Scientific Publications 2010
2010. "Plasma Proteome Response to Severe Burn Injury Revealed by 18O-Labeled “Universal” Reference-based Quantitative Proteomics." Journal of Proteome Research 9(9):4779-4789. Abstract A burn injury represents one of the most severe forms of human trauma and is responsible for significant mortality worldwide. Here, we present the first quantitative proteomics investigation of the blood plasma proteome response to severe burn injury by comparing the plasma protein concentrations in samples collected from10 healthy control subjects with those in samples collected from 15 severe burn patients at two different time-points following the injuries. The overall analytical strategy for this work integrated immunoaffinity depletion of the 12 most abundant plasma proteins with cysteinyl-peptide enrichment-based fractionation prior to LC-MS analyses of individual patient samples. Incorporation of an 18O-labeled “universal” reference among the sample sets ensured accurate relative quantification across samples. In total, 313 plasma proteins confidently identified with two or more unique peptides were quantified. Following statistical analysis, 110 proteins exhibited significant abundance changes in response to thermal injury. The observed changes in protein concentrations suggest significant inflammatory and hypermetabolic response to the injury, which is supported by the fact that many of the identified proteins are associated with acute phase response signaling, complement system, and coagulation system pathways. The regulation of ~35 proteins observed in this study is in agreement with previous results reported for inflammatory or burn response. There are approximately 50 potentially novel proteins previously not known to be associated with burn response or inflammation. Elucidating proteins involved in the response to severe burn injury may reveal novel targets for therapeutic interventions, as well as potential predictive biomarkers for patient outcomes such as multiple organ failure.
2010. "Thermodynamic Instability at the Stoichiometric LaAlO3/SrTiO3(001) Interface." Journal of Physics. Condensed matter 22(31):Art. No. 312201. doi:10.1088/0953-8984/22/31/312201 Abstract Fully stoichiometric epitaxial LaAlO3 grown on the TiO2-terminated SrTiO3(001) by off-axis pulsed laser deposition is shown to exhibit strong La-Sr cation intermixing. This result is predicted by classical and quantum mechanical calculations of the relative stabilities of abrupt and intermixed states. The extensive cation intermixing has a marked impact on the electronic properties of the interface.
2010. "Structural and Operational Complexity of the Geobacter Sulfurreducens Genome." Genome Research 20:1304-1311. doi:10.1101/gr.107540.110 Abstract Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale, such as metabolism and transcriptional regulation. Here, we describe a systems approach to simultaneously determine the structural and operational annotation of the Geobacter sulfurreducens genome. Integration of proteomics, transcriptomics, RNA polymerase, and sigma factor-binding information with deep-sequencing-based analysis of primary 59-end transcripts allowed for a most precise annotation. The structural annotation is comprised of numerous previously undetected genes, noncoding RNAs, prevalent leaderless mRNA transcripts, and antisense transcripts. When compared with other prokaryotes, we found that the number of antisense transcripts reversely correlated with genome size. The operational annotation consists of 1453 operons, 22% of which have multiple transcription start sites that use different RNA polymerase holoenzymes. Several operons with multiple transcription start sites encoded genes with essential functions, giving insight into the regulatory complexity of the genome. The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes.