Quantitative reactivity profiling predicts functional cysteines in proteomes

Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here we describe a proteomics method to profile quantitatively the intrinsic reactivity of cysteine residues en masse directly in native biological systems. Hyper-reactivity was a rare feature among cysteines and it was found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyper-reactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and is involved in iron-sulphur protein biogenesis. We also demonstrate that quantitative reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs.     

Western Scrub-Jay breeding biology in central Colorado

The breeding ecology of the Western Scrub-Jay ( Aphelocoma californica ) in the midwestern United States is relatively unknown compared with Aphelocoma species in other geographic regions. We examined Western Scrub-Jay breeding biology in Colorado between 1970 and 1992. Incubation was initiated in early April and lasted 16 days, while the nestling stage lasted approximately 17-18 days. Clutch size averaged 4.0 eggs per nest, reproductive success was 25%, and productivity averaged 0.66 fledglings per nest. The low reproductive success and productivity measures may be due to high predator densities in the surrounding suburban landscape. Western Scrub-Jays preferred nesting in eastern red cedar ( Juniperus virginianus ) with nests placed on southern exposures. Western Scrub-Jays bred monogamously and were more similar in their breeding biology to the Island Scrub-Jay ( Aphelocoma insularis ) than to the Florida Scrub-Jay ( Aphelocoma coerulescens ).     

A novel retinoblastoma therapy from genomic and epigenetic analyses

Retinoblastoma is an aggressive childhood cancer of the developing retina that is initiated by the biallelic loss of RB1. Tumours progress very quickly following RB1 inactivation but the underlying mechanism is not known. Here we show that the retinoblastoma genome is stable, but that multiple cancer pathways can be epigenetically deregulated. To identify the mutations that cooperate with RB1 loss, we performed whole-genome sequencing of retinoblastomas. The overall mutational rate was very low; RB1 was the only known cancer gene mutated. We then evaluated the role of RB1 in genome stability and considered non-genetic mechanisms of cancer pathway deregulation. For example, the proto-oncogene SYK is upregulated in retinoblastoma and is required for tumour cell survival. Targeting SYK with a small-molecule inhibitor induced retinoblastoma tumour cell death in vitro and in vivo. Thus, retinoblastomas may develop quickly as a result of the epigenetic deregulation of key cancer pathways as a direct or indirect result of RB1 loss.