The Mitochondrial Genome of Acropora tenuis (Cnidaria; Scleractinia) Contains a Large Group I Intron and a Candidate Control Region

The complete nucleotide sequence of the mitochondrial genome of the coral Acropora tenuis has been determined. The 18,338 bp A. tenuis mitochondrial genome contains the standard metazoan complement of 13 protein-coding and two rRNA genes, but only the same two tRNA genes (trnM and trnW) as are present in the mtDNA of the sea anemone, Metridium senile. The A. tenuis nad5 gene is interrupted by a large group I intron which contains ten protein-coding genes and rns; M. senile has an intron at the same position but this contains only two protein-coding genes. Despite the large distance (about 11.5 kb) between the 5?-exon and 3?-exon boundaries, the A. tenuis nad5 gene is functional, as we were able to RT-PCR across the predicted intron splice site using total RNA from A. tenuis. As in M. senile, all of the genes in the A. tenuis mt genome have the same orientation, but their organization is completely different in these two zoantharians: The only common gene boundaries are those at each end of the group I intron and between trnM and rnl. Finally, we provide evidence that the rns-cox3 intergenic region in A. tenuis may correspond to the mitochondrial control region of higher animals. This region contains repetitive elements, and has the potential to form secondary structures of the type characteristic of vertebrate D-loops. Comparisons between a wide range of Acropora species showed that a long hairpin predicted in rns-cox3 is phylogenetically conserved, and allowed the tentative identification of conserved sequence blocks.     

Molecular and genetic analysis of factors controlling host range in Agrobacterium tumefaciens

Summary We have investigated the factors which contribute to the host specificity of a tumor inducing plasmid of Agrobacterium, pTiAg162, which confers a narrow host range. Determinants both within the T-DNA and virulence regions contribute to host specificity. Within the T-DNA a defective cytokinin biosynthetic gene limits host range. Nucleotide sequence analysis revealed a large deletion in the 5 coding region of this gene when compared with the homologous gene from the wide host range tumor inducing plasmid, pTiA6. Introduction of the wide host range cytokinin biosynthesis gene into the T-DNA of the limited host range strain expanded the host range and suppressed the rooty morphology of tumors incited by the limited host range strain. Two genes from the virulence region of the wide host range plasmid, designated virA and virC, must also be introduced into the limited host range strain in order to restore a wide host range phenotype. The wide host range strain is avirulent on some cultivars of Vitis plants on which the limited host range strain induces tumors. This avirulence is apparently due to a hypersensitive response in which infected plant cells are killed at the site of inoculation. Mutations within the virC locus of the wide host range plasmid prevented the hypersensitive response and allowed the formation of tumors by the wide host range strain.     

A vehicle for the introduction of transposons into plant-associated pseudomonads

A recombinant plasmid with wide-host-range transfer functions, narrow-host-range replication functions, and carrying a kanamycin-resistant transposon transferred kanamycin resistance to a number of plant-associated pseudomonads. Southern hybridization studies suggest that only a small portion of the plasmid, coinciding with the location of the transposon, is present in the kanamycin-resistant Pseudomonas derivatives. The plasmid sequences appear to be inserted at a number of different sites in the recipient genome. This plasmid can thus be used as a vehicle for the introduction of transposons into some plant-associated pseudomonads and should be useful in both genetic and ecological studies of these bacteria.     

A Recurrent PDGFRB Mutation Causes Familial Infantile Myofibromatosis

Infantile myofibromatosis (IM) is the most common benign fibrous tumor of soft tissues affecting young children. By using whole-exome sequencing, RNA sequencing, and targeted sequencing, we investigated germline and tumor DNA in individuals from four distinct families with the familial form of IM and in five simplex IM cases with no previous family history of this disease. We identified a germline mutation c.1681C>T (p.Arg561Cys) in platelet-derived growth factor receptor β (PDGFRB) in all 11 affected individuals with familial IM, although none of the five individuals with nonfamilial IM had mutations in this gene. We further identified a second heterozygous mutation in PDGFRB in two myofibromas from one of the affected familial cases, indicative of a potential second hit in this gene in the tumor. PDGFR-β promotes growth of mesenchymal cells, including blood vessels and smooth muscles, which are affected in IM. Our findings indicate p.Arg561Cys substitution in PDGFR-β as a cause of the dominant form of this disease. They provide a rationale for further investigations of this specific mutation and gene to assess the benefits of targeted therapies against PDGFR-β in aggressive life-threatening familial forms of the disease.     

Initial soil amendments still affect plant community composition after nine years in succession on a heavy metal contaminated mountainside

Many efforts to restore disturbed landscapes seek to meet ecological goals over timescales from decades to centuries. It is thus crucial to know how different actions available to restoration practitioners may affect ecosystems in the long term, yet few such data exist. Here, we test the effects of seed and compost applications on plant community composition 9 years after their application, by taking advantage of a well‐controlled restoration experiment on a mountainside severely degraded by over 80 years of zinc smelting emissions. We asked whether plots have converged on similar plant communities regardless of initial seed and compost treatments, or if these initial treatments have given rise to lasting differences in whole plant communities or in the richness and abundance of native, exotic, and planted species. We found that compost types significantly affected plant communities 9 years later, but seed mix species composition did not. Observed differences in species richness and vegetative cover were negatively correlated, and both were related to the differences in plant communities associated with different compost types. These observed differences are due primarily to the number and abundance of species not in original seed mixes, of which notably many are native. Our results underscore the importance of soils in shaping the aboveground composition of ecosystems. Differences in soil characteristics can affect plant diversity and cover, which are both common restoration targets. Even in highly polluted and devegetated sites, compost and seed application can reinstate high vegetative cover and allow continued colonization of native species.     

A topological data analytic approach for discovering biophysical signatures in protein dynamics

Identifying structural differences among proteins can be a non-trivial task. When contrasting ensembles of protein structures obtained from molecular dynamics simulations, biologically-relevant features can be easily overshadowed by spurious fluctuations. Here, we present SINATRA Pro, a computational pipeline designed to robustly identify topological differences between two sets of protein structures. Algorithmically, SINATRA Pro works by first taking in the 3D atomic coordinates for each protein snapshot and summarizing them according to their underlying topology. Statistically significant topological features are then projected back onto a user-selected representative protein structure, thus facilitating the visual identification of biophysical signatures of different protein ensembles. We assess the ability of SINATRA Pro to detect minute conformational changes in five independent protein systems of varying complexities. In all test cases, SINATRA Pro identifies known structural features that have been validated by previous experimental and computational studies, as well as novel features that are also likely to be biologically-relevant according to the literature. These results highlight SINATRA Pro as a promising method for facilitating the non-trivial task of pattern recognition in trajectories resulting from molecular dynamics simulations, with substantially increased resolution.     

Environmental heterogeneity and alternative mating tactics in the damselfly Protoneura amatoria

Conditional male mating strategies have been studied extensivelyin relation to male attributes, such as size and resource-holdingpotential, but few studies have considered the effects of environmentalheterogeneity on the use of alternative mating tactics. In somesystems, environmental heterogeneity may be the key to understandingthe evolution and maintenance of such polyphenisms. I examinedthe influence of the physical environment on the use of alternativetactics by the damselfly Protoneura amatoria. Male P. amatoriareversibly use 2 tactics to gain matings: 1) sit and wait inthe canopy for passing females or 2) hover over the water andattempt to grab females that are ovipositing in floating debris.Observations in 3 streams indicated that the use of the hoveringtactic was greater under high-light than low-light conditionsand at higher densities of ovipositing females. The densityof ovipositing females was correlated with both the light conditionsand the availability of oviposition substrate, indicating thatphysical factors exert indirect as well as direct influenceson tactic use. Experimental manipulations showed that both malesand females responded directly to light conditions and suggestedthat males responded directly to the density of ovipositingfemales. These results can be explained largely in terms ofthe cues and constraints inherent in different light environments.Thus, the conditional mating strategy of P. amatoria appearsto have evolved in response to, and been maintained by, fine-scalevariation in the physical environment. These findings are discussedin relation to flight dynamics and predation risk.