Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome.

With the availability of a new highly contiguous Bos taurus reference genome assembly (ARS-UCD1.2), it is the opportune time to upgrade the bovine gene set by seeking input from researchers. Furthermore, advances in graphical genome annotation tools now make it possible for researchers to leverage sequence data generated with the latest technologies to collaboratively curate genes. For many years the Bovine Genome Database (BGD) has provided tools such as the Apollo genome annotation editor to support manual bovine gene curation. The goal of this paper is to explain the reasoning behind the decisions made in the manual gene curation process while providing examples using the existing BGD tools. We will describe the sources of gene annotation evidence provided at the BGD, including RNA-seq and Iso-Seq data. We will also explain how to interpret various data visualizations when curating gene models, and will demonstrate the value of manual gene annotation. The process described here can be applied to manual gene curation for other species with similar tools. With a better understanding of manual gene annotation, researchers will be encouraged to edit gene models and contribute to the enhancement of livestock gene sets.

Structural studies of EcoRII methylase: exploring similarities among methylases.

EcoRII methyltransferase (M.EcoRII) is a cytosine-C5 DNA methylating enzyme. A model of its three-dimensional structure is proposed on the basis of homology modeling. Crystal structures of two members of the same family of enzymes, HaeIII and HhaI methyltransferases (M.HaeIII and M.HhaI respectively), were used as template molecules. Molecular dynamics was used to ensure sampling of conformationally stable structures. The final model has good geometry. The DNA and cofactor binding residues are in expected positions and form proper interactions. M.EcoRII is 147 amino acids longer than the template molecules, and hence the model contains several loops that are significantly longer than those in M.HaeIII and M.HhaI. The model provides a framework for interpretation and designing site-directed mutants that have a potential to improve crystallization experiments of this enzyme, and possibly other similar enzymes.

Polyurethane foam extraction of platinum-tin halide complexes.

The sorptive capacity of the polyether-based foam was determined to be between 0.85 and 0.92 moles/kg for the platinum-tin(II) chloride complex. At hydrochloric and hydrobromic acid concentrations up to 3.0M, the platinum-tin(II) bromide complex had higher extraction efficiencies than the platinum-tin(II) chloride complex. Sorptions were optimized at 5.0M hydrochloric acid and 3.0M hydrobromic acid and distribution ratios as high as 2.0 x 10(5) 1./kg were observed at high foam:platinum ratios. The percent of platinum extracted increased when the alkali metal cations are added in the order K(+) < Na(+) < Li(+) for polyether foam, and decreased in the order K(+) > Na(+) > Li(+) for polyester foam. Also, the sorption efficiencies increased as the proportion of poly(ethylene oxide) of the foam was increased. A Scatchard plot analysis shows that there is a 2:1 ratio of loosely bound platinum to tightly bound platinum with the polyether foam, however, the experimental results are consistent with a weak-base anion exchange mechanism as the prominent method of sorption. For polyester foam, results are consistent with a solvent-like ion-pair sorption mechanism.