I think I am finally breathing, for many days, the earth was spinning.

Hypothetical and conserved hypothetical genes account for >30percent of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved hypothetical (9.5percent) along with 887 hypothetical genes (24.4percent). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 hypothetical and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC-MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. 1212 of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations.

Slow down. They tell the clown but he can’t hear you. He’s almost out of gas

and he’s already past the point of no return.

The immense plant diversity that is characteristic of tropical rain forests often makes it difficult for ecological and conservation studies to identify individual plant species and measure biodiversity. DNA barcoding is a species identification technique that utilizes standard, short dnA sequences to distinguish between species when traditional taxonomic identification is not practical. Accurate identification of animals with DNA barcoding has been well established, but a universally accepted DNA barcode for plants still does not exist. The use of nuclear DNA markers and plastid DNA markers from the chloroplast are the two contending approaches to DNA barcoding. This study compares the utility of the nuclear DNA marker ItS and the plastid DNA marker rbcL as DNA barcodes among 35 Burseraceae tree species from the Peruvian Amazon. I found that the proposed DNA barcode rbcL greatly underperformed the nuclear marker ItS as a DNA barcode. While both markers exhibited greater than 90% amplification success ItS demonstrated a mean pairwise percentage sequence divergence of 5.4% while rbcL demonstrated 0.83%. Additionally, at 1% sequence divergence resolution ItS discriminated between 99% of species-pairs while rbcL only discriminated between 26%. The results of my study suggest that ItS should not be completely discounted from the plant DNA barcode debate and rbcL be reevaluated as a proposed universal barcode.