Dystrophin deficiency leads to disturbance of LAMP1-vesicle-associated protein secretion

Duchenne muscular dystrophy results from loss of the protein dystrophin, which links the intracellular cytoskeletal network with the extracellular matrix, but deficiency in this function does not fully explain the onset or progression of the disease. While some intracellular events involved in the degeneration of dystrophin-deficient muscle fibers have been well characterized, changes in their secretory profile are undescribed. To analyze the secretome profile of mdx myotubes independently of myonecrosis, we labeled the proteins of mdx and wild-type myotubes with stable isotope-labeled amino acids (SILAC), finding marked enrichment of vesicular markers in the mdx secretome. These included the lysosomal-associated membrane protein, LAMP1, that co-localized in vesicles with an over-secreted cytoskeletal protein, myosin light chain 1. These LAMP1/MLC1-3-positive vesicles accumulated in the cytosol of mdx myotubes and were secreted into the culture medium in a range of abnormal densities. Restitution of dystrophin expression, by exon skipping, to some 30 % of the control value, partially normalized the secretome profile and the excess LAMP1 accumulation. Together, our results suggest that a lack of dystrophin leads to a general dysregulation of vesicle trafficking. We hypothesize that disturbance of the export of proteins through vesicles occurs before, and then concurrently with, the myonecrotic cascade and contributes chronically to the pathophysiology of DMD, thereby presenting us with a range of new potential therapeutic targets.     

Natural enemy assemblages on native and reseeded grasslands in southwestern Montana: a family-level analysis

We conducted a 2-year survey, using sweep sampling and family-level taxon identification, of the predatory and parasitoid insects on grassland sites in the Gallatin Valley of southwestern Montana. The 25 sites were divided into 4 habitat classes: 2 native habitat types ( Stipa comata/Bouteloua gracilis and Festuca idahoensis/Agropyron spicatum ) and 2 that had been reseeded with either crested wheatgrass ( Agropyron cristatum ) or smooth brome ( Bromus inermis ). Our major goal was to make quantitative comparisons of the abundance of insects among native and reseeded habitats. Of 51 families in 5 insect orders identified, 7 Hymenoptera (Encyrtidae, Braconidae, Ichneumonidae, Pteromalidae, Eulophidae, Scelionidae, and Torymidae), 3 Hemiptera (Lygaeidae, Nabidae, and Reduviidae), 1 Coleoptera (Coccinellidae), and 1 Diptera (Asilidae) comprised 90% of the natural enemies sampled. Ordination analyses provided no strong evidence that the 4 habitat classes contained distinct overall natural enemy communities. However, contiguous native and reseeded sites usually had relatively different overall natural enemy assemblages, suggesting that vegetation was often a more important correlate of community composition than was close spatial proximity of sites. Furthermore, several common families exhibited differential abundances across habitat classes in one or both years. For example, in 1989, Eulophidae, Pteromalidae, and Torymidae were more abundant on native Festuca/Agropyron sites, whereas Encyrtidae and Nabidae were more abundant on Festuca/Agropyron sites reseeded with Bromus inermis . Although analyses of insect assemblages classified to the family level provide somewhat limited information on functional ecological differences among habitats, they allow one to survey a broad array of taxa to identify focal groups for future conservation and land management studies.     

Human gut microbiome viewed across age and geography

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.     

A Cenozoic record of the equatorial Pacific carbonate compensation depth

Atmospheric carbon dioxide concentrations and climate are regulated on geological timescales by the balance between carbon input from volcanic and metamorphic outgassing and its removal by weathering feedbacks; these feedbacks involve the erosion of silicate rocks and organic-carbon-bearing rocks. The integrated effect of these processes is reflected in the calcium carbonate compensation depth, which is the oceanic depth at which calcium carbonate is dissolved. Here we present a carbonate accumulation record that covers the past 53 million years from a depth transect in the equatorial Pacific Ocean. The carbonate compensation depth tracks long-term ocean cooling, deepening from 3.0-3.5?kilometres during the early Cenozoic (approximately 55?million years ago) to 4.6 kilometres at present, consistent with an overall Cenozoic increase in weathering. We find large superimposed fluctuations in carbonate compensation depth during the middle and late Eocene. Using Earth system models, we identify changes in weathering and the mode of organic-carbon delivery as two key processes to explain these large-scale Eocene fluctuations of the carbonate compensation depth.     

Crystal structure of the non-haem iron halogenase SyrB2 in syringomycin biosynthesis

Non-haem Fe(II)/alpha-ketoglutarate (alphaKG)-dependent enzymes harness the reducing power of alphaKG to catalyse oxidative reactions, usually the hydroxylation of unactivated carbons, and are involved in processes such as natural product biosynthesis, the mammalian hypoxic response, and DNA repair. These enzymes couple the decarboxylation of alphaKG with the formation of a high-energy ferryl-oxo intermediate that acts as a hydrogen-abstracting species. All previously structurally characterized mononuclear iron enzymes contain a 2-His, 1-carboxylate motif that coordinates the iron. The two histidines and one carboxylate, known as the 'facial triad', form one triangular side of an octahedral iron coordination geometry. A subclass of mononuclear iron enzymes has been shown to catalyse halogenation reactions, rather than the more typical hydroxylation reaction. SyrB2, a member of this subclass, is a non-haem Fe(II)/alphaKG-dependent halogenase that catalyses the chlorination of threonine in syringomycin E biosynthesis. Here we report the structure of SyrB2 with both a chloride ion and alphaKG coordinated to the iron ion at 1.6 A resolution. This structure reveals a previously unknown coordination of iron, in which the carboxylate ligand of the facial triad is replaced by a chloride ion.     

Predator learning favours mimicry of a less-toxic model in poison frogs

Batesian mimicry--resemblance of a toxic model by an edible mimic--depends on deceiving predators. Mimetic advantage is considered to be dependent on frequency because an increase in mimic abundance leads to breakdown of the warning signal. Where multiple toxic species are available, batesian polymorphism is predicted--that is, mimics diversify to match sympatric models. Despite the prevalence of batesian mimicry in nature, batesian polymorphism is relatively rare. Here we explore a poison-frog mimicry complex comprising two parapatric models and a geographically dimorphic mimic that shows monomorphism where models co-occur. Contrary to classical predictions, our toxicity assays, field observations and spectral reflectances show that mimics resemble the less-toxic and less-abundant model. We examine "stimulus generalization" as a mechanism for this non-intuitive result with learning experiments using naive avian predators and live poison frogs. We find that predators differ in avoidance generalization depending on toxicity of the model, conferring greater protection to mimics resembling the less-toxic model owing to overlap of generalized avoidance curves. Our work supports a mechanism of toxicity-dependent stimulus generalization, revealing an additional solution for batesian mimicry where multiple models coexist.