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Open Access Publications from the University of California

Scholarly Works (21 results)

  • Thesis
  • Peer Reviewed
UC Santa Cruz Electronic Theses and Dissertations (2023)

The circadian clock is a cell autonomous clock that drives the daily rhythms of biological processes. Emerging literature shows a clear relationship between the circadian clock and the immune system, but the mechanisms behind this relationship are not well understood. Due to their genetic tractability and similarity to humans, zebrafish (Danio rerio) are an appealing model to study the connection between the clock and immunity. However, no studies have investigated how bacterial exposure affects the clock in this model organism. In this thesis, we show that heat killed (HK) Streptococcus pneumoniae (Spn) and Escherichia coli augment the expression of the light driven genes, per2 and cry1a, in zebrafish cells. Further investigation into the mechanism by which HK Spn alters circadian gene expression revealed that inhibition of reactive oxygen species (ROS) abolishes the response to HK Spn exposure, indicating an ROS dependent mechanism of per2 and cry1a augmentation by HK Spn. In addition to investing how zebrafish cells respond to bacteria, we also generated circadian reporter fish and tested how these reporters respond to bacteria. We found that the reporters behaved as previously reported in the literature in different lighting conditions, but that Spn infection did not alter their circadian rhythms. Together, these results illustrate how multiple environmental signals can converge via a common pathway to induce changes in circadian gene expression in zebrafish cells, and how live circadian zebrafish reporters can be used to study the circadian response to bacteria.

    • Article
    • Peer Reviewed
    UC Santa Cruz Previously Published Works (2016)
    Research in recent years has focused significantly on the role of selective macroautophagy in targeting intracellular pathogens for lysosomal degradation, a process termed xenophagy. In this review we evaluate the proposed roles for xenophagy in controlling bacterial infection, highlighting the concept that successful pathogens have evolved ways to subvert or exploit this defense, minimizing the actual effectiveness of xenophagy in innate immunity. Instead, studies in animal models have revealed that autophagy-associated proteins often function outside of xenophagy to influence bacterial pathogenesis. In light of current efforts to manipulate autophagy and the development of host-directed therapies to fight bacterial infections, we also discuss the implications stemming from the complicated relationship that exists between autophagy and bacterial pathogens.
      Cover page: Bacterial Pathogens versus Autophagy: Implications for Therapeutic Interventions
      • Article
      • Peer Reviewed
      UC Santa Cruz Previously Published Works (2022)
      Streptococcus pneumoniae (Spn) is the primary agent of community-acquired pneumonia. Neutrophils are innate immune cells that are essential for bacterial clearance during pneumococcal pneumonia but can also do harm to host tissue. Neutrophil migration in pneumococcal pneumonia is therefore a major determinant of host disease outcomes. During Spn infection, detection of the bacterium leads to an increase in proinflammatory signals and subsequent expression of integrins and ligands on both the neutrophil as well as endothelial and epithelial cells. These integrins and ligands mediate the tethering and migration of the neutrophil from the bloodstream to the site of infection. A gradient of host-derived and bacterial-derived chemoattractants contribute to targeted movement of neutrophils. During pneumococcal pneumonia, neutrophils are rapidly recruited to the pulmonary space, but studies show that some of the canonical neutrophil migratory machinery is dispensable. Investigation of neutrophil migration is necessary for us to understand the dynamics of pneumococcal infection. Here, we summarize what is known about the pathways that lead to migration of the neutrophil from the capillaries to the lung during pneumococcal infection.
        Cover page: Neutrophil Recruitment in Pneumococcal Pneumonia.
        • Thesis
        • Peer Reviewed
        UC Santa Cruz Electronic Theses and Dissertations (2021)

        Circadian rhythms regulate changes in physiology and allow organisms to respond to predictable environmental demands over 24 hours. Recent studies have shown that the circadian system is an essential regulator of immune function. Additionally, disruption of the circadian clock affects our immune response. However, how bacterial infection affects our circadian clock, which affects our immune response, remains unclear. Here, we found that the addition of heat-killed S. pneumoniae (HK Spn) to mouse lung fibroblast cells impacts their circadian rhythms through acute induction of clock protein PER2. Due to the acute induction of PER2, it resets the cells to a different phase. Moreover, HK Spn can affect the PER2 rhythm throughout the clock, and interestingly, HK Spn resets the clock of these mouse lung fibroblasts to the same circadian time. Furthermore, we also identify the dose-dependent effect of HK Spn on PER2 rhythm. Gram-positive bacteria and gram-negative bacteria are evolutionarily different from each other. Nonetheless, we find that all tested bacteria trigger the same PER2 response. Therefore, this response is an evolutionarily conserved response within all bacteria. Furthermore, we identify that TLR2 and TLR4 are not responsible for this bacterially induced PER2 induction. My work also focuses on the downstream of the signaling pathway, where we characterize that the PER2 response is post-transcriptional and likely mTOR-independent. Together, our results advance understanding of the bidirectionality effect between circadian rhythms and bacterial infections.

          • Article
          • Peer Reviewed
          UC Santa Cruz Previously Published Works (2022)
          Circadian clocks are universally used to coordinate biological processes with the Earth's 24-h solar day and are critical for the health and environmental success of an organism. Circadian rhythms in eukaryotes are driven by a cell-intrinsic transcription-translation feedback loop that controls daily oscillations in gene expression which regulate diverse physiological functions. Substantial evidence now exists demonstrating that immune activation and inflammatory responses during infection are under circadian control, however, the cellular mechanisms responsible for this are not well understood. The zebrafish (Danio rerio) is a powerful model organism to study vertebrate circadian biology and immune function. Zebrafish contain homologs of mammalian circadian clock genes which, to our current knowledge, function similarly to impart timekeeping ability. Consistent with studies in mammalian models, several studies in fish have now demonstrated a bidirectional relationship between the circadian clock and inflammation: the circadian clock regulates immune activity, and inflammation can alter circadian rhythms. This review summarizes our current understanding of the molecular mechanisms of the zebrafish clock and the bi-directional relationship between the circadian clock and inflammation in fish.
            Cover page: Immunity, Infection, and the Zebrafish Clock
            • Article
            • Peer Reviewed
            UC Santa Cruz Previously Published Works (2024)
            The circadian clock is a cell-autonomous process that regulates daily internal rhythms by interacting with environmental signals. Reports across species show that infection can alter the expression of circadian genes; however, in teleosts, these effects are influenced by light exposure. Currently, no reports analyze the direct effects of bacterial exposure on the zebrafish clock. Using zebrafish Z3 cells, we demonstrate that exposure to heat-killed Streptococcus pneumoniae (HK-Spn) augments the expression of core repressive factors in a light- and time-dependent manner. In constant darkness, HK-Spn highly upregulated cry1a, per3, and per1b expression. In the presence of light, HK-Spn exposure rapidly and strongly upregulated per2 and cry1a, and this was proportionally increased with light intensity. The combinatorial effect of light and HK-Spn on per2 and cry1a was not duplicated with H2O2, a known byproduct of light exposure. However, the ROS inhibitor N-acetyl cysteine was sufficient to block HK-Spn augmentation of per2, cry1a, and per3. These findings demonstrate that exposure to an inactive bacteria influences the expression of zebrafish clock genes under different light conditions.
              Cover page: Heat-inactivated Streptococcus pneumoniae augments circadian clock gene expression in zebrafish cells.
              • Article
              • Peer Reviewed
              UC Santa Cruz Previously Published Works (2021)
              Group B Streptococcus (GBS) is a leading cause of neonatal morbidity and mortality, and the primary source of exposure is the maternal vagina. Intrapartum antibiotic prophylaxis for GBS-positive mothers has reduced the incidence of GBS early-onset disease, however, potential long-lasting influence of an antibiotic-altered neonatal microbiota, and the frequent clinical sequelae in survivors of invasive GBS infection, compels alternative treatment options for GBS. Here, we examined the role of transcription factor hypoxia-inducible factor 1 alpha (HIF-1α), widely recognized as a regulator of immune activation during infection, in the host response to GBS. Given the importance of endogenous HIF-1α for innate immune defense, and the potential utility of HIF-1α stabilization in promoting bacterial clearance, we hypothesized that HIF-1α could play an important role in coordinating host responses to GBS in colonization and systemic disease. Counter to our hypothesis, we found that GBS infection did not induce HIF-1α expression in vaginal epithelial cells or murine macrophages, nor did HIF-1α deficiency alter GBS colonization or pathogenesis in vivo. Furthermore, pharmacological enhancement of HIF-1α did not improve control of GBS in pathogenesis and colonization models, while displaying inhibitory effects in vaginal epithelial cytokines and immune cell killing in vitro. Taken together, we conclude that HIF-1α is not a prominent aspect of the host response to GBS colonization or invasive disease, and its pharmacological modulation is unlikely to provide significant benefit against this important neonatal pathogen.
                Cover page: Hypoxia-Inducible Factor 1 Alpha Is Dispensable for Host Defense of Group B Streptococcus Colonization and Infection
                • Article
                • Peer Reviewed
                UC Santa Cruz Previously Published Works (2017)
                Mycobacterium tuberculosis infection results in 1.5 million deaths annually. Type I interferon (IFN) signaling through its receptor IFNAR correlates with increased severity of disease, although how this increases susceptibility to M. tuberculosis remains uncertain. ISG15 is one of the most highly induced interferon stimulated genes (ISGs) during M. tuberculosis infection. ISG15 functions by conjugation to target proteins (ISGylation), by noncovalent association with intracellular proteins, and by release from the cell. Recent studies indicated that ISG15 can function via conjugation-independent mechanisms to suppress the type I IFN response. These data raised the question of whether ISG15 may have diverse and sometimes opposing functions during M. tuberculosis infection. To address this, we analyzed ISGylation during M. tuberculosis infection and show that ISGylated proteins accumulate following infection in an IFNAR-dependent manner. Type I IFN and ISG15 both play transient roles in promoting bacterial replication. However, as the disease progresses, ISGylation deviates from the overall effect of type I IFN and, ultimately, mice deficient in ISGylation are significantly more susceptible than IFNAR mice. Our data demonstrate that ISGs can both protect against and promote disease and are the first to report a role for ISGylation during M. tuberculosis infection.
                  Cover page: The impact of ISGylation during Mycobacterium tuberculosis infection in mice
                  • Article
                  • Peer Reviewed
                  UC Santa Cruz Previously Published Works (2016)
                  Mycobacterium tuberculosis (Mtb) is one of the world's most successful pathogens. Millions of new cases of tuberculosis occur each year, emphasizing the need for better methods of treatment. The design of novel therapeutics is dependent on our understanding of factors that are essential for pathogenesis. Many bacterial pathogens use pili and other adhesins to mediate pathogenesis. The recently identified Mycobacterium tuberculosis pilus (MTP) and the hypothetical, widely conserved Flp pilus have been speculated to be important for Mtb virulence based on in vitro studies and homology to other pili, respectively. However, the roles for these pili during infection have yet to be tested. We addressed this gap in knowledge and found that neither MTP nor the hypothetical Flp pilus is required for Mtb survival in mouse models of infection, although MTP can contribute to biofilm formation and subsequent isoniazid tolerance. However, differences in mtp expression did affect lesion architecture in infected lungs. Deletion of mtp did not correlate with loss of cell-associated extracellular structures as visualized by transmission electron microscopy in Mtb Erdman and HN878 strains, suggesting that the phenotypes of the mtp mutants were not due to defects in production of extracellular structures. These findings highlight the importance of testing the virulence of adhesion mutants in animal models to assess the contribution of the adhesin to infection. This study also underscores the need for further investigation into additional strategies that Mtb may use to adhere to its host so that we may understand how this pathogen invades, colonizes and disseminates.
                    Cover page: Analysis of the contribution of MTP and the predicted Flp pilus genes to Mycobacterium tuberculosis pathogenesis
                    • Article
                    • Peer Reviewed
                    UC Santa Cruz Previously Published Works (2020)
                    Serological testing to evaluate antigen-specific antibodies in plasma is generally performed by rapid lateral flow test strips that lack quantitative results or by high complexity immunoassays that are time- and labor-intensive but provide quantitative results. Here, we describe a novel application of biolayer interferometry for the rapid detection of antigen-specific antibody levels in plasma samples, and demonstrate its utility for quantification of SARS-CoV-2 antibodies. Our biolayer interferometry immunosorbent assay (BLI-ISA) utilizes single-use biosensors in an automated “dip-and-read” format, providing real-time optical measurements of antigen loading, plasma antibody binding, and antibody isotype detection. Complete quantitative results are obtained in less than 20 minutes. BLI-ISA meets or exceeds the performance of high complexity methods such as Enzyme-Linked Immunosorbent Assay (ELISA) and Chemiluminescent Immunoassay. Importantly, our method can be immediately implemented on existing BLI platforms for urgent COVID-19 studies, such as serosurveillance and the evaluation of vaccine candidates. In a broader sense, BLI-ISA can be developed as a novel diagnostic platform to evaluate antibodies and other biomolecules in clinical specimens.
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