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Open Access Publications from the University of California

Scholarly Works (27 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2019)

Post-translational modifications (PTMs) on histone proteins affect many essential biological processes. With the abundance of PTMs on histone proteins, these modifications can collectively work together to alter chromatin structure and impact gene expression in this complex system. Detection and understanding of these PTMs, as well as the enzymes that mediate them, can elucidate their biological outcomes and connection to pathogenesis. Mass spectrometry (MS) is a powerful tool that is most often used for identification and characterization of modification patterns, and it has greatly expanded the library of histone modifications. However, MS does require coupling to separation techniques, such as reversed-phase liquid chromatography and hydrophilic interaction chromatography, in order to reduce sample complexity and improve analysis. While chromatographic techniques have been widely used, multiple columns and long separation times are required for peptides that are more challenging to separate. For instance, methylation does not alter the charge of lysine residues; in addition, it introduces only subtle changes in size and hydrophobicity. Recently, there has been an increasing interest in synthetic receptors that have affinity for lysine methylation. Such receptors include water-soluble calixarenes, cucurbiturils, and deep cavitands. Capillary electrophoresis (CE) is an extremely suitable separation method that can be combined with these synthetic receptors, which can be easily included in the separation buffer. In this work, we first developed a method to induce mobility shifts for methylated small guests and peptides. After combining the high resolving power of CE and the selective recognition of host molecules, separation of modified and unmodified peptides was achieved. This host-assisted CE method was able to discriminate between different lysine methylation levels; essentially, this enabled the monitoring of various PTM enzyme reactions, including demethylation, methylation, and phosphorylation. This technique has also demonstrated its capability for analysis of a crosstalk event in which a pre-existing histone modification can impact the activity of an enzyme for another PTM. Furthermore, there is potential of host-assisted CE to separate proteins with PTMs as well.

    Cover page: Separation of Modified Biomolecules With Synthetic Receptors in Capillary Electrophoresis
    • Thesis
    • Peer Reviewed
    UC Irvine Electronic Theses and Dissertations (2021)

    Decades of scholarly work continue to document the marginalization of children from nondominant backgrounds in mathematics classrooms. Learning to equitably teach children from linguistically, ethnically, racially, and culturally diverse backgrounds remains a priority. This dissertation approaches this broader problem in society by understanding how to prepare elementary teacher candidates to center equity in their mathematics teaching. The first study explores how an innovative pedagogical activity elicits and has candidates confront their expectations, assumptions, and biases about children and their mathematical thinking. The study conceptualizes a framework that captures the extent of candidates’ self-awareness of their assumptions and biases. The second study conceptualizes teacher candidates’ conceptions of equity in mathematics teaching and explores their prior mathematics experiences. The third study tells the story of how a researcher-practitioner collaboration developed and shifted the mathematics course to integrate an equity lens over time. Research data include candidates’ written reflections, interviews, and other artifacts they produced in the methods course; field notes of class observations; teacher educators’ interviews and syllabi; and other documentations of idea exchanges between the teacher educator and researcher. Qualitative analytic methods were employed.The study findings reflect the importance of self-confrontation and critical self-reflection in a mathematics methods course to support candidates to center equity in their practice. The three studies contribute to the field of teacher preparation in the following ways: (1) a conceptual framework for candidates’ self-awareness of their biases and assumptions and a conceptual framework for centering equity in mathematics teaching; (2) a typology for teacher candidates’ conceptions of equity in mathematics teaching and a more nuanced understanding of candidates’ prior mathematical experiences; (3) an illustrative example of how a collaborative relationship between a researcher and practitioner developed over shared sensemaking experiences.

      Cover page: Developing Teacher Candidates' Self-Awareness and Vision for Equitable Mathematics Teaching through a Researcher-Teacher Educator Partnership
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2016)

      Background

      Few studies have examined ambulatory cardiovascular physiological parameters of taxi drivers while driving in relation to their occupational hazards. This study aims to investigate and quantify the impact of worksite physical hazards as a whole on ambulatory heart rate of professional taxi drivers while driving without their typical worksite psychosocial stressors.

      Methods

      Ambulatory heart rate (HRdriving) of 13 non-smoking male taxi drivers (24 to 67 years old) while driving was continuously assessed on their 6-hour experimental on-road driving in Los Angeles. Percent maximum HR range (PMHRdriving) of the drivers while driving was estimated based on the individual HRdriving values and US adult population resting HR (HRrest) reference data. For analyses, the HRdriving and PMHRdriving data were split and averaged into 5-min segments. Five physical hazards inside taxi cabs were also monitored while driving. Work stress and work hours on typical work days were self-reported.

      Results

      The means of the ambulatory 5-min HRdriving and PMHRdriving values of the 13 drivers were 80.5 bpm (11.2 bpm higher than their mean HRrest) and 10.7 % (range, 5.7 to 19.9 %), respectively. The means were lower than the upper limits of ambulatory HR and PMHR for a sustainable 8-hour work (35 bpm above HRrest and 30 % PMHR), although 15-27 % of the 5-min HRdriving and PMHRdriving values of one driver were higher than the limits. The levels of the five physical hazards among the drivers were modest: temperature (26.4 ± 3.0 °C), relative humidity (40.7 ± 10.4 %), PM2.5 (21.5 ± 7.9 μg/m3), CO2 (1,267.1 ± 580.0 ppm) and noise (69.7 ± 3.0 dBA). The drivers worked, on average, 72 h per week and more than half of them reported that their job were often stressful.

      Conclusions

      The impact of physical worksite hazards alone on ambulatory HR of professional taxi drivers in Los Angeles generally appeared to be minor. Future ambulatory heart rate studies including both physical and psychosocial hazards of professional taxi drivers are warranted.
        Cover page: Ambulatory heart rate of professional taxi drivers while driving without their typical psychosocial work stressors: a pilot study
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2019)
        Lower extremity peripheral artery disease (PAD) burden differs by race/ethnicity. Although familial aggregation and heritability studies suggest a genetic basis, little is known about the genetic susceptibility to PAD, especially in non-European descent populations. Genome-wide association studies (GWAS) of the ankle brachial index (ABI) and PAD (defined as an ABI < 0.90) have not been conducted in Hispanics/Latinos. We performed a GWAS of PAD and the ABI in 7,589 participants aged >45 years from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). We also performed GWAS for ABI stratified by Hispanic/Latino ethnic subgroups: Central American, Mexican, and South American (Mainland group), and Cuban, Dominican, and Puerto Rican (Caribbean group). We detected two genome-wide significant associations for the ABI in COMMD10 in Puerto Ricans, and at SYBU in the Caribbean group. The lead SNP rs4466200 in the COMMD10 gene had a replication p = 0.02 for the ABI in Multi-Ethnic Study of Atherosclerosis (MESA) African Americans, but it did not replicate in African Americans from the Cardiovascular Health Study (CHS). In a regional look-up, a nearby SNP rs12520838 had Bonferroni adjusted p = 0.05 (unadjusted p = 7.5 × 10-5) for PAD in MESA Hispanics. Among three suggestive associations (p < 10-7) in subgroup-specific analyses, DMD on chromosome X, identified in Central Americans, replicated in MESA Hispanics (p = 2.2 × 10-4). None of the previously reported ABI and PAD associations in whites generalized to Hispanics/Latinos.
          Cover page: Variants Associated with the Ankle Brachial Index Differ by Hispanic/Latino Ethnic Group: a genome-wide association study in the Hispanic Community Health Study/Study of LatinosCreative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2019)
          The pharmacokinetic properties of antibodies are largely dictated by the pH-dependent binding of the IgG fragment crystallizable (Fc) domain to the human neonatal Fc receptor (hFcRn). Engineered Fc domains that confer a longer circulation half-life by virtue of more favorable pH-dependent binding to hFcRn are of great therapeutic interest. Here we developed a pH Toggle switch Fc variant containing the L309D/Q311H/N434S (DHS) substitutions, which exhibits markedly improved pharmacokinetics relative to both native IgG1 and widely used half-life extension variants, both in conventional hFcRn transgenic mice and in new knock-in mouse strains. engineered specifically to recapitulate all the key processes relevant to human antibody persistence in circulation, namely: (i) physiological expression of hFcRn, (ii) the impact of hFcγRs on antibody clearance and (iii) the role of competing endogenous IgG. DHS-IgG retains intact effector functions, which are important for the clearance of target pathogenic cells and also has favorable developability.
            Cover page: An engineered human Fc domain that behaves like a pH-toggle switch for ultra-long circulation persistenceCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2019)
            An amendment to this paper has been published and can be accessed via a link at the top of the paper.
              Cover page: Publisher Correction: An engineered human Fc domain that behaves like a pH-toggle switch for ultra-long circulation persistenceCreative Commons 'BY' version 4.0 license
              • Article
              • Peer Reviewed
              UCLA Previously Published Works (2022)
              Rare variants in ten genes have been reported to cause Mendelian sleep conditions characterised by extreme sleep duration or timing. These include familial natural short sleep (ADRB1, DEC2/BHLHE41, GRM1 and NPSR1), advanced sleep phase (PER2, PER3, CRY2, CSNK1D and TIMELESS) and delayed sleep phase (CRY1). The association of variants in these genes with extreme sleep conditions were usually based on clinically ascertained families, and their effects when identified in the population are unknown. We aimed to determine the effects of these variants on sleep traits in large population-based cohorts. We performed genetic association analysis of variants previously reported to be causal for Mendelian sleep and circadian conditions. Analyses were performed using 191,929 individuals with data on sleep and whole-exome or genome-sequence data from 4 population-based studies: UK Biobank, FINRISK, Health-2000-2001, and the Multi-Ethnic Study of Atherosclerosis (MESA). We identified sleep disorders from self-report, hospital and primary care data. We estimated sleep duration and timing measures from self-report and accelerometery data. We identified carriers for 10 out of 12 previously reported pathogenic variants for 8 of the 10 genes. They ranged in frequency from 1 individual with the variant in CSNK1D to 1,574 individuals with a reported variant in the PER3 gene in the UK Biobank. No carriers for variants reported in NPSR1 or PER2 were identified. We found no association between variants analyzed and extreme sleep or circadian phenotypes. Using sleep timing as a proxy measure for sleep phase, only PER3 and CRY1 variants demonstrated association with earlier and later sleep timing, respectively; however, the magnitude of effect was smaller than previously reported (sleep midpoint ~7 mins earlier and ~5 mins later, respectively). We also performed burden tests of protein truncating (PTVs) or rare missense variants for the 10 genes. Only PTVs in PER2 and PER3 were associated with a relevant trait (for example, 64 individuals with a PTV in PER2 had an odds ratio of 4.4 for being "definitely a morning person", P = 4x10-8; and had a 57-minute earlier midpoint sleep, P = 5x10-7). Our results indicate that previously reported variants for Mendelian sleep and circadian conditions are often not highly penetrant when ascertained incidentally from the general population.
                Cover page: The impact of Mendelian sleep and circadian genetic variants in a population settingCreative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2020)

                Background

                Sleep Disordered Breathing (SDB) is associated with a wide range of pathophysiological changes due, in part, to hypoxemia during sleep. We sought to identify gene transcription associations with measures of SDB and hypoxemia during sleep, and study their response to treatment.

                Methods

                In two discovery cohorts, Framingham Offspring Study (FOS; N = 571) and the Multi-Ethnic Study of Atherosclerosis (MESA; N = 580), we studied gene expression in peripheral blood mononuclear cells in association with three measures of SDB: Apnea Hypopnea Index (AHI); average oxyhemoglobin saturation (avgO2) during sleep; and minimum oxyhemoglobin saturation (minO2) during sleep. Associated genes were used for analysis of gene expression in the blood of 15 participants with moderate or severe obstructive sleep apnea (OSA) from the Heart Biomarkers In Apnea Treatment (HeartBEAT) trial. These genes were studied pre- and post-treatment (three months) with continuous positive airway pressure (CPAP). We also performed Gene Set Enrichment Analysis (GSEA) on all traits and cohort analyses.

                Findings

                Twenty-two genes were associated with SDB traits in both MESA and FOS. Of these, lower expression of CD1D and RAB20 was associated with lower avgO2 in MESA and FOS. CPAP treatment increased the expression of these genes in HeartBEAT participants. Immunity and inflammation pathways were up-regulated in subjects with lower avgO2; i.e., in those with a more severe SDB phenotype (MESA), whereas immuno-inflammatory processes were down-regulated following CPAP treatment (HeartBEAT).

                Interpretation

                Low oxygen saturation during sleep is associated with alterations in gene expression and transcriptional programs that are partially reversed by CPAP treatment.
                  Cover page: Low oxygen saturation during sleep reduces CD1D and RAB20 expressions that are reversed by CPAP therapyCreative Commons 'BY' version 4.0 license
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2022)
                  Rationale: Obstructive sleep apnea (OSA) is a common disorder associated with increased risk for cardiovascular disease, diabetes, and premature mortality. There is strong clinical and epidemiologic evidence supporting the importance of genetic factors influencing OSA but limited data implicating specific genes. Objectives: To search for rare variants contributing to OSA severity. Methods: Leveraging high-depth genomic sequencing data from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and imputed genotype data from multiple population-based studies, we performed linkage analysis in the CFS (Cleveland Family Study), followed by multistage gene-based association analyses in independent cohorts for apnea-hypopnea index (AHI) in a total of 7,708 individuals of European ancestry. Measurements and Main Results: Linkage analysis in the CFS identified a suggestive linkage peak on chromosome 7q31 (LOD = 2.31). Gene-based analysis identified 21 noncoding rare variants in CAV1 (Caveolin-1) associated with lower AHI after accounting for multiple comparisons (P = 7.4 × 10-8). These noncoding variants together significantly contributed to the linkage evidence (P < 10-3). Follow-up analysis revealed significant associations between these variants and increased CAV1 expression, and increased CAV1 expression in peripheral monocytes was associated with lower AHI (P = 0.024) and higher minimum overnight oxygen saturation (P = 0.007). Conclusions: Rare variants in CAV1, a membrane-scaffolding protein essential in multiple cellular and metabolic functions, are associated with higher CAV1 gene expression and lower OSA severity, suggesting a novel target for modulating OSA severity.
                    Cover page: Targeted Genome Sequencing Identifies Multiple Rare Variants in&nbsp;Caveolin-1 Associated with Obstructive Sleep Apnea.
                    • Article
                    • Peer Reviewed
                    UC Santa Cruz Previously Published Works (2016)
                    Molecular understanding of serological immunity to influenza has been confounded by the complexity of the polyclonal antibody response in humans. Here we used high-resolution proteomics analysis of immunoglobulin (referred to as Ig-seq) coupled with high-throughput sequencing of transcripts encoding B cell receptors (BCR-seq) to quantitatively determine the antibody repertoire at the individual clonotype level in the sera of young adults before and after vaccination with trivalent seasonal influenza vaccine. The serum repertoire comprised between 40 and 147 clonotypes that were specific to each of the three monovalent components of the trivalent influenza vaccine, with boosted pre-existing clonotypes accounting for ∼60% of the response. An unexpectedly high fraction of serum antibodies recognized both the H1 and H3 monovalent vaccines. Recombinant versions of these H1 + H3 cross-reactive antibodies showed broad binding to hemagglutinins (HAs) from previously circulating virus strains; several of these antibodies, which were prevalent in the serum of multiple donors, recognized the same conserved epitope in the HA head domain. Although the HA-head-specific H1 + H3 antibodies did not show neutralization activity in vitro, they protected mice against infection with the H1N1 and H3N2 virus strains when administered before or after challenge. Collectively, our data reveal unanticipated insights regarding the serological response to influenza vaccination and raise questions about the added benefits of using a quadrivalent vaccine instead of a trivalent vaccine.
                      Cover page: Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination
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