Zebrafish ProVEGF-C Expression, Proteolytic Processing and Inhibitory Effect of Unprocessed ProVEGF-C during Fin Regeneration

BACKGROUND: In zebrafish, vascular endothelial growth factor-C precursor (proVEGF-C) processing occurs within the dibasic motif HSIIRR(214) suggesting the involvement of one or more basic amino acid-specific proprotein convertases (PCs) in this process. In the present study, we examined zebrafish proVEGF-C expression and processing and the effect of unprocessed proVEGF-C on caudal fin regeneration. METHODOLOGY/PRINCIPAL FINDINGS: Cell transfection assays revealed that the cleavage of proVEGF-C, mainly mediated by the proprotein convertases Furin and PC5 and to a less degree by PACE4 and PC7, is abolished by PCs inhibitors or by mutation of its cleavage site (HSIIRR(214) into HSIISS(214)). In vitro, unprocessed proVEGF-C failed to activate its signaling proteins Akt and ERK and to induce cell proliferation. In vivo, following caudal fin amputation, the induction of VEGF-C, Furin and PC5 expression occurs as early as 2 days post-amputation (dpa) with a maximum levels at 4-7 dpa. Using immunofluorescence staining we localized high expression of VEGF-C and the convertases Furin and PC5 surrounding the apical growth zone of the regenerating fin. While expression of wild-type proVEGF-C in this area had no effect, unprocessed proVEGF-C inhibited fin regeneration. CONCLUSIONS/SIGNIFICANCES: Taken together, these data indicate that zebrafish fin regeneration is associated with up-regulation of VEGF-C and the convertases Furin and PC5 and highlight the inhibitory effect of unprocessed proVEGF-C on fin regeneration

Claudin 13, a Member of the Claudin Family Regulated in Mouse Stress Induced Erythropoiesis

Mammals are able to rapidly produce red blood cells in response to stress. The molecular pathways used in this process are important in understanding responses to anaemia in multiple biological settings. Here we characterise the novel gene Claudin 13 (Cldn13), a member of the Claudin family of tight junction proteins using RNA expression, microarray and phylogenetic analysis. We present evidence that Cldn13 appears to be co-ordinately regulated as part of a stress induced erythropoiesis pathway and is a mouse-specific gene mainly expressed in tissues associated with haematopoietic function. CLDN13 phylogenetically groups with its genomic neighbour CLDN4, a conserved tight junction protein with a putative role in epithelial to mesenchymal transition, suggesting a recent duplication event. Mechanisms of mammalian stress erythropoiesis are of importance in anaemic responses and expression microarray analyses demonstrate that Cldn13 is the most abundant Claudin in spleen from mice infected with Trypanosoma congolense. In mice prone to anaemia (C57BL/6), its expression is reduced compared to strains which display a less severe anaemic response (A/J and BALB/c) and is differentially regulated in spleen during disease progression. Genes clustering with Cldn13 on microarrays are key regulators of erythropoiesis (Tal1, Trim10, E2f2), erythrocyte membrane proteins (Rhd and Gypa), associated with red cell volume (Tmcc2) and indirectly associated with erythropoietic pathways (Cdca8, Cdkn2d, Cenpk). Relationships between genes appearing co-ordinately regulated with Cldn13 post-infection suggest new insights into the molecular regulation and pathways involved in stress induced erythropoiesis and suggest a novel, previously unreported role for claudins in correct cell polarisation and protein partitioning prior to erythroblast enucleation

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

Biology is encoded in molecular sequences: deciphering this encoding remains a grand scientific challenge. Functional regions of DNA, RNA, and protein sequences often exhibit characteristic but subtle motifs; thus, computational discovery of motifs in sequences is a fundamental and much-studied problem. However, most current algorithms do not allow for insertions or deletions (indels) within motifs, and the few that do have other limitations. We present a method, GLAM2 (Gapped Local Alignment of Motifs), for discovering motifs allowing indels in a fully general manner, and a companion method GLAM2SCAN for searching sequence databases using such motifs. glam2 is a generalization of the gapless Gibbs sampling algorithm. It re-discovers variable-width protein motifs from the PROSITE database significantly more accurately than the alternative methods PRATT and SAM-T2K. Furthermore, it usefully refines protein motifs from the ELM database: in some cases, the refined motifs make orders of magnitude fewer overpredictions than the original ELM regular expressions. GLAM2 performs respectably on the BAliBASE multiple alignment benchmark, and may be superior to leading multiple alignment methods for “motif-like” alignments with N- and C-terminal extensions. Finally, we demonstrate the use of GLAM2 to discover protein kinase substrate motifs and a gapped DNA motif for the LIM-only transcriptional regulatory complex: using GLAM2SCAN, we identify promising targets for the latter. GLAM2 is especially promising for short protein motifs, and it should improve our ability to identify the protein cleavage sites, interaction sites, post-translational modification attachment sites, etc., that underlie much of biology. It may be equally useful for arbitrarily gapped motifs in DNA and RNA, although fewer examples of such motifs are known at present. GLAM2 is public domain software, available for download at http://bioinformatics.org.au/glam2

Rediscovering ancient glass technologies through the examination of opacifier crystals

International audienceThe aim of the study is to understand how antimonate opacifying crystals were obtained throughout history. Two archaeological glass productions opacified with calcium and lead antimonates are studied in this paper, in order to rediscover ancient opaque glass technologies: Roman mosaic tesserae (1st cent. B.C.-4th cent. A.D.) and Nevers lampworking glass (18th cent. A.D.). The fine examination of crystalline phases and of the vitreous matrix is undertaken using various and complementary techniques. Results are compared with a modern reference production, for which the technological process is well known. We demonstrate that Ca-antimonate opacifiers in Roman mosaic tesserae, as well as in Nevers lampworking glass, were obtained by in situ crystallization. Nevertheless, Roman and Nevers glass would have undergone different firing processes. We propose that the addition of previously synthesized crystals or the use of "anime" could be the process used to obtain Pb-antimonate opacified glass, for both productions studied.We demonstrate that CaO, PbO and Sb2O3 concentrations in the bulk compositions and in the matrices, and their evolution with the crystallinity ratio, offer robust criteria for the distinction of the opacification process used. Also, the different crystalline structures help to provide information on the experimental condition

Characterizing the decay of ancient chinese silk fabrics by microbeam synchrotron radiation diffraction

Scanning synchrotron radiation microdiffraction with an approximately 1 X 1 mu m(2) beam has been used as a novel method for characterizing the decay of several T'ang dynasty (618-907 AD) silk fabrics. The crystalline fraction could be visualized based on beta-sheet 210 reflection intensities, extracted by recursive peak fits from several thousand diffraction patterns recorded during mesh scans. The azimuthal width of the 210 reflection, which is related to the orientation distribution of the crystalline domains within nanofibrils and the macroscopic orientation of the fibers traversed by the beam, was found to be sensitive to the overall state of decay of the fabric. The fine structure of the histogram of azimuthal width was related to the fiber hierarchical microstructure and the fabric morphology. SAXS/WAXS analysis supports the assumption of an initial loss of the random chain network with decay. At a subsequent state of aging, decay proceeds into the nanofibrils and the silk fibers break up into even smaller fractions

Trapping of rare earth-doped nanorods using quasi Bessel beam optical fiber tweezers

International audienceWe demonstrate optical trapping of rare earth-doped NaYF 4 :Er/Yb nanorods of high aspect ratio (length 1.47 µm and diameter 140 nm) using a quasi Bessel beam (QBB) generated by positive axicon optical fiber tips. Propulsion or trapping of the nanorods is demonstrated using either single or dual fiber nano-tip geometries. The optical force exerted on the trapped nanorods, their velocities, and their positions have been analyzed. We determine the trap stiffness for a single nanorod to be 0.12 pN/µm (0.003 pN/µm) by power spectrum analysis and 0.13 pN/µm (0.015 pN/µm) by Boltzmann statistics in the direction perpendicular to (along) the fiber axes for an average optical power of 34 mW. The experiments illustrate the advantage of using a QBB for multiple nanorod trapping over a large distance of up to 30 µm

Lines, spots and trails: a microscopic and mineralogical study of antimonate-opacified glass beads from Lofkënd, Albania

This study focuses on a group of decorated glass beads (twelfth–tenth century BC), belonging to a larger assemblage that was excavated from the prehistoric burial tumulus at Lofkënd, Albania. The bulk glass, opaque glass decorations, and corroded areas were examined and analyzed using variable pressure-scanning electron microscopy with energy-dispersive spectroscopy (VP-SEM-EDS) and X-ray diffraction (XRD). The four glass beads analyzed were made using a plant ash-based alkali and colored with an iron containing chromophore which gave the glass its dark green color. Calcium antimonate was the predominant white opacifier used. Sodium antimonate was found as the opacifier in one sample. Its occurrence is likely accidental and formed due to a low concentration of calcium in the glass. Lead antimonate was identified in one sample and, along with calcium antimonate which was also present, would have acted as an opacifier for the white glass

Active control of light extraction in the near-IR range with sub-wavelength periodic structures

International audienceDue to their narrow reflection peak as well as their compact structure, Guided Mode Resonance Filters (GMRFs) are attractive for many applications. We demonstrate the possibility to modulate the properties of a GMRF by associating with liquid crystals (LCs). By impregnating the diffraction grating with LCs, it is possible to switch between an active and an inactive state depending on the polarization of the light or the applied voltage. In this paper we fabricated and characterized the first diffraction order of LC-impregnated gratings with different periods (0,8 to 5,0μm) and depths (130 to 840nm) to test the ability of liquid crystals to adjust the diffraction properties. Finally, 99.8% of diffraction turn off with a 90° rotation polarization at zero voltage and 90 to 99% by applying a voltage of 30 V according to the grating dimensions. The effect of the grating dimension on the diffraction modulation capacity will be discussed