Melanization of the alimentary tract in lizardfishes (Teleostei, Aulopiformes, Synodontidae)

Investigating the alimentary tract in several species of lizardfishes (Synodontidae, Teleostei) of the genera Saurida, Synodus and Trachinocephalus, from various sites of their distribution, revealed melanization of the tract wall. This phenomenon was observed in several species of the genus Saurida, but not in the other two genera. This melanization is caused by layers of melanosomes rich in melanin granules and deposited within the connective tissue of the submucosa, between the muscular wall and the muscularis submucosa. From this site this black submucosa extends into the folds of the mucosa. In S. tumbil and S. filamentosa, the entire alimentary tract is black, whereas in S. macrolepis only the stomach is partially or entirely black. This phenomenon and its possible importance are discussed.     

Mutations in ARL2BP,Encoding ADP-Ribosylation-Factor-Like 2 Binding Protein,Cause Autosomal-Recessive Retinitis Pigmentosa

Retinitis pigmentosa (RP) is a genetically heterogeneous retinal degeneration characterized by photoreceptor death, which results in visual failure. Here, we used a combination of homozygosity mapping and exome sequencing to identify mutations in ARL2BP, which encodes an effector protein of the small GTPases ARL2 and ARL3, as causative for autosomal-recessive RP (RP66). In a family affected by RP and situs inversus, a homozygous, splice-acceptor mutation, c.101−1G>C, which alters pre-mRNA splicing of ARLBP2 in blood RNA, was identified. In another family, a homozygous c.134T>G (p.Met45Arg) mutation was identified. In the mouse retina, ARL2BP localized to the basal body and cilium-associated centriole of photoreceptors and the periciliary extension of the inner segment. Depletion of ARL2BP caused cilia shortening. Moreover, depletion of ARL2, but not ARL3, caused displacement of ARL2BP from the basal body, suggesting that ARL2 is vital for recruiting or anchoring ARL2BP at the base of the cilium. This hypothesis is supported by the finding that the p.Met45Arg amino acid substitution reduced binding to ARL2 and caused the loss of ARL2BP localization at the basal body in ciliated nasal epithelial cells. These data demonstrate a role for ARL2BP and ARL2 in primary cilia function and that this role is essential for normal photoreceptor maintenance and function.     

Arrestin binding to calmodulin: a direct interaction between two ubiquitous signaling proteins

Arrestins serve as multi-functional regulators of G-protein coupled receptors, interacting with hundreds of different receptor subtypes and a variety of other signaling proteins. Here we identify calmodulin as a novel arrestin interaction partner using three independent methods in vitro and in cells. Arrestin preferentially binds calcium-loaded calmodulin with a Kd value of approximately 7 microM, which is within range of endogenous calmodulin concentrations. The calmodulin binding site is localized on the concave side of the C-domain and a loop in the center of the arrestin molecule, significantly overlapping with receptor and microtubule-binding sites. Using purified proteins, we found that arrestins sequester calmodulin, preventing its binding to microtubules. Nanomolar affinity of arrestins for their cognate receptors makes calmodulin an ineffective competitor for arrestin binding at relatively high receptor concentrations. The arrestin-calmodulin interaction likely regulates the localization of both proteins and their availability for other interaction partners.     

A simple plant regeneration-ability assay in a range of Lycopersicon species

Plant growth regulator-dependent (PGR-dependent) in vitro shoot organogenesis has been extensively studied in tomato (Lycopersicon esculentum), whereas PGR-independent adventitious shoot organogenesis received marginal attention in L. esculentum and no consideration at all in other Lycopersicon species. In the present study, induction of PGR-independent adventitious shoots was by decapitation of the apex and removal of preexisting shoot meristems of the seedling, and seedling culture on a medium with no PGR supplements. The existence of PGR-independent regeneration-ability was verified in L. esculentum genotypes (high pigment photomorphogenic mutants and wild-type counterparts) and was uncover amongst L. cheesmanii, L. chilense, L. chmielewskii, L. hirsutum, L. parviflorum, L.␣peruvianum and L. pimpinellifolium. Compared to species other than L. esculentum, high pigment photomorphogenic mutants displayed the weakest PGR-independent regeneration-ability. Our results imply that decapitated seedlings cultured on a medium without PGRs can serve as a convenient assay system for genotypic variation in self-controlled, PGR-independent, shoot regeneration-ability in a wide range of Lycopersicon species. Using transverse thin slices of the hypocotyl placed onto a medium supplemented with 0.2 μM zeatin reboside and 0.04 μM IAA, we assessed PGR-mediated shoot regeneration in L. esculentum genotypes. In a given genotype, more plants per seedling were established by PGR-mediated than by PGR-independent regeneration. However, with both modes of organogenesis, only a fraction of shoot buds eventually grew into normal plants, while others developed into abnormal regenerants having no stem. Percentage of stem-deficiency, in a given genotype, was higher in PGR-treated cultures, which indicates that PGRs amplify the formation frequency of imperfect adventitious apical shoot meristems. Unlike L. esculentum, adventitious shoot buds of other Lycopersicon species, induced by wounding seedlings that were not treated with PGRs, rarely formed regenerants lacking a stem.     

Numerical solutions of the Lamm equation. I. Numerical procedure

This paper gives an account, of the numerical technique used to derive results to he presented in future papers of this series.     

A structural model for human dihydrolipoamide dehydrogenase

The hypothesis that dihydrolipoamide dehydrogenases (E₃s) have tertiary structures very similar to that of human glutathione reductase (GR) was tested in detail by three separate criteria: (1) by analyzing each putative secondary structural element for conservation of appropriate polar/nonpolar regions, (2) by detailed comparison of putative active site residues in E₃s with their authentic counterparts in human GR, and (3) by comparison of residues at the putative dimeric interface of the E₃s with the authentic residues in GR. All three criteria are satisfied in a convincing way for the 7 E₃s that were considered, supporting the conclusion that the structural scaffolding and the overall tertiary structure (which determines the location of functional sites and residues) are remarkably similar for the E₃s and for GR. These analyses together with the crystal structures of human erythrocyte GR formed the basis for construction of a molecular model for human E₃. The cofactor FAD and the substrakes NAD and lipoic acid were also included in the model. Unexpectedly, the surface residues in the cleft that holds the lipoamide were found to be highly charged and predominantly acidic, allowing us to predict that the region around the lipoamide in the sub-unit should be basic in nature. The molecular model can be tested by site-directed mutagenesis of residues predicted to be in the dihydrolipoamide acetyltransferase subunit binding cleft. © 1992 Wiley-Liss, Inc.     

The proteomic profile of hereditary inclusion body myopathy

Hereditary inclusion body myopathy (HIBM) is an adult onset, slowly progressive distal and proximal myopathy. Although the causing gene, GNE, encodes for a key enzyme in the biosynthesis of sialic acid, its primary function in HIBM remains unknown. The goal of this study was to unravel new clues on the biological pathways leading to HIBM by proteomic comparison. Muscle cultures and biopsies were analyzed by two dimensional gel electrophoresis (2-DE) and the same biopsy extracts by isobaric tag for relative and absolute quantitation (iTRAQ). Proteins that were differentially expressed in all HIBM specimens versus all controls in each analysis were identified by mass spectrometry. The muscle cultures 2-DE analysis yielded 41 such proteins, while the biopsies 2-DE analysis showed 26 differentially expressed proteins. Out of the 400 proteins identified in biopsies by iTRAQ, 41 showed altered expression. In spite of the different nature of specimens (muscle primary cultures versus muscle biopsies) and of the different methods applied (2D gels versus iTRAQ) the differentially expressed proteins identified in each of the three analyses where related mainly to the same pathways, ubiquitination, stress response and mitochondrial processes, but the most robust cluster (30%) was assigned to cytoskeleton and sarcomere organization. Taken together, these findings indicate a possible novel function of GNE in the muscle filamentous apparatus that could be involved in the pathogenesis of HIBM.     

Dynamic conformational changes in munc18 prevent syntaxin binding

The Sec1/munc18 protein family is essential for vesicle fusion in eukaryotic cells via binding to SNARE proteins. Protein kinase C modulates these interactions by phosphorylating munc18a thereby reducing its affinity to one of the central SNARE members, syntaxin-1a. The established hypothesis is that the reduced affinity of the phosphorylated munc18a to syntaxin-1a is a result of local electrostatic repulsion between the two proteins, which interferes with their compatibility. The current study challenges this paradigm and offers a novel mechanistic explanation by revealing a syntaxin-non-binding conformation of munc18a that is induced by the phosphomimetic mutations. In the present study, using molecular dynamics simulations, we explored the dynamics of the wild-type munc18a versus phosphomimetic mutant munc18a. We focused on the structural changes that occur in the cavity between domains 3a and 1, which serves as the main syntaxin-binding site. The results of the simulations suggest that the free wild-type munc18a exhibits a dynamic equilibrium between several conformations differing in the size of its cavity (the main syntaxin-binding site). The flexibility of the cavity's size might facilitate the binding or unbinding of syntaxin. In silico insertion of phosphomimetic mutations into the munc18a structure induces the formation of a conformation where the syntaxin-binding area is rigid and blocked as a result of interactions between residues located on both sides of the cavity. Therefore, we suggest that the reduced affinity of the phosphomimetic mutant/phosphorylated munc18a is a result of the closed-cavity conformation, which makes syntaxin binding energetically and sterically unfavorable. The current study demonstrates the potential of phosphorylation, an essential biological process, to serve as a driving force for dramatic conformational changes of proteins modulating their affinity to target proteins.