J. Robert Newman

Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the deep sequencing of ribosome-protected mRNA fragments and enables genome-wide investigation of translation with subcodon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control in both determining absolute protein abundance and responding to environmental stress. We also observed distinct phases during translation that involve a large decrease in ribosome density going from early to late peptide elongation as well as widespread regulated initiation at non-adenine-uracil-guanine (AUG) codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible.

Four studies evaluated the success of behaviors and strategies used to self-regulate bad moods, raise energy, and reduce tension. Study 1 (N = 102) used an open-ended questionnaire to identify behavioral categories. Studies 2 and 4 surveyed a representative sample (N = 308) with a fixed-response questionnaire to quantify behaviors, general strategies, and individual differences. Study 3 used psychotherapist (N = 26) judgments of the likely success of the strategies. Therapist and self-rating converged on success of strategies and gender differences. These studies clarify and confirm previous research findings, particularly gender differences in controlling depression. Exercise appears to be the most effective mood-regulating behavior, and the best general strategy to change a bad mood is a combination of relaxation, stress management, cognitive, and exercise techniques. Results support a 2-dimensional biopsychological model of mood.

In eukaryotes, the combinatorial association of sequence-specific DNA binding proteins is essential for transcription. We have used protein arrays to test 492 pairings of a nearly complete set of coiled-coil strands from human basic-region leucine zipper (bZIP) transcription factors. We find considerable partnering selectivity despite the bZIPs' homologous sequences. The interaction data are of high quality, as assessed by their reproducibility, reciprocity, and agreement with previous observations. Biophysical studies in solution support the relative binding strengths observed with the arrays. New associations provide insights into the circadian clock and the unfolded protein response.