Skip to main content
eScholarship
Open Access Publications from the University of California

Scholarly Works (110 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2013)

Micron-scale spatial reorganization of cell membrane receptor protein clusters is emerging as an important early modulator of inter- and intracellular signaling input. Detailed within is an in-vitro investigative technique utilizing cultured cells, nanolithograpically-patterned supports for fluid biomolecule-functionalized phospholipid bilayer membranes and inverted optical microscopy. This method allows the user to visualize and, if desired, restrict the formation and transport of these transient macroclusters as they coalesce on the membrane of a stimulated cell. Multi-color fluorescence imaging allows the simultaneous tracking of multiple molecules, permitting real-time analysis of coupling between surface receptors and intracellular signaling and structural proteins. The two systems examined are the T cell immunological synapse and ephrinA1-EphA2 interactions in highly invasive breast cancer cells. In both cases, it is demonstrated that induced restrictions of receptor-mediated cytoskeletal reorganization is sufficient to alter downstream signaling outcomes, and the molecular mechanisms of feedback coupling are investigated.

    Cover page: Spatial Frustration: Using Pharmacological and Mechanical Disruption of Membrane Receptor Transport to Probe Cell Signaling Dynamics on Supported Lipid Bilayers
    • Thesis
    • Peer Reviewed
    UC Riverside Electronic Theses and Dissertations (2010)

    To come - will be 350 words or less.

      Cover page: "We Ain't Scared of No Mayor": LA's Skid Row Residents Fight for Their Right to the City
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2019)
      Studying how arthropod-borne viruses interact with their arthropod vectors is critical to understanding how these viruses replicate and are transmitted. Until recently, these types of studies were limited in scale because of the lack of classical tools available to study virus-host interaction for non-model viruses and non-model organisms. Advances in systems biology "-omics"-based techniques such as next-generation sequencing (NGS) and mass spectrometry can rapidly provide an unbiased view of arbovirus-vector interaction landscapes. In this mini-review, we discuss how arbovirus-vector interaction studies have been advanced by systems biology. We review studies of arbovirus-vector interactions that occur at multiple time and length scales, including intracellular interactions, interactions at the level of the organism, viral and vector populations, and how new techniques can integrate systems-level data across these different scales.
        Cover page: Mapping Arbovirus-Vector Interactions Using Systems Biology Techniques
        • Article
        • Peer Reviewed
        SSOE Research Symposium Dean's Awards (2023)
        Traditional methods of watering plants based on timers have been shown to be wasteful when compared to sensor based watering. While sensor based irrigation systems do exist, current implementations are both costly and needlessly complex. Our goal was to design an irrigation sensor system is cheap, easy to implement, and saves more water than traditional watering systems. Our approach was to create a sensor node network that is both reliable and cost effective when installing it. With this approach we were able to create a dependable tree like sensor network that could read moisture data from soil and have it visualized in an Android application. In regards to our Android application, we were able to implement features such as sensor calibration in order to obtain accurate readings. Our tree like network was also able to be consistent in being able to send data packets back and forth with each sensor having a reach of up to 100 meters and being able to have a total of 3125 radio modules in use. In conclusion we were able to create a reliable and cost effective irrigation system that could be used for both farms and home gardens. We were able to meet our initial goals which were to create an user friendly application that could be used to read and visualize data as well creating a sensor network that is low-power and is low cost.  Advisor: Professor Sitao Huang, Department of Electrical Engineering and Computer Science
          Cover page: Automatic Irrigation System (AIS)Creative Commons 'BY' version 4.0 license
          • Article
          Other Recent Work (2006)

          This is a study of contemporary global party formation in world historical perspective. Recent efforts to organize progressive forces are intended to have a democratizing effect on global governance and the operation of the world economy. The activists want to avoid the mistakes of the past while organizing an effective effort move in the direction of a more just global system. This new project needs to be understood in world historical context with attention to the implications of the history of transnational social movements, world revolutions and the evolution of global governance over the last four centuries.

            Cover page: Global Party Formation in World Historical Perspective
            • Article
            LBL Publications (2013)
              Cover page: T-cell triggering thresholds are modulated by the number of antigen within individual T-cell receptor clusters
              • Article
              • Peer Reviewed
              Joint Genome Institute (2017)
              Antibiotic resistance genes (ARGs) are pervasive in gut microbiota, but it remains unclear how often ARGs are transferred, particularly to pathogens. Traditionally, ARG spread is attributed to horizontal transfer mediated either by DNA transformation, bacterial conjugation or generalized transduction. However, recent viral metagenome (virome) analyses suggest that ARGs are frequently carried by phages, which is inconsistent with the traditional view that phage genomes rarely encode ARGs. Here we used exploratory and conservative bioinformatic strategies found in the literature to detect ARGs in phage genomes, and experimentally assessed a subset of ARG predicted using exploratory thresholds. ARG abundances in 1181 phage genomes were vastly overestimated using exploratory thresholds (421 predicted vs 2 known), due to low similarities and matches to protein unrelated to antibiotic resistance. Consistent with this, four ARGs predicted using exploratory thresholds were experimentally evaluated and failed to confer antibiotic resistance in Escherichia coli. Reanalysis of available human- or mouse-associated viromes for ARGs and their genomic context suggested that bona fide ARG attributed to phages in viromes were previously overestimated. These findings provide guidance for documentation of ARG in viromes, and reassert that ARGs are rarely encoded in phages.
                • Article
                • Peer Reviewed
                UC San Diego Previously Published Works (2014)

                Background

                Heat and air pollution are both associated with increases in mortality. However, the interactive effect of temperature and air pollution on mortality remains unsettled. Similarly, the relationship between air pollution, air temperature, and social deprivation has never been explored.

                Methods

                We used daily mortality data from 2004 to 2009, daily mean temperature variables and relative humidity, for Paris, France. Estimates of chronic exposure to air pollution and social deprivation at a small spatial scale were calculated and split into three strata. We developed a stratified Poisson regression models to assess daily temperature and mortality associations, and tested the heterogeneity of the regression coefficients of the different strata. Deaths due to ambient temperature were calculated from attributable fractions and mortality rates were estimated.

                Results

                We found that chronic air pollution exposure and social deprivation are effect modifiers of the association between daily temperature and mortality. We found a potential interactive effect between social deprivation and chronic exposure with regards to air pollution in the mortality-temperature relationship.

                Conclusion

                Our results may have implications in considering chronically polluted areas as vulnerable in heat action plans and in the long-term measures to reduce the burden of heat stress especially in the context of climate change.
                  Cover page: Chronic air pollution and social deprivation as modifiers of the association between high temperature and daily mortality
                  • Article
                  LBL Publications (2011)
                  T cells react to extremely small numbers of activating agonist peptides. Spatial organization of T-cell receptors (TCR) and their peptide-major histocompatibility complex (pMHC) ligands into microclusters is correlated with T-cell activation. Here we have designed an experimental strategy that enables control over the number of agonist peptides per TCR cluster, without altering the total number engaged by the cell. Supported membranes, partitioned with grids of barriers to lateral mobility, provide an effective way of limiting the total number of pMHC ligands that may be assembled within a single TCR cluster. Observations directly reveal that restriction of pMHC content within individual TCR clusters can decrease T-cell sensitivity for triggering initial calcium flux at fixed total pMHC density. Further analysis suggests that triggering thresholds are determined by the number of activating ligands available to individual TCR clusters, not by the total number encountered by the cell. Results from a series of experiments in which the overall agonist density and the maximum number of agonist per TCR cluster are independently varied in primary T cells indicate that the most probable minimal triggering unit for calcium signaling is at least four pMHC in a single cluster for this system. This threshold is unchanged by inclusion of coagonist pMHC, but costimulation of CD28 by CD80 can modulate the threshold lower.
                    Cover page: T-cell triggering thresholds are modulated by the number of antigen within individual T-cell receptor clusters.
                    • Article
                    Other Recent Work (2006)

                    Little systematic research has been done on the social composition of the hundreds of thousands of people that attend the World Social Forum, or how their background characteristics and political affiliations might shape their political views. This paper addresses these questions through an analysis of original survey data of 640 participants of the 2005 World Social Forum in Porto Alegre, Brazil. We found that most WSF participants were young, from Brazil and neighboring countries, expressed radical views, and actively participated in social movements. Most also belonged to relatively privileged social groups; most were highly educated (a proxy measure for class), and “white” was the most common racial identity. Results from our logistic regression analysis indicate that there were statistically significant differences among respondents’ political goals and preferred strategies for social change based on their world system position, race, and membership in different types of organizations; there were not statistically significant differences in respondents’ political views based on their gender, age, or years of education however.

                      Cover page: Alliances and Divisions within the“Movement of Movements”:Survey Findings from the 2005 World Social Forum
                      Top