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Open Access Publications from the University of California

Scholarly Works (417 results)

  • Article
Lawrence Berkeley National Laboratory (2008)
    Cover page: Depth-resolved soft x-ray photoelectron emission microscopy in nanostructures via standing-wave excited photoemission
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2019)
    It is important to draw causal inference from observational studies, but this becomes challenging if the confounders have missing values. Generally, causal effects are not identifiable if the confounders are missing not at random. In this article we propose a novel framework for nonparametric identification of causal effects with confounders subject to an outcome-independent missingness, which means that the missing data mechanism is independent of the outcome, given the treatment and possibly missing confounders. We then propose a nonparametric two-stage least squares estimator and a parametric estimator for causal effects.
      Cover page: Causal inference with confounders missing not at random
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2011)
        Cover page: APE/Ref-1, a druggable target for the therapy of human melanomaCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2019)
        In response to stress, cells must quickly reprogram gene expression to adapt and survive. This is achieved in part by altering levels of mRNAs and their translation into proteins. Recently, the formation of two stress-induced messenger ribonucleoprotein (mRNP) assemblies named stress granules and processing bodies has been postulated to directly impact gene expression during stress. These assemblies sequester and concentrate specific proteins and RNAs away from the larger cytoplasm during stress, thereby providing a layer of posttranscriptional gene regulation with the potential to directly impact mRNA levels, protein translation, and cell survival. The function of these granules has generally been ascribed either by the protein components concentrated into them or, more broadly, by global changes that occur during stress. Recent proteome- and transcriptome-wide studies have provided a more complete view of stress-induced mRNP granule composition in varied cell types and stress conditions. However, direct measurements of the phenotypic and functional consequences of stress granule and processing body formation are lacking. This leaves our understanding of their roles during stress incomplete. Continued study into the function of these granules will be an important part in elucidating how cells respond to and survive stressful environmental changes. This article is categorized under: Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Export and Localization > RNA Localization.
          Cover page: Stress‐induced mRNP granules: Form and function of processing bodies and stress granules
          • Article
          LBL Publications (2003)
            Cover page: A heat exchanger between forced flow helium gas at 14 to 18 K and liquid hydrogen at 20 K circulated by natural convection
            • Thesis
            • Peer Reviewed
            UC San Diego Electronic Theses and Dissertations (2021)

            During times of unpredictable stress, organisms must adapt their gene expression to maximize survival. Along with changes in transcription, one conserved means of gene regulation during conditions that quickly represses translation is the formation of cytoplasmic phase-separated mRNP (messenger ribonucleoprotein) granules. Two well-known stress-induced mRNP granules are processing bodies (P-bodies) and stress granules. Previously, we identified that distinct steps in gene expression can be coupled during glucose starvation stress as promoter sequences in the nucleus are able to direct the subcellular localization to or excluded from the phase-separated granules and translatability of mRNAs in the cytosol. During my Ph.D., I have been investigating the underlying mechanisms of how promoter dictates the cytoplasmic fate of mRNAs during glucose starvation. Chapter 1 is a background introduction of the questions I asked. In chapter 2, I led a discovery of a promoter-directed mechanism mediated by AAA+ proteins Rvb1/Rvb2 that couple the transcription, mRNA cytoplasmic localization, and translation of select genes during glucose starvation. In chapter 3, colleagues and I reviewed recent findings regarding stress-related phase-separated granules and shared our insights. Chapter 4 describes 3 projects that aimed to answer the promoter-dictation question from other perspectives, such as expression timing and promoter motifs. Finally, Chapter 5 discusses insights and future directions for my thesis work. I anticipate that these studies will provide us with more insights into complex gene regulation during stressful and pathological conditions.

            • 4 supplemental ZIPs
            Cover page: Investigating promoter-driven mRNA localization and translational control during stress
            • Article
            LBL Publications (2003)
              Cover page: Focusing solenoids for the MICE cooling channel
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2012)
              Background: A detailed analysis of whole genomes can be now achieved with next generation sequencing. Epstein Barr Virus (EBV) transformation is a widely used strategy in clinical research to obtain an unlimited source of a subject's DNA. Although the mechanism of transformation and immortalization by EBV is relatively well known at the transcriptional and proteomic level, the genetic consequences of EBV transformation are less well understood. A detailed analysis of the genetic alterations introduced by EBV transformation is highly relevant, as it will inform on the usefulness and limitations of this approach.Results: We used whole genome sequencing to assess the genomic signature of a low-passage lymphoblastoid cell line (LCL). Specifically, we sequenced the full genome (40X) of an individual using DNA purified from fresh whole blood as well as DNA from his LCL. A total of 217.33 Gb of sequence were generated from the cell line and 238.95 Gb from the normal genomic DNA. We determined with high confidence that 99.2% of the genomes were identical, with no reproducible changes in structural variation (chromosomal rearrangements and copy number variations) or insertion/deletion polymorphisms (indels).Conclusions: Our results suggest that, at this level of resolution, the LCL is genetically indistinguishable from its genomic counterpart and therefore their use in clinical research is not likely to introduce a significant bias. © 2012 Nickles et al.; licensee BioMed Central Ltd.
                Cover page: In depth comparison of an individual's DNA and its lymphoblastoid cell line using whole genome sequencing
                • Article
                LBL Publications (2003)
                  Cover page: A 201 MHz RF cavity design with non-stressed pre-curved Be windows for muon cooling channels
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2016)
                  In the United States, 19.2% of Neisseria gonorrhoeae isolates are resistant to ciprofloxacin. We evaluated a real-time PCR assay to predict ciprofloxacin susceptibility using residual DNA from the Roche Cobas 4800 CT/NG assay. The results of the assay were 100% concordant with agar dilution susceptibility test results for 100 clinical isolates. Among 76 clinical urine and swab specimens positive for N. gonorrhoeae by the Cobas assay, 71% could be genotyped. The test took 1.5 h to perform, allowing the physician to receive results in time to make informed clinical decisions.
                    Cover page: Performance and Verification of a Real-Time PCR Assay Targeting the gyrA Gene for Prediction of Ciprofloxacin Resistance in Neisseria gonorrhoeae
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