Codon usage bias analysis of genes linked with esophagus cancer

Esophageal cancer involves multiple genetic alternations. A systematic codon usage bias analysis was completed to investigate the bias among the esophageal cancer responsive genes. GC-rich genes were low (average effective number of codon value was 49.28). CAG and GTA are over-represented and under-represented codons, respectively. Correspondence analysis, neutrality plot, and parity rule 2 plot analysis confirmed the dominance over mutation pressure in modulating the codon usage pattern of genes linked with esophageal cancer.     

Alkylresorcinol biosynthesis in plants: New insights from an ancient enzyme family?

Alkylresorcinols are members of an extensive family of bioactive compounds referred to as phenolic lipids, which occur primarily in plants, fungi and bacteria. In plants, alkylresorcinols and their derivatives are thought to serve important roles as phytoanticipins and allelochemicals, although direct evidence for this is still somewhat lacking. Specialized type III polyketide synthases (referred to as ‘alkylresorcinol synthases’), which catalyze the formation of 5-alkylresorcinols using fatty acyl-CoA starter units and malonyl-CoA extender units, have been characterized from several microbial species; however, until very recently little has been known concerning their plant counterparts. Through the use of sorghum and rice EST and genomic data sets, significant inroads have now been made in this regard. Here we provide additional information concerning our recent report on the identification and characterization of alkylresorcinol synthases from Sorghum bicolor and Oryza sativa, as well as a brief consideration of the emergence of this intriguing subfamily of enzymes.Key words: alkylresorcinol, polyketide synthase, alkylresorcinol synthase, phenolic lipid, antifungal     

Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales

Powerful analyses of population structure require information from multiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers that span conserved intron-exon junctions in a wide variety of animal phyla. We test the utility of exon-primed, intron-crossing amplifications by analyzing the variability of actin intron sequences from humpback, blue, and bowhead whales and comparing the results with mitochondrial DNA (mtDNA) haplotype data. Humpback actin introns fall into two major clades that exist in different frequencies in different oceanic populations. It is surprising that Hawaii and California populations, which are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due either to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to offspring, between separate breeding grounds. Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden patterns of structure in natural populations.      

Probing allelochemical biosynthesis in sorghum root hairs

Allelopathic interaction between plants is thought to involve the release of phytotoxic allelochemicals by one species, thus inhibiting the growth of neighboring species in competition for limited resources. Sorgoleone represents one of the more potent allelochemicals characterized to date, and its prolific production in root hair cells of Sorghum spp. has made the investigation of its biosynthetic pathway ideally-suited for functional genomics investigations. Through the use of a recently-released EST data set generated from isolated Sorghum bicolor root hair cells, significant inroads have been made toward the identification of genes and the corresponding enzymes involved in the biosynthesis of this compound in root hairs. Here we provide additional information concerning our recent report on the identification of a 5-n-alk(en) ylresorcinol utilizing O-methyltransferase, as well as other key enzymes likely to participate in the biosynthesis of this important allelochemical.Key words: allelopathy, sorgoleone, root hair, EST, O-methyltransferase