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Open Access Publications from the University of California

Scholarly Works (95 results)

  • Article
Hydrology (2011)

Since 2009, one in eight San Francisco Unified School District (SFUSD) elementary schools has received a rainwater cistern or barrels and increased garden space under the Tap the Sky initiative.  A quarter of San Francisco elementary schools and two of the city's nine alternative configured schools are planned to have received a cistern system by the end of next year.

This report seeks to identify the impacts and key components of this rainwater capture initiative, both in terms of sustainable water management and environmental education goals, while also suggesting recommendations for the ongoing implementation and expansion of this practice in San Francisco elementary schools.

    Cover page: Rainwater Harvesting in San Francisco Schools
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2015)
    Human telomerase acts on telomeres during the genome synthesis phase of the cell cycle, accompanied by its concentration in Cajal bodies and transient colocalization with telomeres. Whether the regulation of human telomerase holoenzyme assembly contributes to the cell cycle restriction of telomerase function is unknown. We investigated the steady-state levels, assembly, and exchange dynamics of human telomerase subunits with quantitative in vivo cross-linking and other methods. We determined the physical association of telomerase subunits in cells blocked or progressing through the cell cycle as synchronized by multiple protocols. The total level of human telomerase RNA (hTR) was invariant across the cell cycle. In vivo snapshots of telomerase holoenzyme composition established that hTR remains bound to human telomerase reverse transcriptase (hTERT) throughout all phases of the cell cycle, and subunit competition assays suggested that hTERT-hTR interaction is not readily exchangeable. In contrast, the telomerase holoenzyme Cajal body-associated protein, TCAB1, was released from hTR in mitotic cells coincident with TCAB1 delocalization from Cajal bodies. This telomerase holoenzyme disassembly was reversible with cell cycle progression without any change in total TCAB1 protein level. Consistent with differential cell cycle regulation of hTERT-hTR and TCAB1-hTR protein-RNA interactions, overexpression of hTERT or TCAB1 had limited if any influence on hTR assembly of the other subunit. Overall, these findings revealed a cell cycle regulation that disables human telomerase association with telomeres while preserving the co-folded hTERT-hTR ribonucleoprotein catalytic core. Studies here, integrated with previous work, led to a unifying model for telomerase subunit assembly and trafficking in human cells.
      Cover page: Dynamics of Human Telomerase Holoenzyme Assembly and Subunit Exchange across the Cell Cycle*
      • Thesis
      • Peer Reviewed
      UC San Francisco Electronic Theses and Dissertations (2018)

      Mild traumatic brain injury (mTBI) is a major public health concern, linked with post-concussive syndrome and chronic traumatic encephalopathy. At present, standard clinical imaging fails to reliably detect traumatic axonal injury associated with mTBI and post-concussive symptoms. Diffusion tensor imaging (DTI) is an MR imaging technique that is sensitive to changes in white matter microstructure. Prior studies using DTI to investigate mTBI did not separate contact sport athletes, a population at high risk for mTBI and subconcussive head traumas, and there has been a dearth of longitudinal studies of mTBI patients. In this study, we used Tract-Based Spatial Statistics to perform cross-sectional and longitudinal analysis describing changes in DTI scalar parameters in emergency room (ER) patients and in scholastic contact sport athletes. In the acute post-injury period, athletes demonstrated an elevated rate of regional decreases in axial diffusivity compared to controls. These decreases were especially pronounced in the cerebellar peduncles, and were more pronounced in contact sport athletes compared to the ER patient population. These results lend credence to the hypothesis that post-concussive symptoms are caused by shearing of axons of an attention network in the brain with timing mediated by the cerebellum, and warrant further study of the correlation between cerebellar DTI findings and clinical outcomes in mTBI patients.

        Cover page: Diffusion Tensor Imaging Analysis of mTBI in Scholastic Athletes
        • Article
        • Peer Reviewed
        UC Santa Cruz Previously Published Works (2020)
        A number of proposed and ongoing experiments search for axion dark matter with a mass nearing the limit set by small scale structure [O(10-21 eV)]. We consider the late universe cosmology of these models, showing that requiring the axion to have a matter-power spectrum that matches that of cold dark matter constrains the magnitude of the axion couplings to the visible sector. Comparing these limits to current and future experimental efforts, we find that many searches require axions with an abnormally large coupling to Standard Model fields, independently of how the axion was populated in the early Universe. We survey mechanisms that can alleviate the bounds, namely, the introduction of large charges, various forms of kinetic mixing, a clockwork structure, and imposing a discrete symmetry. We provide an explicit model for each case and explore their phenomenology and viability to produce detectable ultralight axion dark matter.
          Cover page: Cosmological tension of ultralight axion dark matter and its solutions
          • Thesis
          • Peer Reviewed
          UC Berkeley Electronic Theses and Dissertations (2018)

          This dissertation investigates the causes and consequences of policy variation and policy polarization in the U.S. states. Chapter 2 describes policy change over time. Since the 1970s, state governments have implemented important policies while national policymaking has slowed, such that Americans' relationships to government are increasingly determined by their states of residence. This policy variation is increasingly associated with party control of state government, and carries major consequences for the lives of residents. Chapter 3 further investigates the measurement of policy outcomes, suggesting that prior measures may understate policy polarization in recent years. Chapter 4 estimates the relationship between public opinion and policy outcomes. Results suggest that this relationship varies widely by policy issue area, with marijuana and LGBT rights policy showing strong responsiveness. While public opinion may play an inconsistent role in state policy change, Chapter 5 suggests that changes in activist group behavior may influence legislative behavior and policy outcomes in the states. The implications of this dissertation challenge traditional theories of federalism and state politics, suggesting that organized and well-resourced political actors, not ordinary voters, have collapsed American politics into a single national arena of contestation over the direction of public policy.

            Cover page: Polarized Federalism: Activists, Voters, and the Resurgence of State Policy in the U.S.
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2024)
            Plant-systemic neonicotinoid (NN) insecticides can exert non-target impacts on organisms like beneficial insects and soil microbes. NNs can affect plant microbiomes, but we know little about their effects on microbial communities that mediate plant-insect interactions, including nectar-inhabiting microbes (NIMs). Here we employed two approaches to assess the impacts of NN exposure on several NIM taxa. First, we assayed the in vitro effects of six NN compounds on NIM growth using plate assays. Second, we inoculated a standardised NIM community into the nectar of NN-treated canola (Brassica napus) and assessed microbial survival and growth after 24 h. With few exceptions, in vitro NN exposure tended to decrease bacterial growth metrics. However, the magnitude of the decrease and the NN concentrations at which effects were observed varied substantially across bacteria. Yeasts showed no consistent in vitro response to NNs. In nectar, we saw no effects of NN treatment on NIM community metrics. Rather, NIM abundance and diversity responded to inherent plant qualities like nectar volume. In conclusion, we found no evidence that NIMs respond to field-relevant NN levels in nectar within 24 h, but our study suggests that context, specifically assay methods, time and plant traits, is important in assaying the effects of NNs on microbial communities.
              Creative Commons 'BY-NC-ND' version 4.0 license
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2021)
              If gravitational perturbations are quantized into gravitons in analogy with the electromagnetic field and photons, the resulting graviton interactions should lead to an entangling interaction between massive objects. We suggest a test of this prediction. To do this, we introduce the concept of interactive quantum information sensing. This novel sensing protocol is tailored to provable verification of weak dynamical entanglement generation between a pair of systems. We show that this protocol is highly robust to typical thermal noise sources. Moreover, the sensitivity can be increased both using an initial thermal state and/or an initial phase of entangling via a nongravitational interaction. We outline a concrete implementation testing the ability of the gravitational field to generate entanglement between an atomic interferometer and a mechanical oscillator. Preliminary numerical estimates suggest that near-term devices could feasibly be used to perform the experiment.
                Cover page: Using an Atom Interferometer to Infer Gravitational Entanglement Generation
                • Article
                • Peer Reviewed
                UC Santa Cruz Previously Published Works (2017)
                The DREAM (Dp/Retinoblastoma(Rb)-like/E2F/MuvB) transcriptional repressor complex acts as a gatekeeper of the mammalian cell cycle by establishing and maintaining cellular quiescence. How DREAM's three functional components, the E2F-DP heterodimer, the Rb-like pocket protein, and the MuvB subcomplex, form and function at target gene promoters remains unknown. The current model invokes that the pocket protein links E2F-DP and MuvB and is essential for gene repression. We tested this model by assessing how the conserved yet less redundant DREAM system in Caenorhabditis elegans is affected by absence of the sole C. elegans pocket protein LIN-35. Using a LIN-35 protein null mutant, we analyzed the assembly of E2F-DP and MuvB at promoters that are bound by DREAM and the level of expression of those "DREAM target genes" in embryos. We report that LIN-35 indeed mediates the association of E2F-DP and MuvB, a function that stabilizes DREAM subunit occupancy at target genes. In the absence of LIN-35, the occupancy of E2F-DP and MuvB at most DREAM target genes decreases dramatically and many of those genes become upregulated. The retention of E2F-DP and MuvB at some target gene promoters in lin-35 null embryos allowed us to test their contribution to DREAM target gene repression. Depletion of MuvB, but not E2F-DP, in the sensitized lin-35 null background caused further upregulation of DREAM target genes. We conclude that the pocket protein functions primarily to support MuvB-mediated repression of DREAM targets and that transcriptional repression is the innate function of the evolutionarily conserved MuvB complex. Our findings provide important insights into how mammalian DREAM assembly and disassembly may regulate gene expression and the cell cycle.
                  Cover page: Loss of the Caenorhabditis elegans pocket protein LIN-35 reveals MuvB's innate function as the repressor of DREAM target genes
                  • Article
                  • Peer Reviewed
                  UC Santa Cruz Previously Published Works (2015)
                  Formation of heterochromatin serves a critical role in organizing the genome and regulating gene expression. In most organisms, heterochromatin flanks centromeres and telomeres. To identify heterochromatic regions in the heavily studied model C. elegans, which possesses holocentric chromosomes with dispersed centromeres, we analyzed the genome-wide distribution of the heterochromatin protein 1 (HP1) ortholog HPL-2 and compared its distribution to other features commonly associated with heterochromatin. HPL-2 binding highly correlates with histone H3 mono- and dimethylated at lysine 9 (H3K9me1 and H3K9me2) and forms broad domains on autosomal arms. Although HPL-2, like other HP1 orthologs, binds H3K9me peptides in vitro, the distribution of HPL-2 in vivo appears relatively normal in mutant embryos that lack H3K9me, demonstrating that the chromosomal distribution of HPL-2 can be achieved in an H3K9me-independent manner. Consistent with HPL-2 serving roles independent of H3K9me, hpl-2 mutant worms display more severe defects than mutant worms lacking H3K9me. HPL-2 binding is enriched for repetitive sequences, and on chromosome arms is anticorrelated with centromeres. At the genic level, HPL-2 preferentially associates with well-expressed genes, and loss of HPL-2 results in up-regulation of some binding targets and down-regulation of others. Our work defines heterochromatin in an important model organism and uncovers both shared and distinctive properties of heterochromatin relative to other systems.
                    Cover page: Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2014)
                    In calves, passive immunity of immunoglobulins can be acquired through ingestion of colostrum or colostrum replacers. Plasma can been used to supplement immunoglobulins in healthy or sick calves. Serum half-life of colostral derived immuglobulin G (IgG) is estimated to be 20 days. Half-life of IgG is important in determining response to antigens and timing of vaccination in calves. To date studies evaluating half-life of colostrum replacer or plasma derived IgG are lacking. The objectives of this study were to compare the serum half-life of IgG derived from colostrum, colostrum replacer and plasma in dairy calves reared up to 35 days of age. Thirty Jersey calves were randomly assigned to receive colostrum or colostrum replacer by oroesophageal tubing or plasma by intravenous administration. Serum samples were collected at 2, 5, 7, 10, 14, 21, 28 and 35 days. Serum IgG concentrations were determined by radial immunodiffusion. The results indicated that half-life for IgG in colostrum fed (28.5 days) or plasma transfused calves (27.3 days) was longer than colostrum replacer fed calves (19.1 days). Further studies are required to evaluate pathogen specific immunoglobulins in order to recommend vaccination timing in calves fed colostrum replacers.
                      Cover page: Comparison of serum immunoglobulin G half-life in dairy calves fed colostrum, colostrum replacer or administered with intravenous bovine plasma
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