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Open Access Publications from the University of California

Scholarly Works (22 results)

  • Article
  • Peer Reviewed
The Undergraduate Historical Journal at UC Merced, Volume 2, Issue 2 (2015)
    Cover page: From Aden to Hong Kong, British Imperialism and the Roots of National ResistanceCreative Commons 'BY-NC-ND' version 4.0 license
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2014)
    Recurrent chromosomal deletions in cancer are typically thought to harbor tumor suppressors. In a recent publication in Nature, Northcott and colleagues identify a novel region of structural variation in medulloblastoma that leads to oncogenic activation of GFI1B and GFI1 by repositioning these genes next to super-enhancers.
      Cover page: When Deletions Gain Functions: Commandeering Epigenetic Mechanisms
      • Article
      UCR Honors Capstones 2016-2017 (2017)
        Cover page: Behavioral Changes of Macrophages and Neutrophils During Biofilm Induction: Neutrophil Aggregate Formation in Response to Bacteria
        • Thesis
        • Peer Reviewed
        UC San Francisco Electronic Theses and Dissertations (2014)

        Alternative splicing plays critical roles in normal development and can promote growth and survival in cancer. Genes that have canonical splice variants that function antagonistically can be ectopically expressed to drive malignant progression. Additionally, aberrant splicing, the production of noncanonical and cancer‐specific mRNA transcripts, can lead to loss‐of‐function in tumor suppressors or activation of oncogenes and cancer pathways. Emerging data suggests that aberrant splicing products and loss of canonically spliced variants correlate with stage and progression in malignancy. Not only do these data illuminate roles for alternative splicing in cancer and intersections between alternative splicing pathways and therapy, but they illustrate the importance of understanding the genetic basis of splicing.

        Using a transgenic model of neuroblastoma, we set up a backcrossed genetic system to derive distinct virtual genomes of over 100 individual mice in which we have profiled exon expression in two different neural tissues. We identified splicing quantitative trait loci (sQTL) which map genetic control of splicing and define key splicing motifs. We identify these motifs as sites of recurrent somatic mutations in cancer. We also use this analysis to identify novel effector splicing events. Among these, we show that a triplet splicing event within FUBP1 modulates levels of the MYC oncoprotein in human neuroblastoma‐derived cell line, and correlates with outcome in neuroblastoma.

          Cover page: The genetics of splicing in cancer
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2014)
          Toward addressing the difficult problems of knee meniscus regeneration, a self-assembling process has been used to re-create the native morphology and matrix properties. A significant problem in such attempts is the recapitulation of the distinct zones of the meniscus, the inner, more cartilaginous and the outer, more fibrocartilaginous zones. In this study, an anisotropic and zonally variant meniscus was produced by self-assembly of the inner meniscus (100% chondrocytes) followed by cell seeding the outer meniscus (coculture of chondrocytes and meniscus cells). After 4 weeks in culture, the engineered, inner meniscus exhibited a 42% increase in both instantaneous and relaxation moduli and a 62% increase in GAG/DW, as compared to the outer meniscus. In contrast, the circumferential tensile modulus and collagen/DW of the outer zone was 101% and 129% higher, respectively, than the values measured for the inner zone. Furthermore, there was no difference in the radial tensile modulus between the control and zonal engineered menisci, suggesting that the inner and outer zones of the engineered zonal menisci successfully integrated. These data demonstrate that not only can biomechanical and biochemical properties be engineered to differ by the zone, but they can also recapitulate the anisotropic behavior of the knee meniscus.
            Cover page: Building an Anisotropic Meniscus with Zonal Variations
            • Article
            • Peer Reviewed
            UC Riverside Previously Published Works (2020)
            Bacterial infections associated with implanted medical devices represents a healthcare crisis due to their persistence, antibiotic tolerance, and immune avoidance. Indwelling devices are rapidly coated with host plasma and extracellular matrix proteins which can then be exploited by bacterial pathogens for adherence and subsequent biofilm development. Our understanding of the host-pathogen interface that determines the fate of biofilm-mediated infections is limited to the experimental models employed by laboratories studying these organisms. Current in vivo models of biofilm-mediated infection, while certainly useful, are typically limited to end-point analyses of bacterial burden enumeration, immune cell profiling, and cytokine/chemokine analysis. Thus, with these models, the complex, real-time assessment of biofilm development and innate immune cell activity remains imperceptible. Here, we describe a novel murine biofilm infection model employing time-lapse intravital multiphoton microscopy which permits concurrent and real-time visualization of Staphylococcus aureus biofilm formation and immune cell activity. Using cell tracking, we found that S. aureus biofilms impede neutrophil chemotaxis, redirecting their migration patterns to prevent biofilm invasion. This approach is the first to directly examine device-associated biofilm development and host-pathogen interactions and will serve to both further our understanding of infection development and help reveal the effects of future antibiofilm treatment strategies.
              Cover page: Intravital Multiphoton Examination of Implant-Associated Staphylococcus aureus Biofilm Infection.
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2014)
              Toward addressing the difficult problems of knee meniscus regeneration, a self-assembling process has been used to re-create the native morphology and matrix properties. A significant problem in such attempts is the recapitulation of the distinct zones of the meniscus, the inner, more cartilaginous and the outer, more fibrocartilaginous zones. In this study, an anisotropic and zonally variant meniscus was produced by self-assembly of the inner meniscus (100% chondrocytes) followed by cell seeding the outer meniscus (coculture of chondrocytes and meniscus cells). After 4 weeks in culture, the engineered, inner meniscus exhibited a 42% increase in both instantaneous and relaxation moduli and a 62% increase in GAG/DW, as compared to the outer meniscus. In contrast, the circumferential tensile modulus and collagen/DW of the outer zone was 101% and 129% higher, respectively, than the values measured for the inner zone. Furthermore, there was no difference in the radial tensile modulus between the control and zonal engineered menisci, suggesting that the inner and outer zones of the engineered zonal menisci successfully integrated. These data demonstrate that not only can biomechanical and biochemical properties be engineered to differ by the zone, but they can also recapitulate the anisotropic behavior of the knee meniscus.
                Cover page: Building an Anisotropic Meniscus with Zonal Variations
                • Article
                Research Reports (2007)

                This research investigates the feasibility of offering demand-responsive transit (DRT) service to the general public in situations of low demand density. The study region is AC Transit District 2 which consists of the cities of Fremont and Newark, California.

                We developed a methodology to evaluate operating efficiencies of existing bus lines and line segments, and identified areas suitable for DRT service based on year 2001 data. We proposed an alternating strategy of checkpoint DRT service and compared it to other strategies. The report also described the schema for an automated reservation and scheduling system.

                Our initial findings are: the service cuts and route changes implemented by AC Transit district 2 after 2001 largely concur with our analysis of the 2001 system; by making very limited additional changes to the fixed routes and using the proposed checkpoint service, AC Transit could have a net savings of 2-3 buses; and finally, this service offers considerable advantage in passenger access, reliability and service cost.

                  Cover page: Design of a Demand-Responsive Transit System
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2018)
                  The efficacy of tandem dehydrogenation-condensation catalysts for the upgrade of bio-derived intermediates is largely determined by their relative (de-)hydrogenation and decarbonylation activity. Here, the effects of support and particle size of heterogeneous PdCu alloy catalysts on (de-)hydrogenation and decarbonlylation reactions were investigated using kinetic measurements, X-ray absorption spectroscopy and density functional theory (DFT). The chemical mismatch of Cu2+ with Ti4+ and Ca2+ prevents the substitution of Cu into the lattice of TiO2 or hydroxyapatite supports, and facilitates its alloying with Pd, resulting in improved selectivity for hydrogenation-dehydrogenation reactions compared to decarbonylation reactions. Based on kinetic measurements of butyraldehyde reactions over Pd and PdCu/SiO2 model catalysts, decarbonylation activity is attributed to the presence of Pd surface ensembles, while (de-)hydrogenation reactions are catalyzed by PdCu sites on the surface. This is consistent with selectivity and CO coverage trends with increasing conversion, and DFT-based microkinetic modeling. Selectivity control can also be achieved using the PdCu nanocluster size. Smaller nanoparticles favor the C-CO bond scission step of the decarbonylation reaction, due to the stronger binding of CO and alkyl species to sites of lower coordination. CO-induced segregation of reactive Pd atoms to under-coordinated step/edge sites also amplifies the geometric effect on the catalytic behavior.
                    Cover page: Selectivity tuning over monometallic and bimetallic dehydrogenation catalysts: effects of support and particle size
                    • Article
                    • Peer Reviewed
                    UC Berkeley Previously Published Works (2017)
                    Herein, we present work on the catalyst development and the kinetics of acetone-butanol-ethanol (ABE) condensation. After examining multiple combinations of metal and basic catalysts reported in the literature, Cu supported on calcined hydrotalcites (HT) was found to be the optimal catalyst for the ABE condensation. This catalyst gave a six-fold increase in reaction rates over previously reported catalysts. Kinetic analysis of the reaction over CuHT and HT revealed that the rate-determining step is the C−H bond activation of alkoxides that are formed from alcohols on the Cu surface. This step is followed by the addition of the resulting aldehydes to an acetone enolate formed by deprotonation of the acetone over basic sites on the HT surface. The presence of alcohols reduces aldol condensation rates, as a result of the coverage of catalytic sites by alkoxides.
                      Cover page: ABE Condensation over Monometallic Catalysts: Catalyst Characterization and Kinetics
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