A combined approach of benthic mapping of Caraguatatuba Bay, Brazil, with recommendations for management practices

Benthic habitat mapping is an important first step towards ecosystem-based management. In a top-down approach, benthic mapping of a semi-enclosed bay in south-eastern Brazil was performed using a combined approach of acoustic RoxAnn survey and benthic samples. An inventory of the benthic macrofauna as well as unsupervised classifications of the acoustic data provided information about sediment patterns and potential areas of ecological importance, and a new zoning scheme is suggested based on the macrofauna analysis. The RoxAnn survey proved suitable to determine sediment characteristics, however, species environment relationships cannot be revealed by acoustic techniques only. Based on the data presented here, acoustic surveys could become an important tool in future monitoring programmes following the bottom-up approach of seabed classification protocols for an ecosystem-based management to improve existing coastal ecosystem management strategies in Brazil. (C) 2012 Elsevier Ltd. All rights reserved.71269274German Academic Exchange Service (DAAD

Codon optimization of the human papillomavirus E7 oncogene induces a CD8+ T cell response to a cryptic epitope not harbored by wild-type E7.

Codon optimization of nucleotide sequences is a widely used method to achieve high levels of transgene expression for basic and clinical research. Until now, immunological side effects have not been described. To trigger T cell responses against human papillomavirus, we incubated T cells with dendritic cells that were pulsed with RNA encoding the codon-optimized E7 oncogene. All T cell receptors isolated from responding T cell clones recognized target cells expressing the codon-optimized E7 gene but not the wild type E7 sequence. Epitope mapping revealed recognition of a cryptic epitope from the +3 alternative reading frame of codon-optimized E7, which is not encoded by the wild type E7 sequence. The introduction of a stop codon into the +3 alternative reading frame protected the transgene product from recognition by T cell receptor gene-modified T cells. This is the first experimental study demonstrating that codon optimization can render a transgene artificially immunogenic through generation of a dominant cryptic epitope. This finding may be of great importance for the clinical field of gene therapy to avoid rejection of gene-corrected cells and for the design of DNA- and RNA-based vaccines, where codon optimization may artificially add a strong immunogenic component to the vaccine