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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UC San Francisco Electronic Theses and Dissertations (2016)

Despite centuries of research, the etiology of Ulcerative Colitis (UC; a chronic form of colonic inflammation) remains a mystery. As such, diagnosis is difficult, relying on clinical manifestations and resulting in an incredibly heterogeneous patient population. Furthermore, no cure (save colectomy) is available for UC, leading to a lifetime of therapies (many having variable efficacy; a consequence of UC patient heterogeneity). As UC prevalence rises, substantial need for enhanced therapies exists.

The gastrointestinal microbiome represents a promising avenue for improved treatment practices for UC. Being a diverse microbial community with substantial metabolic activity, opportunity exists for commensal microbes to influence host health, specifically the immune system. Indeed, several common colonizers of the mammalian gut regulate specific aspects of host immunity relevant to UC (such as Th17 and regulatory T-cell abundance, lymphocyte recruitment, and epithelial barrier function) through production of immunomodulatory metabolites. While UC was originally described as non-infectious diarrhea, studies demonstrating the potential efficacy of microbe-based treatments (i.e., probiotics) and the impact of microbes on animal models of UC suggest the microbiome contributes in a non-classical form of pathogenesis. Building on this, independent researchers found the gastrointestinal microbiome of UC patients to be less diverse and more compositionally variable compared to healthy people. Though these findings implicate the gastrointestinal microbiome in UC, questions remain regarding the therapeutic potential of gut microbes to improve patient outcomes.

This thesis addresses the clinical utility of the gastrointestinal microbiome in improving UC treatment. The therapeutic potential of microbiome manipulation was demonstrated using a murine model of UC and indicated gastrointestinal niches upstream of the colon harbor microbial activity associated with both disease induction and remission, suggesting patients might benefit from remodeling of microbial communities throughout the intestines. Additionally, a human study was conducted to demonstrate the utility of the microbiome with respect to improved stratification of UC patients. This work indicated discrete microbial states exist within the UC population, associate with symptom severity, and, via unique metabolic programming, differentially regulate T-cell activity. Together, this work highlights the microbiome as a resource for the development of both novel therapies and personalized treatment regimens for UC.

    Cover page: Investigating the Clinical Utility of the Gastrointestinal Microbiome in Ulcerative Colitis
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2013)
    Gene regulation in bacteria is usually described as an adaptive response to an environmental change so that genes are expressed when they are required. We instead propose that most genes are under indirect control: their expression responds to signal(s) that are not directly related to the genes' function. Indirect control should perform poorly in artificial conditions, and we show that gene regulation is often maladaptive in the laboratory. In Shewanella oneidensis MR-1, 24% of genes are detrimental to fitness in some conditions, and detrimental genes tend to be highly expressed instead of being repressed when not needed. In diverse bacteria, there is little correlation between when genes are important for optimal growth or fitness and when those genes are upregulated. Two common types of indirect control are constitutive expression and regulation by growth rate; these occur for genes with diverse functions and often seem to be suboptimal. Because genes that have closely related functions can have dissimilar expression patterns, regulation may be suboptimal in the wild as well as in the laboratory.
      Cover page: Indirect and suboptimal control of gene expression is widespread in bacteria.
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2010)
      In Saccharomyces cerevisiae, the DNA damage response (DDR) is activated by the spatio-temporal colocalization of Mec1-Ddc2 kinase and the 9-1-1 clamp. In the absence of direct means to monitor Mec1 kinase activation in vivo, activation of the checkpoint kinase Rad53 has been taken as a proxy for DDR activation. Here, we identify serine 378 of the Rad55 recombination protein as a direct target site of Mec1. Rad55-S378 phosphorylation leads to an electrophoretic mobility shift of the protein and acts as a sentinel for Mec1 activation in vivo. A single double-stranded break (DSB) in G1-arrested cells causes phosphorylation of Rad55-S378, indicating activation of Mec1 kinase. However, Rad53 kinase is not detectably activated under these conditions. This response required Mec1-Ddc2 and loading of the 9-1-1 clamp by Rad24-RFC, but not Rad9 or Mrc1. In addition to Rad55-S378, two additional direct Mec1 kinase targets are phosphorylated, the middle subunit of the ssDNA-binding protein RPA, RPA2 and histone H2A (H2AX). These data suggest the existence of a truncated signaling pathway in response to a single DSB in G1-arrested cells that activates Mec1 without eliciting a full DDR involving the entire signaling pathway including the effector kinases.
        Cover page: A truncated DNA-damage-signaling response is activated after DSB formation in the G1 phase of Saccharomyces cerevisiae
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2018)
        Gut microbiota dysbiosis and metabolic dysfunction in infancy precedes childhood atopy and asthma development. Here we examined gut microbiota maturation over the first year of life in infants at high risk for asthma (HR), and whether it is modifiable by early-life Lactobacillus supplementation. We performed a longitudinal comparison of stool samples collected from HR infants randomized to daily oral Lactobacillus rhamnosus GG (HRLGG) or placebo (HRP) for 6 months, and healthy (HC) infants. Meconium microbiota of HRP participants is distinct, follows a delayed developmental trajectory, and is primarily glycolytic and depleted of a range of anti-inflammatory lipids at 6 months of age. These deficits are partly rescued in HRLGG infants, but this effect was lost at 12 months of age, 6 months after cessation of supplementation. Thus we show that early-life gut microbial development is distinct, but plastic, in HR infants. Our findings offer a novel strategy for early-life preventative interventions.
          Cover page: Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2013)
          The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA-barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4-fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate-derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance.
            Cover page: Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates.
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