Browsing by Author "Liu, Ying"

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    Computational Simulation of Secondary Organic Aerosol (SOA) Formation from Toluene Oxidation
    (2012-09-05) Liu, Ying; Griffin, Robert J.; Cohan, Daniel S.; Wong, Michael S.
    Toluene is one of the most prevalent aromatic volatile organic compounds (VOCs) in the atmosphere and has large secondary organic aerosol (SOA) yields compared to many other aromatic VOCs. Recent photo-oxidation studies highlight that toluene oxidation produces more SOA than observed previously, particularly at low levels of nitrogen oxides (NOx). This study focuses on: 1.) the development of a gas-phase chemical mechanism describing toluene oxidation by hydroxyl radicals (OH); 2.) the prediction of SOA formation from toluene oxidation products; and 3.) the impact of NOx level on SOA formation. The oxidation mechanism, which includes multiple pathways after the initial OH attack, has been incorporated into the Caltech Atmospheric Chemistry Mechanism (CACM). Toluene concentrations simulated in chamber experiments by the updated CACM as a function of time are typically within 5% of observed values for most experiments. Predicted ozone and NO2 concentrations are typically within 15% of the experimental values. The gas-phase mechanism indicates the importance of bicyclic peroxy radical reactions in determining the product distribution and thus the likelihood of SOA formation. A gas-aerosol partitioning model is used in conjunction with the gas-phase mechanism to simulate SOA formation. Predicted SOA concentrations are typically within 15% of the experimental values. Under low NOx conditions, simulation shows that more than 98% of SOA mass is contributed by bicyclic products from reactions between bicyclic peroxy radicals and other peroxy radicals. Increasing NOx levels cause bicyclic peroxy radicals to react with NO or nitrate radical, leading to fragmentation products that are less likely to form SOA. SOA yield dropped from 19.26% with zero initial NOx to 13.27% with 100 ppb initial NO because of the change in the amount of toluene consumed. Composition of NOx also has an impact on SOA yield and formation, showing that NO has a greater impact on SOA yield and formation than NO2.
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    Evolution of the activation domain in a Hox transcription factor
    (UPV/EHU Press, 2018) Liu, Ying; Huang, Annie; Booth, Rebecca M.; Mendes, Gabriela Geraldo; Merchant, Zabeena; Matthews, Kathleen S.; Bondos, Sarah E.
    Linking changes in amino acid sequences to the evolution of transcription regulatory domains is often complicated by the low sequence complexity and high mutation rates of intrinsically disordered protein regions. For the Hox transcription factor Ultrabithorax (Ubx), conserved motifs distributed throughout the protein sequence enable direct comparison of specific protein regions, despite variations in the length and composition of the intervening sequences. In cell culture, the strength of transcription activation by Drosophila melanogaster Ubx correlates with the presence of a predicted helix within its activation domain. Curiously, this helix is not preserved in species more divergent than flies, suggesting the nature of transcription activation may have evolved. To determine whether this helix contributes to Drosophila Ubx function in vivo, wild-type and mutant proteins were ectopically expressed in the developing wing and the phenotypes evaluated. Helix mutations alter Drosophila Ubx activity in the developing wing, demonstrating its functional importance in vivo. The locations of activation domains in Ubx orthologues were identified by testing the ability of truncation mutants to activate transcription in yeast one-hybrid assays. In Ubx orthologues representing 540 million years of evolution, the ability to activate transcription varies substantially. The sequence and the location of the activation domains also differ. Consequently, analogous regions of Ubx orthologues change function over time, and may activate transcription in one species, but have no activity, or even inhibit transcription activation in another species. Unlike homeodomain-DNA binding, the nature of transcription activation by Ubx has substantially evolved.
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    Exploration of DNA binding selectivity, transcriptional regulation, and evolutionary relationships of the Hox protein Ultrabithorax
    (2007) Liu, Ying; Matthews, Kathleen S.
    Hox transcription factors direct differentiation in all tissue layers and many organ systems and therefore have highly specific tissue-dependent functions. The DNA-binding homeodomain of Hox proteins can bind a wide array of nucleotide sequences with similar high affinities, suggesting regions outside the homeodomain must impact DNA interaction. Utilizing a series of deletion mutants, we identified three binding affinity modulation regions outside the homeodomain. DNA binding is inhibited ∼2-fold by the YPWM motif and microexon regions (I1) and ∼40-fold by the large disordered I2 region. High affinity binding is partially restored by the N-terminal 174 residues (R region) in a length-dependent manner. Both I2 and R regions partially overlap the Ubx transcription activation domain, allowing communication between these functional systems. Evolutionary variations in the amino acid sequences of most of these regions potentially differentiate Ubx•DNA interactions.