Pseudoreplication in tropical forests and the resulting effects on biodiversity conservation.

Tropical forest ecosystems are threatened by habitat conversion and other anthropogenic actions. Timber production forests can augment the conservation value of primary forest reserves, but studies of logging effects often yield contradictory findings and thus inhibit efforts to develop clear conservation strategies. We hypothesized that much of this variability reflects a common methodological flaw, simple pseudoreplication, that confounds logging effects with preexisting spatial variation.

Detection of fused genes in eukaryotic genomes using gene deFuser: analysis of the Tetrahymena thermophila genome.

Background: Fused genes are important sources of data for studies of evolution and protein function. To date no service has been made available online to aid in the large-scale identification of fused genes in sequenced genomes. We have developed a program, Gene deFuser, that analyzes uploaded protein sequence files for characteristics of gene fusion events and presents the results in a convenient web interface.

1+1 = 3: a fusion of 2 enzymes in the methionine salvage pathway of Tetrahymena thermophila creates a trifunctional enzyme that catalyzes 3 steps in the pathway.

The methionine salvage pathway is responsible for regenerating methionine from its derivative, methylthioadenosine. The complete set of enzymes of the methionine pathway has been previously described in bacteria. Despite its importance, the pathway has only been fully described in one eukaryotic organism, yeast.

Patterns of codon usage in two ciliates that reassign the genetic code: Tetrahymena thermophila and Paramecium tetraurelia.

We used the recently sequenced genomes of the ciliates Tetrahymena thermophila and Paramecium tetraurelia to analyze the codon usage patterns in both organisms; we have analyzed codon usage bias, Gln codon usage, GC content and the nucleotide contexts of initiation and termination codons in Tetrahymena and Paramecium. We also studied how these trends change along the length of the genes and in a subset of highly expressed genes. Our results corroborate some of the trends previously described in Tetrahymena, but also negate some specific observations.