A Genetic Discontinuity in a Continuously Distributed Species: Mitochondrial DNA in the American Oyster, Crassostrea Virginica

Restriction site variation in mitochondrial DNA (mtDNA) of the American oyster (Crassostrea virginica) was surveyed in continuously distributed populations sampled from the Gulf of St. Lawrence, Canada, to Brownsville, Texas. mtDNA clonal diversity was high, with 82 different haplotypes revealed among 212 oysters with 13 endonucleases. The mtDNA clones grouped into two distinct genetic arrays (estimated to differ by about 2.6% in nucleotide sequence) that characterized oysters collected north vs. south of a region on the Atlantic mid-coast of Florida. The population genetic "break" in mtDNA contrasts with previous reports of near uniformity of nuclear (allozyme) allele frequencies throughout the range of the species, but agrees closely with the magnitude and pattern of mtDNA differentiation reported in other estuarine species in the southeastern United States. This concordance of mtDNA phylogenetic pattern across independently evolving species provides strong evidence for vicariant biogeographic processes in initiating intraspecific population structure. The post-Miocene ecological history of the region suggests that reduced precipitation levels in an enlarged Floridian peninsula may have created discontinuities in suitable estuarine habitat for oysters during glacial periods, and that today such population separations are maintained by the combined influence of ecological gradients and oceanic currents on larval dispersal. The results are consistent with the hypothesis that historical vicariant events, in conjunction with contemporary environmental influences on gene flow, can result in genetic discontinuities in continuously distributed species with high dispersal capability.     

Sesquiterpene lactones and a myoinositol from glandular trichomes of Viguiera quinqueremis (Heliantheae; Asteraceae)

The extract of the floral parts of Viguiera quinqueremis afforded, in addition to known compounds, six new sesquiterpene lactones as well as a new myoinositol derivative. All compounds were detected in glandular trichomes which were collected micromechanically from the anther appendages and were analyzed by HPLC. Structure identification was performed by 1H NMR measurements including LC NMR and LC MS experiments.     

Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes

Spliceosomal (pre-mRNA) introns have previously been found in eukaryotic protein-coding genes, in the small nuclear RNAs of some fungi, and in the small- and large-subunit ribosomal DNA genes of a limited number of ascomycetes. How the majority of these introns originate remains an open question because few proven cases of recent and pervasive intron origin have been documented. We report here the widespread occurrence of spliceosomal introns (69 introns at 27 different sites) in the small- and large-subunit nuclear-encoded rDNA of lichen-forming and free-living members of the Ascomycota. Our analyses suggest that these spliceosomal introns are of relatively recent origin, i.e., within the Euascomycetes, and have arisen through aberrant reverse-splicing (in trans) of free pre-mRNA introns into rRNAs. The spliceosome itself, and not an external agent (e.g., transposable elements, group II introns), may have given rise to these introns. A nonrandom sequence pattern was found at sites flanking the rRNA spliceosomal introns. This pattern (AG-intron-G) closely resembles the proto-splice site (MAG-intron-R) postulated for intron insertions in pre-mRNA genes. The clustered positions of spliceosomal introns on secondary structures suggest that particular rRNA regions are preferred sites for insertion through reverse-splicing.     

Sesquiterpene lactones in Viguiera eriophora and Viguiera puruana (Heliantheae; Asteraceae)

Extracts of the aerial parts of Viguiera eriophora ssp. eriophora and Viguiera puruana afforded, in addition to known compounds, six new heliangolides and a germacrolide, whose structures were determined by spectral analysis. HPLC analysis and LC NMR experiments revealed the natural occurrence of the compounds in glandular trichomes. The taxonomic relevance of the results is briefly discussed.     

Good to the bone: microbial community thrives within bone cavities of a bison carcass at Yellowstone National Park

The discovery of unanticipated microbial diversity in remote, often hostile environments has led to a greater appreciation of the complexity and richness of the natural world. Yellowstone National Park (YNP) has long been a focus of work on taxa that inhabit extreme environments. Here we report the finding of microbial flora that inhabit an unexpected niche: the cavities of bone remnants from a bison carcass in Norris Geyser Basin in YNP. Although bleached white on the surface, the bone cavities are bright green due to the presence of Stichococcus-like trebouxiophyte green algae. The cavities also harbour different fungi and bacteria. Stichococcus species are common lichen photobionts and the Thelebolales fungi present in the bone cavities have previously been found in association with animal remains. Scanning electron microscope analysis suggests the fungi and algae do not form lichen-like associations in the bone. Rather these taxa and the bacteria appear to be opportunists that have colonized an isolated oasis that provides nutrients and protection from desiccation and UV radiation.     

Bioactive principles in the bark of Pilidiostigma tropicum

The crude dichloromethane bark extract of Pilidiostigma tropicum (Myrtaceae) from north Queensland, Australia, shows antibacterial and cytotoxic activity. Bioactivity-directed separation led to the isolation of rhodomyrtoxin B and ursolic acid-3-p-coumarate as the biologically active materials. The structures of these compounds were elucidated on the basis of spectral analysis. The intercalation interaction of rhodomyrtoxin B with DNA was investigated using molecular mechanics and ab initio molecular-orbital techniques. A favorable pi-pi interaction between rhodomyrtoxin B and the cytosine-guanine base pair is predicted, but the orientation of the interaction cannot be predicted based on frontier molecular orbitals.     

Evaluation of transmembrane helix predictions in 2014

Experimental structure determination continues to be challenging for membrane proteins. Computational prediction methods are therefore needed and widely used to supplement experimental data. Here, we re‐examined the state of the art in transmembrane helix prediction based on a nonredundant dataset with 190 high‐resolution structures. Analyzing 12 widely‐used and well‐known methods using a stringent performance measure, we largely confirmed the expected high level of performance. On the other hand, all methods performed worse for proteins that could not have been used for development. A few results stood out: First, all methods predicted proteins in eukaryotes better than those in bacteria. Second, methods worked less well for proteins with many transmembrane helices. Third, most methods correctly discriminated between soluble and transmembrane proteins. However, several older methods often mistook signal peptides for transmembrane helices. Some newer methods have overcome this shortcoming. In our hands, PolyPhobius and MEMSAT‐SVM outperformed other methods. Proteins 2015; 83:473–484. © 2014 Wiley Periodicals, Inc.