Assessing the effect of prevalence on the predictive performance of species distribution models using simulated data

Aim The proportion of sampled sites where a species is present is known as prevalence. Empirical studies have shown that prevalence can affect the predictive performance of species distribution models. This paper uses simulated species data to examine how prevalence and the form of species environmental dependence affect the assessment of the predictive performance of models. Methods Simulated species data were based on various functions of simulated environmental data with differing degrees of spatial correlation. Seven model performance measures – sensitivity, specificity, class‐average (CA), overall prediction success, kappa (κ), normalized mutual information (NMI) and area under the receiver operating characteristic curve (AUC) – were applied to species models fitted by three regression methods. The response of the performance measures to prevalence was then assessed. Three probability threshold selection methods used to convert fitted logistic model values to presence or absence were also assessed. Results The study shows that the extent to which prevalence affects model performance depends on the modelling technique and its degree of success in capturing dominant environmental determinants. It also depends on the statistic used to measure model performance and the probability threshold method. The response based on κ generally preferred models with medium prevalence. All performance measures were least affected by prevalence when the probability threshold was chosen to maximize predictive performance or was based directly on prevalence. In these cases, the responses based on AUC, CA and NMI generally preferred models with small or large prevalence. Main conclusions The effect of prevalence on the predictive performance of species distribution models has a methodological basis. Relevant factors include the success of the fitted distribution model in capturing the dominant environmental determinant, the model performance measure and the probability threshold selection method. The fixed probability threshold method yields a marked response of model performance to prevalence and is therefore not recommended. The study explains previous empirical results obtained with real data.     

Codon optimization for high level expression of human bone morphogenetic protein-2 in Escherichia coli

Codons in the open reading frame (ORF) encoding for human bone morphogenetic protein-2 (hBMP-2) were optimized to reach high level expression in Escherichia coli. The optimization was done by the computer programs DNA works and DNA Star according to Thermodynamically Balanced Inside Out (TBIO) approach. The ORF consisting of 342 base pairs (bp) was assembled using two-steps Polymerase Chain Reaction, cloned into a pGEM-T vector with a mutation rate of 6.38 bp per kb and transformed into E. coli JM109. After a DNA sequence confirmation, mutation-free ORF was subcloned into pET32b and transformed into E. coli BL21(DE3). The rhBMP-2 was produced as a thioredoxin-his-tag fusion protein at relatively high level, approximately 60% of total intracellular proteins as inclusion bodies (IB), with a yield of 1.39 g per liter culture. Solubilization of IB gave soluble monomer rhBMP-2 with a recovery of 13.6% and refolding of soluble rhBMP-2 produced dimeric forms with a yield of 8.7%. The size and identity of the purified rhBMP-2 was confirmed by nano-LC-MS/MS2 analysis. Our work demonstrates for the first time that by using TBIO approach, a codon-optimized ORF encoding for rhBMP-2 protein can be expressed at high level in E. coli expression system.