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Open Access Publications from the University of California

Scholarly Works (3 results)

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

In recent years, advances in sequencing have enabled the mapping of DNA methylation variation across many different populations of human cell types and the identification of candidate DNA methylation biomarkers for clinical applications. The clinical development of DNA methylation biomarkers has been limited, however, due to the high cost and the lack of flexibility in using the current experimental and bioinformatics tools.

We made improvements to the design of bisulfite padlock probes (BSPP) to greatly increase efficiency and throughput for targeted DNA methylation quantification. The cost effectiveness and scalability of this approach was demonstrated on hundreds of samples using a set of 330,000 probes. We also developed a bioinformatics pipeline that performs SNP calling on bisulfite data and DNA methylation quantitation with reduced errors from various different assay types.

Despite many available bioinformatics tools for differential DNA methylation analysis, there is a need for a more general computational tool to characterize DNA methylation variability on reference data. Therefore, we developed a new differential methylation identification method and variability score to quantify DNA methylation variation across multiple groups of samples. For simulated 5X average depth of coverage datasets, cgDMR-miner, identified 42% of simulated DMRs with 73% precision while the next best approach identified 23% of simulated DMRs with 96% precision. Thus cgDMR-miner can identify potential targets from a shallow, low accuracy initial screen that can later be validated with a deeper screen using a targeted assay.

Lastly, the coordinated methylation of nearby CpG sites was investigated in order to identify more robust biomarkers for cancer. Starting with a set of identified 147,888 regions of tightly coupled CpG methylation or methylation haplotype blocks (MHBs), the linked status of CpGs within these regions were found useful for biomarker identification in human tissue samples and human cell free DNA.

    Cover page: Novel molecular and bioinformatics approaches to investigate DNA methylation in human epigenome
    • Article
    • Peer Reviewed
    UC Santa Barbara Previously Published Works (2021)
    Resistance to currently available antifungal drugs has quietly been on the rise but overshadowed by the alarming spread of antibacterial resistance. There is a striking lack of attention to the threat of drug-resistant fungal infections, with only a handful of new drugs currently in development. Given that metal complexes have proven to be useful new chemotypes in the fight against diseases such as cancer, malaria, and bacterial infections, it is reasonable to explore their possible utility in treating fungal infections. Herein we report a series of cobalt(III) Schiff base complexes with broad-spectrum antifungal activity. Some of these complexes show minimum inhibitory concentrations (MIC) in the low micro- to nanomolar range against a series of Candida and Cryptococcus yeasts. Additionally, we demonstrate that these compounds show no cytotoxicity against both bacterial and human cells. Finally, we report the first in vivo toxicity data on these compounds in Galleria mellonella, showing that doses as high as 266 mg kg-1 are tolerated without adverse effects, paving the way for further in vivo studies of these complexes.
      Cover page: Nontoxic Cobalt(III) Schiff Base Complexes with Broad-Spectrum Antifungal Activity.
      • Article
      • Peer Reviewed
      UC Santa Barbara Previously Published Works (2022)
      There are currently fewer than 10 antifungal drugs in clinical development, but new fungal strains that are resistant to most current antifungals are spreading rapidly across the world. To prevent a second resistance crisis, new classes of antifungal drugs are urgently needed. Metal complexes have proven to be promising candidates for novel antibiotics, but so far, few compounds have been explored for their potential application as antifungal agents. In this work, we report the evaluation of 1039 metal-containing compounds that were screened by the Community for Open Antimicrobial Drug Discovery (CO-ADD). We show that 20.9% of all metal compounds tested have antimicrobial activity against two representative Candida and Cryptococcus strains compared with only 1.1% of the >300,000 purely organic molecules tested through CO-ADD. We identified 90 metal compounds (8.7%) that show antifungal activity while not displaying any cytotoxicity against mammalian cell lines or hemolytic properties at similar concentrations. The structures of 21 metal complexes that display high antifungal activity (MIC ≤1.25 μM) are discussed and evaluated further against a broad panel of yeasts. Most of these have not been previously tested for antifungal activity. Eleven of these metal complexes were tested for toxicity in the Galleria mellonella moth larva model, revealing that only one compound showed signs of toxicity at the highest injected concentration. Lastly, we demonstrated that the organo-Pt(II) cyclooctadiene complex Pt1 significantly reduces fungal load in an in vivo G. mellonella infection model. These findings showcase that the structural and chemical diversity of metal-based compounds can be an invaluable tool in the development of new drugs against infectious diseases.
        Cover page: Metal Complexes as Antifungals? From a Crowd-Sourced Compound Library to the First In Vivo Experiments.
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