The Dynamic Codon Biaser: calculating prokaryotic codon usage biases

Bacterial genomes often reflect a bias in the usage of codons. These biases are often most notable within highly expressed genes. While deviations in codon usage can be attributed to selection or mutational biases, they can also be functional, for example controlling gene expression or guiding protein structure. Several different metrics have been developed to identify biases in codon usage. Previously we released a database, CBDB: The Codon Bias Database, in which users could retrieve precalculated codon bias data for bacterial RefSeq genomes. With the increase of bacterial genome sequence data since its release a new tool was needed. Here we present the Dynamic Codon Biaser (DCB) tool, a web application that dynamically calculates the codon usage bias statistics of prokaryotic genomes. DCB bases these calculations on 40 different highly expressed genes (HEGs) that are highly conserved across different prokaryotic species. A user can either specify an NCBI accession number or upload their own sequence. DCB returns both the bias statistics and the genome’s HEG sequences. These calculations have several downstream applications, such as evolutionary studies and phage–host predictions. The source code is freely available, and the website is hosted at www.​cbdb.​info

Electrocatalytic Reduction of CO₂ to CO With Re-Pyridyl-NHCs: Proton Source Influence on Rates and Product Selectivities

A series of four electron-deficient-substituted Re­(I) pyridyl <i>N</i>-heterocyclic carbene (pyNHC) complexes have been synthesized, and their electrocatalytic reduction of CO₂ has been evaluated by cyclic voltammetry and controlled potential electrolysis experiments. All of the catalysts were evaluated by cyclic voltammetry under inert atmosphere and under CO₂ and compared to the known benchmark catalyst Re­(bpy)­(CO)₃Br. Among the four Re-NHC catalysts, Re­(pyNHC-PhCF₃)­(CO)₃Br (<b>2</b>) demonstrated the highest catalytic rate (<i>i</i>_cat/<i>i</i>_p)² at the first and second reduction events with a value of 4 at the second reduction potential (TOF = 0.8 s^–1). The rate of catalysis was enhanced through the addition of proton sources (PhOH, TFE, and H₂O; TOF up to 100 s^–1; (<i>i</i>_cat/<i>i</i>_p)² = 700). Controlled potential electrolysis shows Faradaic efficiencies (FE) for CO production and accumulated charge for the Re­(pyNHC-PhCF₃)­(CO)₃Br catalyst exceed those of the benchmark catalyst in the presence of 2 M H₂O (92%, 13 C at 1 h versus 61%, 3 C for the benchmark catalyst) under analogous experimental conditions. A peak FE of 100% was observed during electrolysis with Re­(pyNHC-PhCF₃)­(CO)₃Br