Browsing by Subject "mass spectrometry"

Now showing 1 - 6 of 6
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    Building maps of plant surface chemistry using literature and citizen-collected mass spectrometry samples
    (2022-06) Nguyen, Dien Le
    Understanding plant chemicals can greatly help achieve the important goals of reducing negative environmental impacts of agriculture and achieving high crop yields. One class of chemicals that has a big influence on plant health and growth is triterpenoid. However, there is a limited number of biological systems in which to study triterpenoids in detail. To increase the number of study systems, and thus our potential to build knowledge of triterpenoid function, there is a critical need to understand which triterpenoids can be found on which plant species' surface. The objective of this project was to build maps of plant surface compound presence with an emphasis on triterpenoids, using published and newly acquired gas chromatography-mass spectrometry data. The maps reveal trends that some triterpenoids are very commonly found on plant surface, while others are rare. In addition, divergent and convergent evolution traits among plants regarding their triterpenoid and other wax compounds presence were also identified.
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    DNA-Protein Cross-links: Formation in Cells and Tissues, Repair, and Inhibition of DNA Transcription
    (2019-04) Park, Daeyoon
    DNA is constantly damaged by exogenous and endogenous agents, generating a range of nucleobase lesions. It is important to understand the biological consequences and repair mechanisms of DNA adducts. Cellular proteins can become covalently trapped on DNA to generate DNA-protein crosslinks (DPCs). Because of their unusually bulky nature, DPCs are anticipated to block many cellular processes including replication, transcription, and repair. However, cellular effects of DPCs have not been fully elucidated. Chapter 1 of this thesis provides background information on the formation, biological consequences, and repair pathways of DPCs studied in previous studies. In Chapter 2, we employed a quantitative nanoLC-ESI+-MS/MS assay to investigate the formation of free radical-induced DPCs between thymidine in DNA and tyrosine sidechains of proteins. This methodology was used to examine the role of SPRTN protease and immunoproteasome in DPC repair in human cells and mouse models. In Chapter 3, a mass spectrometry based CTAB assay was used to study the effects of DNA-peptide crosslinks on transcription in human cells. We constructed plasmid molecules containing DPCs between C5 of dC and lysine sidechains of polypeptides in order to mimic conjugates that form endogenously at DNA epigenetic marks (5-formylc-dC). Lesion bearing and control plasmids were transfected into human cells, and the amounts of RNA transcripts were determined using a mass spectrometry based approach. Moreover, DNA lesion bearing plasmid models were used to determine the importance of NER pathway in DPC repair. In Chapter 4, we investigated in vivo formation of DPCs in cells exposed to monofunctional alkylating agent, methyl methanesulfonate (MMS). A mass spectrometry-based TMT proteomics approach was used to characterize MMS-induced DNA-protein cross-linking in Chinese hamster lung fibroblasts (V79). utilizing Our results revealed that DPCs can be produced via nucleophilic attack of proteins at the C8 position of N7-methylguanine (MdG). Our results revealed novel DPC formation mechanisms and the toxicities of monofunctional agent induced DPCs. In summary, mass spectrometry-based quantification was used to the amounts of free radical induced DPCs in cells, providing evidence for the role of DPC proteolysis in repair, while CTAB assay demonstrated the effect of endogenously formed DPCs on transcription. Moreover, a mass spectrometry-based methodology was applied to examine a novel DPC formation mechanism following treatment with monofunctional alkylating agents.
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    Ecosystem-atmosphere fluxes of reactive carbon from the 2021 Flux Closure Study (FluCS) at Manitou Experimental Forest
    (2023-06-15) Vermeuel, Michael P; Millet, Dylan B; Farmer, Delphine K; Pothier, Matson A; Link, Michael F; dbm@umn.edu; Millet, Dylan B; University of Minnesota Atmospheric Chemistry Group
    This archive contains hourly observed and modeled fluxes of ambient volatile organic compounds (VOCs) over Manitou Experimental Forest in Woodland Park, CO during the FluCS 2021 study throughout August and September 2021. Observations were collected via the eddy covariance method using mass spectrometry for VOC concentrations and a sonic anemometer for vertical windspeed. Model fluxes were simulated using the GEOS-Chem (v13.3) model. Also included are observed and simulated meteorology during this time period.
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    Ethnic differences in the metabolism of 1,3-butadiene and lung cancer risk
    (2019-01) Boldry, Emily
    Cigarette smoking remains one of the most preventable causes of death in the world, and is the leading cause of lung cancer. Epidemiological studies show inherent differences in lung cancer risk among smokers of different ethnic groups, with Native Hawaiian and African Americans have the highest risk, European Americans having an intermediate risk, and Latinos and Japanese Americans having the lowest risk. It has been proposed that these disparities in risk are due to ethnic differences in the metabolism, and ultimately bioactivation, of carcinogens in present in cigarette smoke. 1,3-butadiene (BD) is one of the most abundant and potent carcinogens present in cigarette smoke. BD is metabolically activated to the reactive species 3,4-epoxy-1-butene (EB), hydroxymethylvinylketone (HMVK), 3,4-epoxy-1,2-butanediol (EBD), and 1,2,3,4-diepoxybutane (DEB), which have the ability to form pro-mutagenic DNA adducts. These species can be detoxified through glutathione conjugation and excreted in urine; EB and HMVK are excreted as 2-(N-acetyl-L-cystein-S-yl)-1-hydroxybut-3-ene/ 1-(N-acetyl-L-cystein-S-yl)-2-hydroxybut-3-ene (MHBMA) and 4-(N-acetyl-L-cystein-S-yl)-1,2-dihydroxybutane (DHBMA). The research presented in this thesis focuses on ethnic differences in BD metabolism and the initial development of a DEB specific biomarker. A high throughput HPLC-ESI--MS/MS method for the simultaneous quantitation of MHBMA and DHBMA in humans previously developed in our laboratory was applied to quantify these mercapturic acids in smokers of different ethnic groups. In a large multi-ethnic study composed of African American, European American, and Japanese American smokers (N = 1,072). Urinary MHBMA and MHBMA/MHBMA+DHBMA were highest in African Americans, followed by European Americans, and Japanese Americans, and strongly influenced by GSTT1 genotype. A genome wide association study (GWAS) revealed strong associations between MHBMA and GSTT1: associations with 136 SNPs were detected, and all of them were located between 24.2—24.4 Mb near the GSTT1 gene on chromosome 22q11. Additional experiments with recombinant human GSTT1 and GSTT2 confirmed EB as a substrate for the first time. The same method was also applied to a separate smaller study of African American and European American smokers (N = 151). In contrast to the previous work, urinary MHBMA was higher in European Americans than African Americans in this study; this is likely due to decreased sample size. Statistical analyses revealed no correlation between urinary MHBMA or DHBMA and urinary N7-(1-hydroxy-3-buten-2-yl)guanine (EBGII), as well no significant associations between urinary EBGII, MHBMA, or DHBMA and various specific SNPs from BD-metabolizing genes (EPHX1 and CYP2E1) and DNA repair genes (FANCE). GSTT1 copy number was also included in this analysis, and showed a significant association with urinary MHBMA. Urinary MHBMA and DHBMA were also quantified in smokers (N=79) receiving treatment with the chemopreventative agent 2-phenethyl isothiocyanate (PEITC). Overall, PEITC treatment resulted in only slight increases in MHBMA and DHBMA as compared to treatment with a placebo, but was found to significantly increase MHBMA in individuals null for GSTT1 or both GSTT1 and GSTM1, indicating a potential protective effect of PEITC in these individuals. Lastly, an HPLC-ESI+-MS/MS method for the of detection of a novel DEB-specific biomarker, Nε, Nε-(2,3-dihydroxybutan-1,4-diyl)-L-lysine (DHB-Lys) was explored. Initial development focused on the use of an ion-pairing agent, perfluoroheptanoic acid (PFHA), which was chosen to increase HPLC retention of DHB-Lys. Though addition of PFHA to the aqueous mobile phase during HPLC-ESI+-MS/MS analysis did result in increased retention of the analyte, its use also presented additional challenges with analyte carryover, sample contamination, and ion suppression. Methodology utilizing derivatization of DHB-Lys through the addition of a 6-aminoquinolyl group (6-AQ) at the alpha nitrogen was tested on DEB-treated O6-alkylguanine DNA alkyltransferase (AGT), and showed a dose dependent increase in DHB-Lys formed.
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    Glycyrrhiza Lepidota Leaf Mass Spectrometry Data
    (2017-03-31) Freund, Dana M; Martin, Amanda C; Cohen, Jerry C; Hegeman, Adrian D; dfreund@umn.edu; Freund, Dana M
    Four different populations of Glycyrrhiza lepidota with nearly identical chemotypes were analyzed with each Mass Spectrometry (MS) method: Leaf Spray, Leaf Dip Extraction, and Bulk Extraction.
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    Ploidy, Genetics, And Metabolomics Of Achillea, A Venerable And Variable Medicinal Plant
    (2022-09) Sammons, Katherine
    Humans have turned to plants for medicine since ancient times. In recent centuries technology has allowed isolation of pure compounds which largely replaced herbal medicines in the USA around the beginning of the 20th century. However, even in today’s world of modern medicine, some herbal medicines can offer support for health in ways that pharmaceutical drugs cannot. With the advent of high resolution analytical instruments it is now possible to reconsider herbal medicines in all of their chemical complexity. Using the ancient medicinal plant Achillea millefolium as a case study, I use high resolution accurate mass-mass spectrometry to chemically profile 115 publicly available accessions of Achillea spp. cultivated in a common garden.In Chapter 1 I describe a brief history of medicine and technology to understand how we arrived at the current reductionist single-active-constituent mindset, and why it is important to broaden our mental model. In Chapter 2 I use flow cytometry and karyology to describe the ploidy of each of the 115 Achillea accessions. I also use DArTseq, a SNP analysis technique, to describe the population structure among these accessions. Finally, in Chapter 3 I use high performance liquid chromatography tandem to a high resolution mass spectrometer to chemically profile the 115 accessions. Altogether, this study helps to better understand the role that ploidy and genotype play in the chemotype of Achillea spp. The high resolution chemical profiling also helps to re-envision plants with a higher level of chemical complexity. Additionally, it serves as a potential model for improving approaches to quality control in the herbal industry.