Integrated Calendar

The development of high throughput molecular measurement approaches enables much deeper understanding of cellular and disease related processes. The introduction of new measurement technology is always tied with computational design and optimization work as well as with the need to develop efficient data analysis and interpretation tools. I will describe data analysis and design methods and results with an emphasis on jointly analyzing data from several molecular measurement sources, such as serum glycomics and tumor transcriptomics. I will also describe the use of synthetic oligonucleotides to address new measurement and optimization questions.

Alkene ozonolysis is a primary oxidation pathway for alkenes emitted into the troposphere and also an important source of atmospheric hydroxyl radicals. Alkene ozonolysis takes place on a reaction path with multiple minima and barriers along the way to OH products. In particular, a key reaction intermediate, known as the Criegee intermediate, R1R2COO, had eluded detection until very recently. In this laboratory, the simplest Criegee intermediate, CH2OO, and methyl-substituted Criegee intermediates, CH3CHOO and (CH3)2COO, have now been generated by an alternative synthetic route, detected by VUV photoionization, and characterized on a strong * transition. Most recently, our studies have focused on vibrational activation of methyl-substituted Criegee intermediates in the vicinity of the barrier for 1,4 hydrogen transfer that leads to OH products. The experiments reveal infrared transitions in the CH stretch overtone region that initiate unimolecular decay as well as the rate of the appearance of OH products through direct time-domain measurements. Comparison with high level theory shows that tunneling through the barrier makes a significant contribution to the decay rate. The dissociation dynamics are also examined through the translational and internal energy distributions of the OH products, which reflect critical configurations along the reaction pathway from the barrier for hydrogen transfer to OH products. Finally, the results will be extended to thermally averaged unimolecular decay of stabilized Criegee intermediates under atmospheric conditions.

Alternative promoter usage contributes to the complexity of genome-encoded transcripts but little is known about its impact on translation. To obtain a global view of transcription start site (TSS) selection effect on translation we performed TSS mapping of the translatome under normal growth condition and following energy stress. Our findings uncovered several levels of coordination of transcription and translation. In this talk I will present the data analysis of these experiments along with in-depth inquiries of several intriguing examples.

Abstract (form the eLife paper:) ): Insertion of helix-forming segments into the membrane and their association determines the structure, function, and expression levels of all plasma membrane proteins. However, systematic and reliable quantification of membrane-protein energetics has been challenging. We developed a deep mutational scanning method to monitor the effects of hundreds of point mutations on helix insertion and self-association within the bacterial inner membrane. The assay quantifies insertion energetics for all natural amino acids at 27 positions across the membrane, revealing that the hydrophobicity of biological membranes is significantly higher than appreciated. We further quantitate the contributions to membrane-protein insertion from positively charged residues at the cytoplasm-membrane interface and reveal large and unanticipated differences among these residues. Finally, we derive comprehensive mutational landscapes in the membrane domains of Glycophorin A and the ErbB2 oncogene, and find that insertion and self-association are strongly coupled in receptor homodimers.