Mapping disease‐related missense mutations in the immunoglobulin‐like fold domain of lamin A/C reveals novel genotype–phenotype associations for laminopathies

Mutations in A‐type nuclear lamins cause laminopathies. However, genotype–phenotype correlations using the 340 missense mutations within the LMNA gene are unclear: partially due to the limited availability of three‐dimensional structure. The immunoglobulin (Ig)‐like fold domain has been solved, and using bioinformatics tools (including Polyphen‐2, Fold X, Parameter OPtimized Surfaces, and PocketPicker) we characterized 56 missense mutations for position, surface exposure, change in charge and effect on Ig‐like fold stability. We find that 21 of the 27 mutations associated with a skeletal muscle phenotype are distributed throughout the Ig‐like fold, are nonsurface exposed and predicted to disrupt overall stability of the Ig‐like fold domain. Intriguingly, the remaining 6 mutations clustered, had higher surface exposure, and did not affect stability. The majority of 9 lipodystrophy or 10 premature aging syndrome mutations also did not disrupt Ig‐like fold domain stability and were surface exposed and clustered in distinct regions that overlap predicted binding pockets. Although buried, the 10 cardiac mutations had no other consistent properties. Finally, most lipodystrophy and premature aging mutations resulted in a ‐1 net charge change, whereas skeletal muscle mutations caused no consistent net charge changes. Since premature aging, lipodystrophy and the subset of 6 skeletal muscle mutations cluster tightly in distinct, charged regions, they likely affect lamin A/C –protein/DNA/RNA interactions: providing a consistent genotype–phenotype relationship for mutations in this domain. Thus, this subgroup of skeletal muscle laminopathies that we term the ‘Skeletal muscle cluster’, may have a distinct pathological mechanism. These novel associations refine the ability to predict clinical features caused by certain LMNA missense mutations. Proteins 2014; 82:904–915. © 2013 Wiley Periodicals, Inc.     

Defective growth in vitro of Duchenne muscular dystrophy myoblasts: The molecular and biochemical basis

As the molecular basis of Duchenne Muscular Dystrophy (DMD) was being discovered, increasing focus was placed on the mechanisms of progressive failure of myoregeneration. In this study, we propose a pathogenesis model for DMD, where an autocrine growth factor release of TGF‐β1—from necrotic myofibers—could contribute to the increasing loss of muscle regeneration. In fact, we report evidence that DMD myoblasts reduce their proliferation rate, in time and later cultures; in connection with this, we observed TGF‐β1 increase in conditioned media of DMD myoblasts, able to control the myoblast growth by reducing fusion and differentiation of DMD satellite cells. J. Cell. Biochem. 76:118–132, 1999. © 1999 Wiley‐Liss, Inc.     

M13 endopeptidases: New conserved motifs correlated with structure,and simultaneous phylogenetic occurrence of PHEX and the bony fish

M13 endopeptidase alignments have focused mainly on mammalian sequences and on the active site region defining the catalytic sequence signatures. Aligning all available M13 from bacteria to human on a full-length basis, we have performed a sequence analysis. This enabled us to highlight the origin and function of the M13 PHEX subtype family endopeptidase (phosphate regulating gene with homologies to endopeptidases on the X chromosome). New evolutionary conserved regions in both prokaryotes and eukaryotes have been detected and eukaryotic-specific regions clearly delineated. Using the recently solved neprilysin structure, we have observed that all new motifs, except one, localize in the spatial vicinity of the previously reported catalytic signatures. Interestingly, a highly hydrophobic pocket containing three newly reported motifs is centered by the C-terminal tryptophan residue. Extensive M13 searches in complete and in progress higher eukaryotic genomes have lead to the identification of Danio rerio as the simplest organism having PHEX. Finally, the human PHEX substrate, the parathyroid hormone-related peptide, PTHrP(107-139), is absent in bony fish: this suggests the existence of further PHEX substrates common to both bony fishes and higher vertebrates.     

Influence of (hydroxymethyl)pyridine and pyridine-carboxylic acids, in trans-position to the isopropylamine and amine ligands, on the cytotoxicity of platinum complexes

trans-Pt(II) Complexes with aliphatic amines and planar amines such as (hydroxymethyl)pyridines, and pyridine-3- and pyridine-4-carboxylic acids were synthesized and screened for their potential cytotoxic activity in different cancer cell lines used at the NCI for in vitro screens, i.e., MCF7, NCIH460, and SF268. The complexes studied were designed to differ in geometrical parameters such as the position of the phenyl-group substituents and the nature of the substituents themselves for gathering information about the structure-activity relationships in the trans-complexes. The variation of the substituents turns to be crucial for their biological activity, as both pyridine-3- and pyridine-4-carboxylic acids in trans-position to both amine and isopropylamine ligands provided complexes which displayed no specificity toward any type of cell tested, while (hydroxymethyl)pyridine in trans-position to isopropylamine ligands led to complexes that were clearly more effective against the cell lines tested.     

Inbreeding depression in an insect with maternal care: influences of family interactions,life stage and offspring sex

Although inbreeding is commonly known to depress individual fitness, the severity of inbreeding depression varies considerably across species. Among the factors contributing to this variation, family interactions, life stage and sex of offspring have been proposed, but their joint influence on inbreeding depression remains poorly understood. Here, we demonstrate that these three factors jointly shape inbreeding depression in the European earwig, Forficula auricularia. Using a series of cross‐breeding, split‐clutch and brood size manipulation experiments conducted over two generations, we first showed that sib mating (leading to inbred offspring) did not influence the reproductive success of earwig parents. Second, the presence of tending mothers and the strength of sibling competition (i.e. brood size) did not influence the expression of inbreeding depression in the inbred offspring. By contrast, our results revealed that inbreeding dramatically depressed the reproductive success of inbred adult male offspring, but only had little effect on the reproductive success of inbred adult female offspring. Overall, this study demonstrates limited effects of family interactions on inbreeding depression in this species and emphasizes the importance of disentangling effects of sib mating early and late during development to better understand the evolution of mating systems and population dynamics.     

Historical biogeography of the coffee family (Rubiaceae,Gentianales) in Madagascar: case studies from the tribes Knoxieae,Naucleeae, Paederieae and Vanguerieae

Aim In Madagascar the family Rubiaceae includes an estimated 650 species representing 95 genera. As many as 98% of the species and 30% of the genera are endemic. Several factors make the Rubiaceae a model system for developing an understanding of the origins of the Malagasy flora. Ancestral area distributions are explicitly reconstructed for four tribes (Knoxieae, Naucleeae, Paederieae and Vanguerieae) with the aim of understanding how many times, and from where, these groups have originated in Madagascar. Location Indian Ocean Basin, with a focus on Madagascar. Methods Bayesian phylogenetic analyses are conducted on the four tribes. The results are used for reconstructing ancestral areas using dispersal–vicariance analyses. Phylogenetic uncertainties in the reconstructions are accounted for by conducting all analyses on the posterior distribution from the analyses. Results Altogether, 11 arrivals in Madagascar (one in Paederieae, five in Knoxieae, three in Vanguerieae, and two in Naucleeae) are reconstructed. The most common pattern is a dispersal event (followed by vicariance) from Eastern Tropical Africa. The Naucleeae and Paederieae in Madagascar differ and originate from Asia. Numerous out‐of‐Madagascar dispersals, mainly in the dioecious Vanguerieae, are reconstructed. Main conclusions The four tribes arrived several times in Madagascar via dispersal events from Eastern Tropical Africa, Southern Africa and Tropical Asia. The presence of monophyletic groups that include a number of species only found in Madagascar indicates that much endemism in the tribes results from speciation events occurring well after their arrival in Madagascar. Madagascar is the source of origin for almost all Rubiaceae found on the neighbouring islands of the Comoros, Mascarenes and Seychelles.     

Caenorhabditis elegans in the study of SMN-interacting proteins: a role for SMI-1, an orthologue of human Gemin2 and the identification of novel components of the SMN complex

Spinal muscular atrophy is a common neuromuscular disorder caused by mutations in the survival motor neuron (SMN) gene. In mammals, SMN is tightly associated with Gemin2. To gain further insight into the functions of SMN and Gemin2, we have cloned and sequenced smi-1 (Survival of Motor neuron-Interacting protein 1), a C. elegans homologue of the human Gemin2 gene. We show that the SMI-1 expression pattern and RNA interference phenotype show considerable overlap with that previously reported for SMN-1. Finally, we demonstrate that the SMN-1 and SMI-1 proteins directly interact. Having demonstrated the utility of the C. elegans genetic model for investigating genes encoding SMN-interacting proteins, we have undertaken a yeast two-hybrid screen of a C. elegans cDNA library to identify novel proteins that interact with SMN-1. We show the direct interaction of SMN-1 with nine novel proteins, several of which may be involved in RNA metabolism.     

Characterization of sarcolemma and sarcoplasmic reticulum isolated from skeletal muscle of the freeze tolerant wood frog, Rana sylvatica: the beta(2)-adrenergic receptor and calcium transport systems in control, frozen and thawed states

In freeze tolerant wood frog Rana sylvatica, the freeze-induced liberation of glucose plays a critical role in survival in response to sub-zero temperature exposure. We have shown that the glycaemic response is linked to selective changes in the expression of hepatic adrenergic receptors through which catecholamines act to produce their hepatic glycogenolytic effects. The purpose of the present study was to determine if skeletal muscle, another catecholamine-sensitive tissue with glycogenolytic potential, displayed similar or different changes. In order to achieve these objectives, skeletal muscle derived from Rana sylvatica was studied in control, frozen and thawed states. In isolated sarcolemmal fractions, freezing effected an 88% decrease in beta(2)-adrenergic receptor expression but was without effect on the calcium pump; while thawing resulted in a recovery of the beta(2)-adrenergic receptor to 60% of control levels and a 2.4-fold increase in calcium transport. In isolated sarcoplasmic reticular fractions, freezing effected a 52% decrease in calcium binding and a 92% decrease in oxalate-stimulated calcium uptake; while thawing elicited partial normalization to control levels to 70% with respect to calcium binding and to 47% with respect to calcium uptake. Freezing and thawing were associated with increases and decreases, receptively, in blood glucose levels but were without effect on skeletal muscle glycogen content. Thus these muscle changes in Rana sylvatica in freezing and thawing are not linked to glycogen breakdown, are different from those previously seen in liver, and may provide a role in recovery of muscle function during thawing by protecting glycogen stores for contraction and maximizing extracellular calcium for excitation-contraction coupling in the frozen state. The involvement of thyroid hormone in triggering these muscle changes is discussed.     

Cofactor‐binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle,cavity, and fold space

Small molecules are recognized in protein‐binding pockets through surface‐exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein–ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise tounexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein–cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein‐binding pockets, and the local folding patterns next to the cofactor‐binding site. State‐of‐the‐art clustering techniques have been applied to group the different protein–cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process. Proteins 2012. © 2011 Wiley Periodicals, Inc.     

Upper Campanian–Maastrichtian chronostratigraphy of the Skælskør‐1 core,Denmark: correlation at the basinal and global scale and implications for changes in sea‐surface temperatures

The lithostratigraphy, calcareous nannofossil biostratigraphy, carbon‐ and oxygen‐isotope stratigraphy and gamma‐ray profile are presented for the Skælskør‐1 core, eastern Denmark. The correlation of carbon isotopes to Gubbio (Italy) and ODP Site 762C (Indian Ocean) provides the chronostratigrahical framework of the core through a tie to magnetostratigraphy. Two new carbon‐isotope excursions are defined for the uppermost Maastrichtian of the core and prove useful for long‐distance correlation. Twenty stratigraphic tie‐points are used for correlation of the upper Campanian–Maastrichtian interval by combining carbon‐isotope and gamma‐ray variations. Significant dissimilarities in the gamma‐ray profiles of the Danish Basin cores preclude the sole use of this tool for basin‐scale correlations. Bulk oxygen‐isotopes and semi‐quantitative abundance changes in the warm‐water calcareous nannofossil Watznaueria barnesiae and the cool‐water Kamptnerius magnificus highlight the following past changes in sea‐surface temperatures (SSTs): relatively warm late Campanian SSTs, cooling across the Campanian–Maastrichtian boundary and through the early Maastrichtian, warming across the early–late Maastrichtian transition, cooling in the late Maastrichtian, intense warming in the latest Maastrichtian chron C29r, followed by a very short episode of cooling immediately before the Cretaceous–Palaeogene boundary. The late Campanian–Maastrichtian evolution in sea water temperatures inferred from the Danish Basin is similar to that delineated at tropical latitude oceanic sites.