subjected to vertical loads; piles and piled structures that are affected by tunnelling induced ground movements. Model results for piles under vertical loads compare well with field and other analytical models, confirming the robustness of the two-stage model. For tunnelling adjacent to or beneath single piles and pile groups, the impact of layered soils, soil yielding, and hyperbolic transfer mechanisms are shown to be significant, indicating that these aspects should be considered in risk assessments when using simplified models. Analyses of tunnelling beneath free-head piles and piled equivalent beams (describing flexible slabs or stiff buildings) confirm that pile-foundation connections and superstructures decrease tunnelling-induced displacements and deformations at the surface level; however, their action can also worsen the foundation distress with respect to force-moment structural capacity. Considering that the envelopes of fully-flexible and perfectly rigid superstructures will not always be conservative, soil-pile-structure interaction models are recommended for design
MIRA: a Multiphysics Approach to Designing a Fusion Power Plant
Fusion systems codes (SCs) are deployed to produce the baseline of the European fusion power reactor (DEMO) within its conceptual design. A DEMO baseline is mostly defined by a radial/vertical reactor sketch and major reactor parameters, such as fusion and net electric power, magnetic fields, and plasma burn time. A baseline shall also meet a set of prescribed reactor requirements, constraints, and architectural features. According to the conceptual design workflow implemented within the EU-DEMO programme, the output from the SC is transferred to the detailed physics and engineering design codes. Presently-available fusion SCs rely on rather basic physics and engineering models (mostly at zero or one-dimensional level). The design codes, instead, are very detailed but run on much longer computing times. To fill the gap between systems and design codes, the multi-fidelity systems/design tool modular integrated reactor analysis (MIRA)—has been recently developed. MIRA incorporates the physics and the engineering insights of the utmost domains of tokamak reactors and relies on a higher spatial resolution, spanning from 1D up to 3D modelling frames. The MIRA approach has been applied to the DEMO 2017 baseline, generated by the EU reference SC PROCESS and used as input to MIRA. In the paper, the architectural and mathematical insights of the MIRA package are described, along with an EU-DEMO 2017 baseline analysis
Ferredoxin containing bacteriocins suggest a novel mechanism of iron uptake in <i>Pectobacterium spp</i>
In order to kill competing strains of the same or closely related bacterial species, many bacteria produce potent narrow-spectrum protein antibiotics known as bacteriocins. Two sequenced strains of the phytopathogenic bacterium <i>Pectobacterium carotovorum</i> carry genes encoding putative bacteriocins which have seemingly evolved through a recombination event to encode proteins containing an N-terminal domain with extensive similarity to a [2Fe-2S] plant ferredoxin and a C-terminal colicin M-like catalytic domain. In this work, we show that these genes encode active bacteriocins, pectocin M1 and M2, which target strains of <i>Pectobacterium carotovorum</i> and <i>Pectobacterium atrosepticum</i> with increased potency under iron limiting conditions. The activity of pectocin M1 and M2 can be inhibited by the addition of spinach ferredoxin, indicating that the ferredoxin domain of these proteins acts as a receptor binding domain. This effect is not observed with the mammalian ferredoxin protein adrenodoxin, indicating that <i>Pectobacterium spp.</i> carries a specific receptor for plant ferredoxins and that these plant pathogens may acquire iron from the host through the uptake of ferredoxin. In further support of this hypothesis we show that the growth of strains of <i>Pectobacterium carotovorum</i> and <i>atrosepticum</i> that are not sensitive to the cytotoxic effects of pectocin M1 is enhanced in the presence of pectocin M1 and M2 under iron limiting conditions. A similar growth enhancement under iron limiting conditions is observed with spinach ferrodoxin, but not with adrenodoxin. Our data indicate that pectocin M1 and M2 have evolved to parasitise an existing iron uptake pathway by using a ferredoxin-containing receptor binding domain as a Trojan horse to gain entry into susceptible cells
Protein tyrosine phosphatases: the problems of a growing family
Protein tyrosine phosphorylation is now recognized as an important component of the control of many fundamental aspects of cellular function, including growth and differentiation, cell cycle and cytoskeletal integrity. In vivo, the net level of phosphorylation of tyrosyl residues in a target substrate reflects the balance between the competing action of kinases and phosphatases. We are examining physiological roles for protein tyrosine phosphorylation, pursuing the problem from the perspective of the enzymes that catalyze the dephosphorylation reaction, the protein tyrosine phosphatases (PTPases). The PTPases have, until recently, been somewhat neglected relative to the protein tyrosine kinases (PTKs). However, considerable progress has been made in identifying new members of the PTPase family, and it appears that they constitute a novel class of signal transducing molecules that rival the PTKs in their structural diversity and complexity.
One of the principal reasons that the study of PTPases has lagged behind that of the..
Integration issues on tritium management of the European DEMO Breeding Blanket and ancillary systems
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