ALBERT

Description: The large number of sexually transmitted diseases and ocular trachoma cases that are caused globally each year by Chlamydia trachomatis has made this organism a World Health Organization priority for vaccine development. However, there is no gene transfer system for Chlamydia to help identify potential vaccine targets. To accelerate discoveries toward this goal, here we analyzed the broadest diversity of C. trachomatis genomes to date, including 25 geographically dispersed clinical and seven reference strains representing 14 of the 19 known serotypes. Strikingly, all 32 genomes were found to have evidence of DNA acquisition by homologous recombination in their history. Four distinct clades were identified, which correspond to all C. trachomatis disease phenotypes: lymphogranuloma venereum (LGV; Clade 1); noninvasive urogenital infections (Clade 2); ocular trachoma (Clade 3); and protocolitis (Clade 4; also includes some noninvasive urogenital infections). Although the ancestral relationship between clades varied, most strains acted as donor and recipient of recombination with no evidence for barriers to genetic exchange. The niche-specific LGV and trachoma clades have undergone less recombination, although the opportunity for mixing with strains from other clades that infect the rectal and ocular mucosa, respectively, is evident. Furthermore, there are numerous occasions for gene conversion events through sequential infections at the same anatomic sites. The size of recombinant segments is relatively small (~357 bp) compared with in vitro experiments of various C. trachomatis strains but is consistent with in vitro estimates for other bacterial species including Escherichia coli and Helicobacter pylori . Selection has also played a crucial role during the diversification of the organism. Clade 2 had the lowest nonsynonymous to synonymous ratio (d N /d S ) but the highest effect of recombination, which is consistent with the widespread occurrence of synonymous substitutions in recombined genomic segments. The trachoma Clade 3 had the highest d N /d S estimates, which may be caused by an increased effect of genetic drift from niche specialization and a reduced effective population size. The degree of drift, selection, and recombination in C. trachomatis suggests that the challenge will remain to identify genomic regions that are stable and cross protective for the development of an efficacious vaccine.

Description: To simulate winds and water levels, numerical weather prediction (NWP) and storm surge models generally use the traditional bulk relation for wind stress, which is characterized by a wind drag coefficient. A still commonly used drag coefficient in those models, some of them were developed in the past, is based on a relation, according to which the magnitude of the coefficient is either constant or increases monotonically with increasing surface wind speed (Bender, 2007; Kim et al., 2008; Kohno and Higaki, 2006). The NWP and surge models are often tuned independently from each other in order to obtain good results. Observations have indicated that the magnitude of the drag coefficient levels off at a wind speed of about 30 m s−1, and then decreases with further increase of the wind speed. Above a wind speed of approximately 30 m s−1, the stress above the air-sea interface starts to saturate. To represent the reducing and levelling off of the drag coefficient, the original Charnock drag formulation has been extended with a correction term. In line with the above, the Delft3D storm surge model is tested using both Charnock's and improved Makin's wind drag parameterization to evaluate the improvements on the storm surge model results, with and without inclusion of the wave effects. The effect of waves on storm surge is included by simultaneously simulating waves with the SWAN model on identical model grids in a coupled mode. However, the results presented here will focus on the storm surge results that include the wave effects. The runs were carried out in the Gulf of Mexico for Katrina and Ivan hurricane events. The storm surge model was initially forced with H*wind data (Powell et al., 2010) to test the effect of the Makin's wind drag parameterization on the storm surge model separately. The computed wind, water levels and waves are subsequently compared with observation data. Based on the good results obtained, we conclude that, for a good reproduction of the storm surges under hurricane conditions, Makin's new drag parameterization is favourable above the traditional Charnock relation. Furthermore, we are encouraged by these results to continue the studies and establish the effect of improved Makin's wind drag parameterization in the wave model. The results from this study will be used to evaluate the relevance of extending the present towards implementation of a similar wind drag parameterization in the SWAN wave model, in line with our aim to apply a consistent wind drag formulation throughout the entire storm surge modelling approach.