Parallel Retention of Pdx2 Genes in Cartilaginous Fish and Coelacanths

The Pdx1 or Ipf1 gene encodes an important homeodomain-containing protein with key roles in pancreas development and function. Mutations in human PDX1 are implicated in developmental defects and disease of the pancreas. Extensive research, including genome sequencing, has indicated that Pdx1 is the only member of its gene family in mammals, birds, amphibians, and ray-finned fish, and with the exception of teleost fish, this gene forms part of the ParaHox gene cluster along with Gsx1 and Cdx2. The ParaHox cluster, however, is a remnant of a 4-fold genome duplication; the three other ParaHox paralogues lack a Pdx-like gene in all vertebrate genomes examined to date. We have used bacterial artificial chromosome cloning and synteny analysis to show that the ancestor of living jawed vertebrates in fact had more ParaHox genes, including two Pdx genes (Pdx1 and Pdx2). Surprisingly, the two Pdx genes have been retained in parallel in two quite distantly related lineages, the cartilaginous fish (sharks, skates, and chimeras) and the Indonesian coelacanth, Latimeria menadoensis. The Pdx2 gene has been lost independently in ray-finned fish and in tetrapods

Large enhancement of the sub-barrier fusion probability for a halo nucleus

The fusion-fission cross sections of the He-4 + U-238 and He-6 + U-238 systems have been measured, at Louvain-la-Neuve, for energies around and below the Coulomb barrier, using an array of Si detectors surrounding a UF4 target. The data taken with 4He are in good agreement with previous data and with the coupled channel fusion calculation performed with ECIS. The He-6 data show a regular trend with a large enhancement below the barrier which is attributed to the halo structure of the He-6 nucleus

Novel transcripts reveal a complex structure of the human TRKA gene and imply the presence of multiple protein isoforms

Publisher Copyright: © 2015 Luberg et al.Background: Tropomyosin-related kinase A (TRKA) is a nerve growth factor (NGF) receptor that belongs to the tyrosine kinase receptor family. It is critical for the correct development of many types of neurons including pain-mediating sensory neurons and also controls proliferation, differentiation and survival of many neuronal and non-neuronal cells. TRKA (also known as NTRK1) gene is a target of alternative splicing which can result in several different protein isoforms. Presently, three human isoforms (TRKAI, TRKAII and TRKAIII) and two rat isoforms (TRKA L0 and TRKA L1) have been described. Results: We show here that human TRKA gene is overlapped by two genes and spans 67 kb-almost three times the size that has been previously described. Numerous transcription initiation sites from eight different 5' exons and a sophisticated splicing pattern among exons encoding the extracellular part of TRKA receptor indicate that there might be a large variety of alternative protein isoforms. TrkA genes in rat and mouse appear to be considerably shorter, are not overlapped by other genes and display more straightforward splicing patterns. We describe the expression profile of alternatively spliced TRKA transcripts in different tissues of human, rat and mouse, as well as analyze putative endogenous TRKA protein isoforms in human SH-SY5Y and rat PC12 cells. We also characterize a selection of novel putative protein isoforms by portraying their phosphorylation, glycosylation and intracellular localization patterns. Our findings show that an isoform comprising mainly of TRKA kinase domain is capable of entering the nucleus. Conclusions: Results obtained in this study refer to the existence of a multitude of TRKA mRNA and protein isoforms, with some putative proteins possessing very distinct properties.publishersversionPeer reviewe

An efficient multi-time step FEM–SFEM iterative coupling procedure for elastic–acoustic interaction problems

An iterative coupling methodology between the Finite Element Method (FEM) and the Spectral Finite Element Method (SFEM) for the modeling of coupled elastic-acoustic problems in the time domain is presented here. Since the iterative coupling procedure allows the use of a nonconforming mesh at the interface between the subdomains, the difference in the element sizes concerning the FEM and SFEM is handled in a straightforward and efficient manner, thereby retaining all the advantages of the SFEM. By means of the HHT time integration method, controllable numerical damping can be introduced in one of the subdomains, increasing the robustness of the method and improving the accuracy of the results; besides, independent time-step sizes can be considered within each subdomain, resulting in a more efficient algorithm. In this work, a modification in the subcycling procedure is proposed, ensuring not only an efficient and accurate methodology but also avoiding the computation of a relaxation parameter. Numerical simulations are presented in order to illustrate the accuracy and potential of the proposed methodology.CAPES, UFJF, UFSJ, FAPEMIG and CNP