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Open Access Publications from the University of California

Scholarly Works (30 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2011)

This study compared the use of grade versus instructional level material for progress monitoring struggling readers by examining the materials' psychometric characteristics and the data's influence on teacher expectations and instructional decision-making. Students were progress monitored with both sets of probes for 6 - 8 weeks. Each set of data was analyzed for sensitivity to growth and predictive validity and evaluated by classroom teachers. Results found no statistical difference in sensitivity to growth or predictive validity (p > .05). Both data based decision rules based on trend analysis and teacher responses to questionnaires indicated that grade level data was more likely to portray student progress as inadequate and the current intervention as needing modification and/or increase in intensity. Limitations of the study and directions for future research are discussed.

    Cover page: Progress Monitoring at Grade vs Instructional Level
    • Thesis
    • Peer Reviewed
    UC Riverside Electronic Theses and Dissertations (2014)

    To improve reading proficiency, evidence-based interventions need to be implemented with integrity in schools. Using a multiple baseline single case design, this study examined the impact of performance feedback from consultants on treatment integrity and student outcomes for Peer Assisted Learning Strategies, an evidence-based, standard protocol, class-wide peer tutoring intervention. Participants were four grade 2 to 5 general education teachers and the students in their classes. Results showed a functional relationship between performance feedback and treatment integrity, including higher treatment integrity of core intervention components. Reading growth rates appeared to have increased, but changes were not statistically significant. Overall, teachers rated the performance feedback procedure and PALS positively. Limitations of the study, implications for practice, and directions for future research are discussed.

      Cover page: The Impact of Performance Feedback on Treatment Integrity and Outcomes for a Class-Wide Peer Tutoring Reading Intervention
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2020)
      Antimicrobial and antiviral materials have attracted significant interest in recent years due to increasing occurrences of nosocomial infections and pathogenic microbial contamination. One method to address this is the combination of photoactive compounds that can produce reactive oxygen species (ROS), such as hydrogen peroxide and hydroxyl radicals to disinfect microbes, with carrier materials that meet the application requirements. Using anthraquinone (AQ) and cellulose nanocrystals (CNCs) as the photoactive and carrier components, respectively, this work demonstrated the first covalent incorporation of AQ onto CNCs. The morphology and the photoactive properties were investigated, revealing the structural integrity of the CNCs and the high degree of photoactivity of the AQ-CNC materials upon UVA exposure. The AQ-CNCs also exhibited an unexpected persistent generation of ROS under darkness, which adds advantages for antimicrobial applications.
        Cover page: Daylight-Active Cellulose Nanocrystals Containing Anthraquinone Structures
        • Article
        LBL Publications (2003)
          Cover page: Functional annotation of mouse mutations in embryonic stem cells using expression profiling
          • Article
          • Peer Reviewed
          Lawrence Berkeley National Laboratory (2004)

          The functional importance of the approximately 98 percent of mammalian genomes not corresponding to protein coding sequences remain largely un-scrutinized 1. To test experimentally whether some extensive regions of non-coding DNA, referred to as gene deserts 2-4, contain critical functions essential for the viability of the organism, we deleted two large non-coding intervals, 1,511 kb and 845 kb in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regards to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further in-depth analysis of the expression of genes bracketing the deletions revealed similar expression characteristics in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (>100bp, 70 percent identity). These studies demonstrate that some large-scale deletions of non-coding DNA can be well tolerated by an organism, bringing into question the role of many human-mouse conserved sequences 5,6, and further supports the existence of potentially "disposable DNAi" in the genomes of mammals.

            Cover page: Megabase deletions of gene deserts result in viable mice
            • Article
            Lawrence Berkeley National Laboratory (2007)

            Ultraconserved elements have been suggested to retain extended perfect sequence identity between the human, mouse, and rat genomes due to essential functional properties. To investigate the necessities of these elements in vivo, we removed four non-coding ultraconserved elements (ranging in length from 222 to 731 base pairs) from the mouse genome. To maximize the likelihood of observing a phenotype, we chose to delete elements that function as enhancers in a mouse transgenic assay and that are near genes that exhibit marked phenotypes both when completely inactivated in the mouse as well as when their expression is altered due to other genomic modifications. Remarkably, all four resulting lines of mice lacking these ultraconserved elements were viable and fertile, and failed to reveal any critical abnormalities when assayed for a variety of phenotypes including growth, longevity, pathology and metabolism. In addition more targeted screens, informed by the abnormalities observed in mice where genes in proximity to the investigated elements had been altered, also failed to reveal notable abnormalities. These results, while not inclusive of all the possible phenotypic impact of the deleted sequences, indicate that extreme sequence constraint does not necessarily reflect crucial functions required for viability.

              Cover page: Deletion of ultraconserved elements yields viable mice
              • Article
              • Peer Reviewed
              UC Riverside Previously Published Works (2023)
              Fluoroalkylether substances (ether PFAS) constitute a large group of emerging PFAS with uncertain environmental fate. Among them, GenX is the well-known alternative to perfluorooctanoic acid and one of the six proposed PFAS to be regulated by the U.S. Environmental Protection Agency. This study investigated the structure-biodegradability relationship for 12 different ether PFAS with a carboxylic acid headgroup in activated sludge communities. Only polyfluorinated ethers with at least one -CH2- moiety adjacent to or a C=C bond in the proximity of the ether bond underwent active biotransformation via oxidative and hydrolytic O-dealkylation. The bioreactions at ether bonds led to the formation of unstable fluoroalcohol intermediates subject to spontaneous defluorination. We further demonstrated that this aerobic biotransformation/defluorination could complement the advanced reduction process in a treatment train system to achieve more cost-effective treatment for GenX and other recalcitrant perfluorinated ether PFAS. These findings provide essential insights into the environmental fate of ether PFAS, the design of biodegradable alternative PFAS, and the development of cost-effective ether PFAS treatment strategies.
                Cover page: Aerobic Biotransformation and Defluorination of Fluoroalkylether Substances (ether PFAS): Substrate Specificity, Pathways, and Applications
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2019)
                Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but its application to plants has been limited. Here, we used the high-throughput Drop-seq approach to profile >12,000 cells from Arabidopsis roots. This identified numerous distinct cell types, covering all major root tissues and developmental stages, and illuminated specific marker genes for these populations. In addition, we demonstrate the utility of this approach to study the impact of environmental conditions on developmental processes. Analysis of roots grown with or without sucrose supplementation uncovers changes in the relative frequencies of cell types in response to sucrose. Finally, we characterize the transcriptome changes that occur across endodermis development and identify nearly 800 genes with dynamic expression as this tissue differentiates. Collectively, we demonstrate that single-cell RNA-seq can be used to profile developmental processes in plants and show how they can be altered by external stimuli.
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2020)
                  Progressive synapse loss is an inevitable and insidious part of age-related neurodegenerative disease. Typically, synapse loss precedes symptoms of cognitive and motor decline. This suggests the existence of compensatory mechanisms that can temporarily counteract the effects of ongoing neurodegeneration. Here, we demonstrate that presynaptic homeostatic plasticity (PHP) is induced at degenerating neuromuscular junctions, mediated by an evolutionarily conserved activity of presynaptic ENaC channels in both Drosophila and mouse. To assess the consequence of eliminating PHP in a mouse model of ALS-like degeneration, we generated a motoneuron-specific deletion of Scnn1a, encoding the ENaC channel alpha subunit. We show that Scnn1a is essential for PHP without adversely affecting baseline neural function or lifespan. However, Scnn1a knockout in a degeneration-causing mutant background accelerated motoneuron loss and disease progression to twice the rate observed in littermate controls with intact PHP. We propose a model of neuroprotective homeostatic plasticity, extending organismal lifespan and health span.
                    Cover page: Presynaptic Homeostasis Opposes Disease Progression in Mouse Models of ALS-Like Degeneration: Evidence for Homeostatic Neuroprotection
                    • Article
                    LBL Publications (2012)
                    In the process of clone-based genome sequencing, initial assemblies frequently contain cloning gaps that can be resolved using cloning-independent methods, but the reason for their occurrence is largely unknown. By analyzing 9,328,693 sequencing clones from 393 microbial genomes we systematically mapped more than 15,000 genes residing in cloning gaps and experimentally showed that their expression products are toxic to the Escherichia coli host. A subset of these toxic sequences was further evaluated through a series of functional assays exploring the mechanisms of their toxicity. Among these genes our assays revealed novel toxins and restriction enzymes, and new classes of small non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses also revealed abundant, short toxic DNA fragments that were predicted to suppress E. coli growth by interacting with the replication initiator dnaA. Our results show that cloning gaps, once considered the result of technical problems, actually serve as a rich source for the discovery of biotechnologically valuable functions, and suggest new modes of antimicrobial interventions.
                      Cover page: A vast collection of microbial genes that are toxic to bacteria
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