Structural characterization of water-soluble atmospheric organic matter by ultrahigh-resolution mass spectrometry

Isolated water-soluble analytes extracted from fog water collected during a radiation fog event near Fresno, CA were analyzed using collision induced dissociation and ultrahigh-resolution mass spectrometry. Tandem mass analysis was performed on scan ranges between 100-400 u to characterize the structures of nitrogen and/or sulfur containing species. CHNO, CHOS, and CHNOS compounds were targeted specifically because of the high number of oxygen atoms contained in their molecular formulas. The presence of 22 neutral losses corresponding to fragment ions was evaluated for each of the 1308 precursors. Priority neutral losses represent specific polar functional groups (H2O, CO2, CH3OH, HNO3, SO3, etc., and several combinations of these). Additional neutral losses represent non-specific functional groups (CO, CH2O, C3H8, etc.) Five distinct monoterpene derived organonitrates, organosulfates, and nitroxy-organosulfates were observed in this study, including C10H16O7S, C10H17NO7S, C10H17 NO8S, C10H17NO9S, and C10H17NO10S. Nitrophenols and linear alkyl benzene sulfonates were present in high abundance. Liquid chromatography/mass spectrometery methodology was developed to isolate and quantify nitrophenols based on their fragmentation behavior.

POPLAR GENE EXPRESSION DATA ANALYSIS PIPELINES

Analyzing large-scale gene expression data is a labor-intensive and time-consuming process. To make data analysis easier, we developed a set of pipelines for rapid processing and analysis poplar gene expression data for knowledge discovery. Of all pipelines developed, differentially expressed genes (DEGs) pipeline is the one designed to identify biologically important genes that are differentially expressed in one of multiple time points for conditions. Pathway analysis pipeline was designed to identify the differentially expression metabolic pathways. Protein domain enrichment pipeline can identify the enriched protein domains present in the DEGs. Finally, Gene Ontology (GO) enrichment analysis pipeline was developed to identify the enriched GO terms in the DEGs. Our pipeline tools can analyze both microarray gene data and high-throughput gene data. These two types of data are obtained by two different technologies. A microarray technology is to measure gene expression levels via microarray chips, a collection of microscopic DNA spots attached to a solid (glass) surface, whereas high throughput sequencing, also called as the next-generation sequencing, is a new technology to measure gene expression levels by directly sequencing mRNAs, and obtaining each mRNA’s copy numbers in cells or tissues. We also developed a web portal (http://sys.bio.mtu.edu/) to make all pipelines available to public to facilitate users to analyze their gene expression data. In addition to the analyses mentioned above, it can also perform GO hierarchy analysis, i.e. construct GO trees using a list of GO terms as an input.