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Open Access Publications from the University of California

Scholarly Works (22 results)

  • Article
  • Peer Reviewed
Research Grants Program Office (RGPO) Funded Publications (2000)
We developed a method to map oxidative-induced DNA damage at the nucleotide level using ligation-mediated polymerase chain reaction (LMPCR) technology. In vivo and in vitro DNA base modification patterns inflicted by reactive oxygen species (ROS) in the human P53 and PGK1 gene were nearly identical in vitro and in vivo. In human male fibroblasts, these patterns are independent of the transition metal used (Cu (II), Fe(II), or Cr(VI). Therefore, local probability of H2O2-mediated DNA base damage is determined primarily by DNA sequence. Moreover, in cells undergoing severe oxidative stress, extranuclear sites contribute metals that enhance nuclear DNA damage. The role of the base excision repair pathway in human cells responsible for the repair of the majority of ROS base damage is also discussed.
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    • Peer Reviewed
    UC Santa Barbara Electronic Theses and Dissertations (2024)

    Sessile colonial marine invertebrates can experience a natural histocompatibility process similar to tissue and organ transplantation observed in humans. The colonial ascidian Botryllus schlosseri has been used for about a century to study this allorecognition phenomenon. When two B. schlosseri colonies enter into contact using their extracorporeal vasculature systems, they can fuse, establishing a chimeric colony or reject, developing an inflammation-like process that prevents communication between the colonies. Allorecognition in B. schlosseri is genetically controlled by a single genomic region, the fuhc (fusion/histocompatibility) locus. Six allorecognition genes have been described within this locus; the fuhc-sec, fuhc-tm, fester, uncle fester, hsp40l and bhf genes.

    Tunicates can be classified into three main groups: Appendicularia, Thaliacea and Ascidia. However, it is unclear which species within these groups exhibit the allorecognition genes. To address this knowledge gap, I explored the emergence and evolution of B. schlosseri allorecognition genes. I searched for the allorecognition genes in the available transcriptomes and genomes of tunicates and discovered that the allorecognition genes appeared in different groups. Importantly, the fuhc-sec gene (a putative determinant in this allorecognition system) is present in species of the Styelidae family. At the same time, I established that the fester and uncle fester genes are indeed a gene family which is present in the colonial ascidians of the Styelidae family. Furthermore, we found that the allorecognition genes are located in a single genomic region in Botrylloides diegensis as in the genome of B. schlosseri. However, these genes are located on two different chromosomes (2 and 14) in the solitary species Styela clava. The presence of the fuhc-sec, fuhc-tm, bhf and hsp40l genes in solitary tunicates is intriguing. Although the functions of these genes are unknown, my work suggests that the allorecognition genes were co-opted from solitary species to perform a histocompatibility function in the colonial species of the Styelidae family.

    At the same time, my analysis of the fester family genes (the putative receptors of this allorecognition system) revealed different mechanisms to generate variability, such as haplotype variation, alternative splicing and polymorphism. I found that the fester family has 30-40 and 19 members in B. schlosseri and B. diegensis, respectively. However, each individual has in its genome just a subset of fester genes, for instance 3-10 fester genes for B. schlosseri, which are different compared to the fester gene set of other individuals. Furthermore, we detected that the fester receptors have two regions, one extracellular and another intracellular, which exhibit alternative splicing. Moreover, we found that several fester genes (FFBs1 and FFBd1) show polymorphism. This is consistent with their proposed role in allorecognition.

    In conclusion, I described the evolution of B. schlosseri allorecognition genes, generating new questions as to the presence and function of these genes in solitary species. Further, my analysis of the fester gene revealed that it is a multigene family with high variability and unique distribution across individuals. The predicted structure of the gene product is consistent with its proposed role as a receptor, though the ligand(s) remains unknown. Collectively, this work sets the stage for important questions that must be addressed to understand the evolution and mechanism of histocompatibility in B. schlosseri.

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    • Article
    • Peer Reviewed
    Research Grants Program Office (RGPO) Funded Publications (1996)
    The kinetics of frank DNA strand breaks and DNA base modifications produced by Cu(II)/ascorbate/H2O2 were simultaneously determined in purified human genomic DNA in vitro. Modified bases were determined by cleavage with Escherichia coli enzymes Nth protein (modified pyrimidines) and Fpg protein (modified purines). Single-stranded lesion frequency before (frank strand breaks) and after (modified bases) Nth or Fpg protein digestion was quantified by neutral glyoxal gel electrophoresis. Dialysis of EDTA-treated genomic DNA purified by standard proteinase K digestion/phenol extraction was necessary to remove low molecular weight species, probably transition metal ions and metal ion chelators, which supported frank strand breaks in the presence of ascorbate + H2O2 without supplemental copper ions. We then established a kinetic model of the DNA-damaging reactions caused by Cu(II) + ascorbate + H2O2. The principal new assumption in our model was that DNA base modifications were caused exclusively by DNA-bound Cu(I) and frank strand breaks by non-DNA-bound Cu(I). The model was simulated by computer using published rate constants. The computer simulation quantitatively predicted: (1) the rate of H2O2 degradation, which was measured using an H2O2-sensitive electrode, (2) the linearity of accumulation of DNA strand breaks and modified bases over the reaction period, (3) the rate of modified base accumulation, and (4) the dependence of modified base and frank strand production on initial Cu(II) concentration. The simulation significantly overestimated the rate of frank strand break accumulation, suggesting either that the ultimate oxidizing species that attacks the sugar-phosphate backbone is a less-reactive species than the hydroxyl radical used in the model and/or an unidentified hydroxyl radical-scavenging species was present in the reactions. Our experimental data are consistent with a model of copper ion-DNA interaction in which DNA-bound Cu(I) primarily mediates DNA base modifications and nonbound Cu(I) primarily mediates frank strand break production.
      • Article
      • Peer Reviewed
      Research Grants Program Office (RGPO) Funded Publications (1995)
      The ligation-mediated polymerase chain reaction was used to map the frequency of reactive oxygen species-induced DNA damage at nucleotide resolution in genomic DNA purified from cultured human male fibroblasts. Damaged pyrimidine and purine bases were recognized and cleaved by the Nth and Fpg proteins from Escherichia coli, respectively. Strand breaks and modified bases were induced in vitro by copper ion-mediated reduction of hydrogen peroxide in the presence of ascorbate; reactant concentrations were adjusted to induce lesions at a frequency of 1 per 2-3 kilobases in purified genomic DNA. Glyoxal gel analysis demonstrated that the ratio of induced strand breaks to induced base damage was 0.8/2.7 in DNA dialyzed extensively to remove adventitious transition metal ions. Ligation-mediated polymerase chain reaction analysis of the damage frequency in the promoter region of the transcriptionally active phosphoglycerate kinase (PGK 1) gene revealed that (Cu(II)/ascorbate/H2O2 caused DNA base damage by a sequence-dependent mechanism, with the 5' bases of d(pGn) and d(pCn) being damage hot spots, as were the most internal guanines of d(pGGGCCC) and d(pCCCGGG). Since base damage occurs after formation of a DNA-Cu(I)-H2O2 complex, these data suggest that the local DNA sequence affects formation of DNA-Cu(I)-H2O2 complexes and/or the efficiency of base oxidation during resolution of this complex.
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2022)
        BACKGROUND: Highly variable insulin sensitivity, susceptibility to hypoglycemia and inability to effectively communicate hypoglycemic symptoms pose significant challenges for young children with type 1 diabetes (T1D). Herein, outcomes during clinical MiniMed™ 670G system use were evaluated in children aged 2-6 years with T1D. METHODS: Participants (N = 46, aged 4.6 ± 1.4 years) at seven investigational centers used the MiniMed™ 670G system in Manual Mode during a two-week run-in period followed by Auto Mode during a three-month study phase. Safety events, mean A1C, sensor glucose (SG), and percentage of time spent in (TIR, 70-180 mg/dl), below (TBR, <70 mg/dl) and above (TAR, >180 mg/dl) range were assessed for the run-in and study phase and compared using a paired t-test or Wilcoxon signed-rank test. RESULTS: From run-in to end of study (median 87.1% time in auto mode), mean A1C and SG changed from 8.0 ± 0.9% to 7.5 ± 0.6% (p < 0.001) and from 173 ± 24 to 161 ± 16 mg/dl (p < 0.001), respectively. Overall TIR increased from 55.7 ± 13.4% to 63.8 ± 9.4% (p < 0.001), while TBR and TAR decreased from 3.3 ± 2.5% to 3.2 ± 1.6% (p = 0.996) and 41.0 ± 14.7% to 33.0 ± 9.9% (p < 0.001), respectively. Overnight TBR remained unchanged and TAR was further improved 12:00 am-6:00 am. Throughout the study phase, there were no episodes of severe hypoglycemia or diabetic ketoacidosis (DKA) and no serious adverse device-related events. CONCLUSIONS: At-home MiniMed™ 670G Auto Mode use by young children safely improved glycemic outcomes compared to two-week open-loop Manual Mode use. The improvements are similar to those observed in older children, adolescents and adults with T1D using the same system for the same duration of time.
          Cover page: Glycemic outcomes of children 2-6 years of age with type 1 diabetes during the pediatric MiniMed™ 670G system trial.
          • Peer Reviewed
          Research Grants Program Office (RGPO) Funded Publications (2002)
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2018)
            Topological insulators are an emerging class of materials that host highly robust in-gap surface or interface states while maintaining an insulating bulk1,2. Most advances in this field have focused on topological insulators and related topological crystalline insulators3 in two dimensions4-6 and three dimensions7-10, but more recent theoretical work has predicted the existence of one-dimensional symmetry-protected topological phases in graphene nanoribbons (GNRs)11. The topological phase of these laterally confined, semiconducting strips of graphene is determined by their width, edge shape and terminating crystallographic unit cell and is characterized by a [Formula: see text] invariant12 (that is, an index of either 0 or 1, indicating two topological classes-similar to quasi-one-dimensional solitonic systems13-16). Interfaces between topologically distinct GNRs characterized by different values of [Formula: see text] are predicted to support half-filled, in-gap localized electronic states that could, in principle, be used as a tool for material engineering11. Here we present the rational design and experimental realization of a topologically engineered GNR superlattice that hosts a one-dimensional array of such states, thus generating otherwise inaccessible electronic structures. This strategy also enables new end states to be engineered directly into the termini of the one-dimensional GNR superlattice. Atomically precise topological GNR superlattices were synthesized from molecular precursors on a gold surface, Au(111), under ultrahigh-vacuum conditions and characterized by low-temperature scanning tunnelling microscopy and spectroscopy. Our experimental results and first-principles calculations reveal that the frontier band structure (the bands bracketing filled and empty states) of these GNR superlattices is defined purely by the coupling between adjacent topological interface states. This manifestation of non-trivial one-dimensional topological phases presents a route to band engineering in one-dimensional materials based on precise control of their electronic topology, and is a promising platform for studies of one-dimensional quantum spin physics.
              Cover page: Topological band engineering of graphene nanoribbons.
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2018)
              Bottom-up graphene nanoribbon (GNR) heterojunctions are nanoscale strips of graphene whose electronic structure abruptly changes across a covalently bonded interface. Their rational design offers opportunities for profound technological advancements enabled by their extraordinary structural and electronic properties. Thus far, the most critical aspect of their synthesis, the control over sequence and position of heterojunctions along the length of a ribbon, has been plagued by randomness in monomer sequences emerging from step-growth copolymerization of distinct monomers. All bottom-up GNR heterojunction structures created so far have exhibited random sequences of heterojunctions and, while useful for fundamental scientific studies, are difficult to incorporate into functional nanodevices as a result. In contrast, we describe a hierarchical fabrication strategy that allows the growth of bottom-up GNRs that preferentially exhibit a single heterojunction interface rather than a random statistical sequence of junctions along the ribbon. Such heterojunctions provide a viable platform that could be directly used in functional GNR-based device applications at the molecular scale. Our hierarchical GNR fabrication strategy is based on differences in the dissociation energies of C-Br and C-I bonds that allow control over the growth sequence of the block copolymers from which GNRs are formed and consequently yields a significantly higher proportion of single-junction GNR heterostructures. Scanning tunneling spectroscopy and density functional theory calculations confirm that hierarchically grown heterojunctions between chevron GNR (cGNR) and binaphthyl-cGNR segments exhibit straddling Type I band alignment in structures that are only one atomic layer thick and 3 nm in width.
                Cover page: Hierarchical On-Surface Synthesis of Graphene Nanoribbon Heterojunctions
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2021)
                Bottom-up graphene nanoribbons (GNRs) have recently been shown to host nontrivial topological phases. Here, we report the fabrication and characterization of deterministic GNR quantum dots whose orbital character is defined by zero-mode states arising from nontrivial topological interfaces. Topological control was achieved through the synthesis and on-surface assembly of three distinct molecular precursors designed to exhibit structurally derived topological electronic states. Using a combination of low-temperature scanning tunneling microscopy and spectroscopy, we have characterized two GNR topological quantum dot arrangements synthesized under ultrahigh vacuum conditions. Our results are supported by density-functional theory and tight-binding calculations, revealing that the magnitude and sign of orbital hopping between topological zero-mode states can be tuned based on the bonding geometry of the interconnecting region. These results demonstrate the utility of topological zero modes as components for designer quantum dots and advanced electronic devices.
                  Cover page: Rationally Designed Topological Quantum Dots in Bottom-Up Graphene Nanoribbons
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2017)

                  Objective

                  We aimed to determine the effect of elevated BMI over time on the progression to type 1 diabetes in youth.

                  Research design and methods

                  We studied 1,117 children in the TrialNet Pathway to Prevention cohort (autoantibody-positive relatives of patients with type 1 diabetes). Longitudinally accumulated BMI above the 85th age- and sex-adjusted percentile generated a cumulative excess BMI (ceBMI) index. Recursive partitioning and multivariate analyses yielded sex- and age-specific ceBMI thresholds for greatest type 1 diabetes risk.

                  Results

                  Higher ceBMI conferred significantly greater risk of progressing to type 1 diabetes. The increased diabetes risk occurred at lower ceBMI values in children <12 years of age compared with older subjects and in females versus males.

                  Conclusions

                  Elevated BMI is associated with increased risk of diabetes progression in pediatric autoantibody-positive relatives, but the effect varies by sex and age.
                    Cover page: Excess BMI in Childhood: A Modifiable Risk Factor for Type 1 Diabetes Development
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