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Open Access Publications from the University of California

Scholarly Works (45 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2017)

LC-MS has been employed as a powerful tool for elucidating structures of compounds as well as providing accurate and unambiguous quantification of analytes. The focus of this dissertation is placed on the development of analytical methods for reliable quantification of chemically modified nucleosides in DNA, including oxidative stress-induced DNA lesions, carboxymethylated DNA adducts, and DNA epigenetic marks.

In chapter 2, I employed a nanoflow liquid chromatography-nanoelectrospray ionization-tandem mass spectrometry (NanoLC-NSI-MS2) coupled with the isotope-dilution method for the simultaneous quantification of oxidatively induced DNA modifications. The quantification data suggested that aberrant copper accumulation may perturb genomic stability by elevating oxidatively induced DNA lesions, and by altering epigenetic pathways of gene regulation.

In chapter 3, I developed a highly sensitive nLC-nESI-MS3 method for the simultaneous quantification of N6-CMdA, O6-CMdG and O6-MedG. I was able to measure the levels of these three lesions with the use of low-microgram quantities of DNA from cultured human skin fibroblasts and human colorectal carcinoma cells treated with azaserine, a DNA carboxymethylating agent. The method reported here will be useful for the future investigations about the repair of the carboxymethylated DNA lesions and about the implications of these lesions in carcinogenesis.

In chapter 4, I employed LC-MS3 and quantified the levels of 5-hmdC in different cancer cells treated with a glycolysis inhibitor or activators of AMP-activated protein kinase (AMPK) to gain insights into the relationship between aberrant metabolism and the levels of 5-hmdC in cancer cells. The data indicated that the altered metabolism in cancer cells could contribute, in part, to the diminished levels of 5-hmdC observed in cancer cells.

    Cover page: Mass Spectrometry-Based Studies of DNA Lesions and Epigenetic Biomarkers
    • Thesis
    • Peer Reviewed
    UC San Diego Electronic Theses and Dissertations (2017)

    The understanding on the mechanical behavior of α-keratin broadens our knowledge in biological materials science. In this study, the hierarchical organization is studied from the intermediate filament to the structural levels. The effects of strain rate, relative humidity, and temperature are evaluated.

    Human hair exhibits a high tensile strength, which is significantly dependent on strain rate and humidity. The strain-rate sensitivity is comparable to that of other keratinous materials. One distinguishing feature, the unwinding of the α-helices and the possible transformation to β-sheet structure of keratin under tension, is analytically evaluated and incorporated into a constitutive equation. The contributions of elastic and plastic strains on reloading are evaluated and correlated to structural changes.

    The dynamic mechanical response over a range of frequencies and temperatures is analyzed. The α-keratin fibers behave more elastically at higher frequencies while they become more viscous at higher temperatures. The stress relaxation behavior of α-keratin fibers is established and fit to a constitutive relaxation equation based on the Maxwell-Wiechert model. The two relaxation constants are connected to two hierarchical levels of relaxation: the amorphous matrix-intermediate filaments interfaces, for the short term, and the cellular components for the long term. Results of creep testing provide important knowledge on the uncoiling and phase transformation of the α-helical structure as hair is uniaxially stretched. As the hairs are chemically treated, they exhibit a similar strain-rate sensitivity of ~0.05, which is attributed to the intermediate filaments. As a result, the strain-rate sensitivity of human hair is reduced by half, while that of horse hair remains unchanged. FTIR data confirms that the human hair is more sensitive to the -S-S- cleavage, resulting in an increase of cysteic acid. Therefore, the disulfide bonds in the matrix are experimentally identified as one source of the strain-rate sensitivity and viscoelasticity in α-keratin fibers.

    In addition to human and horse hair that comprise the primary goal of this investigation, boar, giraffe, elephant, and bear hair were tested in tension, to establish the mechanisms of deformation and failure. In spite of differences in strength attributed to the condition of the hair, no significant changes were observed.

      Cover page: Structural and mechanical properties of α-keratin fibers
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2023)
      Traumatic joint injuries such as anterior cruciate ligament (ACL) rupture or meniscus tears commonly lead to post-traumatic osteoarthritis (PTOA) within 10-20 years following injury. Understanding the early biological processes initiated by joint injuries (e.g., inflammation, matrix metalloproteinases (MMPs), cathepsin proteases, bone resorption) is crucial for understanding the etiology of PTOA. However, there are few options for in vivo measurement of these biological processes, and the early biological responses may be confounded if invasive surgical techniques or injections are used to initiate OA. In our studies of PTOA, we have used commercially available near-infrared protease activatable probes combined with fluorescence reflectance imaging (FRI) to quantify protease activity in vivo following non-invasive compression-induced ACL injury in mice. This non-invasive ACL injury method closely recapitulates clinically relevant injury conditions and is completely aseptic since it does not involve disrupting the skin or the joint capsule. The combination of these injury and imaging methods allows us to study the time course of protease activity at multiple time points following a traumatic joint injury.
        Cover page: Non-Invasive Compression-Induced Anterior Cruciate Ligament (ACL) Injury and In Vivo Imaging of Protease Activity in Mice.
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2015)
        Propionibacterium acnes , plays an important role in acne vulgaris and other diseases. However, understanding of the exact mechanisms of P. acnes pathogenesis is limited. Few studies have investigated its proteome, which is essential for vaccine development. Here, we comprehensively investigate the proteome of P. acnes strain ATCC 6919, including secreted, cell wall, membrane, and cytosolic fractions in three types of growth media. A total of 531 proteins were quantified using an Orbitrap mass spectrometer and bioinformatically categorized for localization and function. Several, including PPA1939, a highly expressed surface and secreted protein, were identified as potential vaccine candidates.
          Cover page: Analysis of the surface, secreted, and intracellular proteome of Propionibacterium acnes
          • Article
          UC Berkeley Previously Published Works (2019)
          We develop a formalism to directly evaluate the matrix of force constants within a Quantum Monte Carlo calculation. We utilize the matrix of force constants to accurately relax the positions of atoms in molecules and determine their vibrational modes, using a combination of Variational and Diffusion Monte Carlo. The computed bond lengths differ by less than 0.007{\AA} from the experimental results for all four tested molecules. For hydrogen and hydrogen chloride, we obtain fundamental vibrational frequencies within 0.1% of experimental results and ~10 times more accurate than leading computational methods. For carbon dioxide and methane, the vibrational frequency obtained is on average within 1.1% of the experimental result, which is at least 3 times closer than results using Restricted Hartree-Fock and Density Functional Theory with a Perdew-Burke-Ernzerhof (PBE) functional and comparable or better than Density Functional Theory with a semi-empirical functional.
            • Article
            • Peer Reviewed
            UC Riverside Previously Published Works (2018)
            A wide spectrum of DNA lesions can be generated from byproducts of endogenous metabolism and/or from environmental exposure. A DNA adductomic approach for the robust quantification of DNA adducts in cellular and tissue DNA may facilitate the use of DNA adducts for biomonitoring studies and enable comprehensive assessment about DNA repair. Normalized retention time (iRT) has been widely used in scheduled selected-reaction monitoring (SRM) methods for highly sensitive and high-throughput analyses of protein samples in complicated matrices. By using a similar method, we established the iRT scores for 36 modified nucleosides from the retention times of the four canonical 2-deoxynucleosides on a nanoflow liquid chromatography-nanospray ionization-tandem mass spectrometry (nLC-NSI-MS/MS) system. The iRT scores facilitated reliable prediction of retention time and were employed for establishing a scheduled SRM method for quantitative assessment of a subset of the DNA adductome. The quantification results of the scheduled SRM method were more accurate and precise than those from an unscheduled method.
              Cover page: Normalized Retention Time for Targeted Analysis of the DNA Adductome.
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2023)
              This study investigated long-term interannual changes in summer circulation and hydrology in the East China Sea (ECS) by performing 35-year high-resolution ocean model simulation from 1981 to 2015. The sea surface temperature (SST) warming trend was considerably weaker in summer than in winter. To the east of the Yangtze Estuary, the interannual variation of SST in summer was mainly dominated by horizontal advection associated with variations in the Taiwan warm current and heat flux in the offshore region north of the Yangtze Estuary. Baroclinic circulation during summer played a crucial role in subsurface mixing. Near the surface, the significant atmospheric wind mode (EOF1) and Kuroshio mode (EOF2) dominate interannual variations in ocean circulation. In the subsurface, local wind around the Tsushima Strait dominated the interannual ocean variation. Anomalous northeasterly winds induced a southwestward pressure gradient due to topographical confinement. These anomalies propagated to the south along the continental shelf through topographic Rossby waves. This study identified two types of anomalous features based on combinations of surface and subsurface EOFs. The combination represents an in-phase contribution between wind and Kuroshio forcings and between the surface and subsurface circulation that enhances the hydrological variability in the ECS. The implication on the relevant biogeochemical and ecological studies in the East China Sea is also very crucial at the interannual time scale.
                Cover page: Interannual changes of the summer circulation and hydrology in the East China Sea: A modeling study from 1981 to 2015
                • Article
                Orthopaedic Surgery (2024)
                Post-traumatic osteoarthritis (PTOA) occursfollowing an injury such as Anterior CruciateLigament (ACL) rupture. Clinically, ACLreconstruction surgery is performedfollowing injury. However, it is unclear howeffective knee restabilization is in slowingPTOA progression. This study hypothesized that knee restabilization would slow the progression of PTOA, but the procedure itself would have some mild PTOA-like joint degeneration.
                  Cover page: Surgical restabilization following ACL rupture in mice slows the progression of post-traumatic osteoarthritis
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2014)

                  Introduction

                  Resveratrol (3,5,4'-trihydroxystilbene) is an antioxidant that has multiple biologic effects including antimicrobial properties. Acne vulgaris is a disease of the pilosebaceous unit, characterized by an inflammatory host immune response to the bacteria Propionibacterium acnes (P. acnes). This study sought to determine whether resveratrol may be a potential treatment for acne vulgaris.

                  Methods

                  Colony-forming unit (CFU) assays together with transmission electron microscopy using P. acnes treated with resveratrol or benzoyl peroxide were used to assess antibacterial effects. Blood was drawn from healthy human volunteers, and 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assays were used to assess cytotoxicity in monocytes and keratinocytes.

                  Results

                  Resveratrol demonstrated sustained antibacterial activity against P. acnes, whereas benzoyl peroxide, a commonly used antibacterial treatment for acne, demonstrated a short-term bactericidal response. A combination of resveratrol and benzoyl peroxide showed high initial antibacterial activity and sustained bacterial growth inhibition. Electron microscopy of P. acnes treated with resveratrol revealed altered bacterial morphology, with loss of membrane definition and loss of well-defined extracellular fimbrial structures. Resveratrol was less cytotoxic than benzoyl peroxide.

                  Conclusion

                  The sustained antibacterial activity and reduced cytotoxicity versus benzoyl peroxide demonstrated by resveratrol in this study highlight its potential as a novel therapeutic option or adjuvant therapy in the treatment of acne vulgaris.
                    Cover page: Resveratrol Demonstrates Antimicrobial Effects Against Propionibacterium acnes In Vitro
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2010)
                    The TGF-β, a tumor suppressive cytokine in normal cells, is abused in cancer to promote the malignancy. In this study, we reported that TGF-β downregulated the mutS homolog 2 (MSH2), a central component of the DNA mismatch repair (MMR) system, in HER2-transformed MCF10A mammary epithelial cells and in breast cancer (BC) cells. This was mediated by a TGF-β-induced micro RNA (miRNA), miR-21, which targeted the 3' untranslated region of MSH2 mRNA and downregulated its expression. A negative correlation between the expression of TGF-β1 and MSH2 was also detected in primary breast tumors. In contrast, TGF-β upregulated MSH2 in nontransformed cells through Smad-mediated, p53-dependent promoter activation, which was absent in BC cells with impaired p53 function. Although this upregulating mechanism also existed in MCF10A/HER2 and p53-proficient BC cells, both basal and TGF-β-induced MSH2 promoter activities were significantly lower than those in MCF10A. Moreover, the basal and TGF-β-induced miR-21 levels were markedly higher in transformed cells, suggesting that the preset levels of miR-21 and MSH2 promoter activity, which is affected by the p53 status, determine the outputs of the bidirectional regulation of MSH2 by TGF-β in a certain cellular context. We further found that by downregulating MSH2, TGF-β contributed to resistance to DNA-damaging chemotherapy agents in cancer cells. Our results indicated a regulatory antagonism between promoter activation and miRNA-mediated posttranscriptional inhibition underlying a dual effect of TGF-β on the DNA repair machinery, which may influence the genomic stability in a context-dependent manner and contribute to chemoresistance in cancer.
                      Cover page: Context-Dependent Bidirectional Regulation of the MutS Homolog 2 by Transforming Growth Factor β Contributes to Chemoresistance in Breast Cancer Cells
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