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Open Access Publications from the University of California

Scholarly Works (193 results)

  • Article
Lawrence Berkeley National Laboratory (2009)
    Cover page: Endothelial Cell Migration and Vascular Endothelial Growth Factor Expression Are the Result of Loss of Breast Tissue Polarity
    • Thesis
    • Peer Reviewed
    UC San Francisco Electronic Theses and Dissertations (2010)

    Purpose: To develop a SYBR® Green qPCR method for quantifying Streptococcus mutans (SM) in salivary samples.

    Methods: SM specific primers were derived from the DNA sequence of AP-PCR amplification products (unpublished). Serial dilutions of overnight mutans streptococci (MS) cultures were blotted on FTA cards (Whatman Bioscience Ltd.) as standards for qPCR. Sixty clinical saliva and swab samples, from children aged 2-10 with or without caries, enumerated for SM by traditional culturing were archived on FTA cards for SM quantification by SYBR® Green qPCR. The specificity of qPCR was analyzed by product melting curves. Correlation of SM quantification by qPCR and culture was analyzed using Pearson correlation test. The correlation of MS quantification by culture, or SM quantification by qPCR, and caries scores were analyzed by Pearson correlation test.

    Results: A total of 60 clinical samples (20 saliva and 40 swab samples) were enumerated by traditional culturing, and analyzed by qPCR. The 20 saliva samples were from caries-active (high caries risk) children, and the 40 swab samples were from both caries-active and caries-free children. The SYBR® Green qPCR method provided high efficiency and good specificity for SM detection in salivary samples archived on FTA cards. qPCR showed good reproducibility with a mean variance (CV) = 0.13 for qPCR samples with log10 SM > 3 CFU/ml. SM quantification by qPCR was significantly correlated (Pearson's correlation) with MS culture enumeration for all clinical samples, (r=0.51, P<0.001), saliva samples (r=0.52, P<0.05), and swab samples (r=0.51, P<0.001).

    In addition for swab samples, qPCR and culture results were significantly correlated with caries status (DS, r=0.32, P<0.05 for qPCR; DMFS and DS r=0.51, P<0.001 and r=0.44, P<0.01, respectively for culture).

    Conclusions: qPCR quantification of SM showed good correlation with traditional culture results. It offers a fast and convenient quantification method for SM in clinical samples and could facilitate SM quantification for private practitioners. Development of qPCR techniques to quantify other cariogenic bacteria is needed for thorough evaluation of bacterial challenge.

      Cover page: Quantification of Streptococcus mutans by qPCR
      • Thesis
      • Peer Reviewed
      UC San Francisco Electronic Theses and Dissertations (2017)

      Many epigenetic changes occur around implantation as pluripotent cells of the epiblast prepare for lineage specification. However, in vivo epigenetic studies during these early developmental stages is technically challenging. Here, we use an in vitro model of the transition from pre- to post-implantation epiblast where embryonic stem cells (ESCs) are differentiated into epiblast-like cells (EpiLCs) to profile the epigenetic changes that occur during this transition and elucidate specific mechanisms that underlie these changes. In Chapter 2, we use this in vitro system to perform an siRNA screen for chromatin modifiers that regulate this transition, identifying the cohesin complex as an important regulator. In Chapter 3, we profile changes in cohesin binding between ESCs and EpiLCs to identify regulators of enhancer activity and uncover the transcription factor GRHL2 as a driver of enhancer activation. We further show that GRHL2-mediated enhancer activation in EpiLCs is part of a larger process of enhancer switching where genes that are expressed at similar levels in ESCs and EpiLCs undergo a switch in enhancer usage from an ESC-specific enhancer to a GRHL2-bound enhancer in EpiLCs. GRHL2 targets are enriched for epithelial genes, indicating that this enhancer switch is necessary for maintaining an epithelial program characteristic of both cell states. In Chapter 4, we focus on the transcription factor, FOXD3, which primes enhancers during the ESC-to-EpiLC transition. We show that FOXD3 simultaneously recruits the nucleosome remodeler, BRG1, and the histone deacetylases, HDAC1/2, to target sites to establish nucleosome-depleted regions while preventing full enhancer activation by inhibiting histone acetylation. We further show that the cohesin complex is not yet present at FOXD3 binding sites, suggesting these enhancers are not yet engaged in stable interactions with their target promoters. Lastly, we provide evidence of an intermediate enhancer state between the traditional “primed” and “active” states that is cohesin-bound (K4me1+/cohesin+/K27Ac-), suggesting that enhancer-promoter looping may occur as a distinct step in enhancer priming. Together, these studies demonstrate the importance of epigenetic regulation during this developmental window and uncover novel mechanisms of enhancer regulation that we believe extend beyond the ESC-to-EpiLC transition.

        Cover page: Epigenetic regulation of the transition from naïve to formative pluripotency
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2018)
        The enhancer landscape of pluripotent stem cells undergoes extensive reorganization during early mammalian development. The functions and mechanisms behind such reorganization, however, are unclear. Here, we show that the transcription factor GRHL2 is necessary and sufficient to activate an epithelial subset of enhancers as naive embryonic stem cells (ESCs) transition into formative epiblast-like cells (EpiLCs). Surprisingly, many GRHL2 target genes do not change in expression during the ESC-EpiLC transition. Instead, enhancers regulating these genes in ESCs diminish in activity in EpiLCs while GRHL2-dependent alternative enhancers become activated to maintain transcription. GRHL2 therefore assumes control over a subset of the naive network via enhancer switching to maintain expression of epithelial genes upon exit from naive pluripotency. These data evoke a model where the naive pluripotency network becomes partitioned into smaller, independent networks regulated by EpiLC-specific transcription factors, thereby priming cells for lineage specification.
          Cover page: GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2022)
          Coronary artery bypass graft (CABG) is associated with a high risk of mortality and morbidity; thus, assessment of surgery quality is necessary. In this perspective, we will focus on the structure, process, and outcomes measured as quality assessment. A set of 21 evidence-based structure, process, and outcome measures were selected as National Quality Forum. Of these, the Society of Thoracic Surgeons ultimately chose 11 individual quality measures grouped them into four domains used to assess the quality of CABGs. These four domains consisted of perioperative medical care, operative care, risk-adjusted operative mortality and postoperative risk-adjusted major morbidity. These measures have been useful as quality improvement tools in assessing the quality of CABG surgery.
            Cover page: Methodology in coronary artery bypass surgery quality assessment.
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2018)
            PROBLEM:Academic medical centers struggle to achieve parity in advancement and promotions between educators and discovery-oriented researchers in part because of narrow definitions of scholarship, lack of clear criteria for measuring excellence, and barriers to making educational contributions available for peer review. Despite recent progress in expanding scholarship definitions and identifying excellence criteria, these advances are not integrated into educator portfolio (EP) templates or curriculum vitae platforms. APPROACH:From 2013 to 2015, a working group from the Academy of Medical Educators (AME) at the University of California, San Francisco (UCSF) designed a streamlined, criteria-based EP (EP 2.0) template highlighting faculty members' recent activities in education and setting rigorous evaluation methods to enable educational scholarship to be objectively evaluated for academic advancement, AME membership, and professional development. OUTCOMES:The EP 2.0 template was integrated into the AME application, resulting in high overall satisfaction among candidates and the selection committee and positive feedback on the template's transparency, ease of use, and streamlined format. In 2016, the EP 2.0 template was integrated into the campus-wide curriculum vitae platform and academic advancement system. NEXT STEPS:The authors plan to increase awareness of the EP 2.0 template by educating promotions committees and faculty at UCSF and partnering with other institutions to disseminate it for use. They also plan to study the impact of the template on supporting educators by making their important scholarly contributions available for peer review, providing guidance for professional development, and decreasing disparities in promotions.
              Cover page: Rethinking the Educator Portfolio: An Innovative Criteria-Based Model.
              • Article
              • Peer Reviewed
              LBL Publications (2015)

              Background

              The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. The cellular processes regulated by many of these EBPs remain unknown.

              Results

              To characterize the σ(54)-dependent regulome of D. vulgaris Hildenborough, we identified EBP binding motifs and regulated genes by a combination of computational and experimental techniques. These predictions were supported by our reconstruction of σ(54)-dependent promoters by comparative genomics. We reassessed and refined the results of earlier studies on regulation in D. vulgaris Hildenborough and consolidated them with our new findings. It allowed us to reconstruct the σ(54) regulome in D. vulgaris Hildenborough. This regulome includes 36 regulons that consist of 201 coding genes and 4 non-coding RNAs, and is involved in nitrogen, carbon and energy metabolism, regulation, transmembrane transport and various extracellular functions. To the best of our knowledge, this is the first report of direct regulation of alanine dehydrogenase, pyruvate metabolism genes and type III secretion system by σ(54)-dependent regulators.

              Conclusions

              The σ(54)-dependent regulome is an important component of transcriptional regulatory network in D. vulgaris Hildenborough and related free-living Deltaproteobacteria. Our study provides a representative collection of σ(54)-dependent regulons that can be used for regulation prediction in Deltaproteobacteria and other taxa.
                Cover page: σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough
                • Article
                LBL Publications (2009)
                  Cover page: Endothelial Cell Migration and Vascular Endothelial Growth Factor Expression Are the Result of Loss of Breast Tissue Polarity
                  • Article
                  • Peer Reviewed
                  LBL Publications (2015)

                  Unlabelled

                  Sulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields. Desulfovibrio vulgaris Hildenborough, a model SRB, carries a cytochrome c-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon. NrfR activates the expression of the nrfHA operon in response to nitrite stress. We also show that nrfR is needed for fitness at low cell densities in the presence of nitrite because inactivation of nrfR affects the rate of nitrite reduction. We also predict and validate the binding sites for NrfR upstream of the nrfHA operon using purified NrfR in gel shift assays. We discuss possible roles for NrfR in regulating nitrate reductase genes in nitrate-utilizing Desulfovibrio spp.

                  Importance

                  The NrfA nitrite reductase is prevalent across several bacterial phyla and required for dissimilatory nitrite reduction. However, regulation of the nrfA gene has been studied in only a few nitrate-utilizing bacteria. Here, we show that in D. vulgaris, a bacterium that does not respire nitrate, the expression of nrfHA is induced by NrfR upon nitrite stress. This is the first report of regulation of nrfA by a sigma54-dependent two-component system. Our study increases our knowledge of nitrite stress responses and possibly of the regulation of nitrate reduction in SRB.
                    • Article
                    • Peer Reviewed
                    UC Merced Previously Published Works (2014)
                    Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae, phylum Bacteroidetes. Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occur in diverse habitats, such as rhizosphere and contaminated soils, viscous wastes, composts, biofilter clean-up facilities on contaminated sites and cave environments, and they are involved in the degradation of complex and toxic compounds. Here we describe the features of O. sitiensis AW-6(T), together with the permanent-draft genome sequence and annotation. The organism was sequenced under the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome Institute and is the first genome sequence of a species within the genus Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%) were assigned to a putative function. The identification of 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates involvement of this organism in the catechol catabolic pathway. In addition, genes encoding for β-1,4-xylanases and β-1,4-xylosidases reveal the xylanolytic action of O. sitiensis.
                      Cover page: High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6T), a diphenol degrader with genes involved in the catechol pathway
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