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Open Access Publications from the University of California

Scholarly Works (10 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2017)
In contrast to small molecules, DNA and RNA macromolecules can be accurately formulated with base "elements" abbreviated as A, T, U, C, and G. However, the development of functionally artificial bases can result in the generation of new biomaterials with unique properties and applications. Therefore, we herein report the design and synthesis of a photoresponsive base as a new functional or molecular "element" for constructing DNA nanomolecules. The new base is made by fusion of an azobenzene with a natural T base (zT). zT, a new molecular element, is not only the most size-expanded T analogue but also a photoresponsive base capable of specific self-assembly through hydrogen bonding. Our results showed that stable and selective self-assembly of double-stranded DNAs occurred through zT-A base pairing, but it could still be efficiently dissociated by light irradiation. The photoresponsive DNA bases will provide the versatility required for constructing desired DNA nanomolecules and nanodevices.
    Cover page: Artificial Base zT as Functional “Element” for Constructing Photoresponsive DNA Nanomolecules
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2015)
    We derive expressions of interatomic force and heat current for many-body potentials such as the Tersoff, the Brenner, and the Stillinger-Weber potential used extensively in molecular dynamics simulations of covalently bonded materials. Although these potentials have a many-body nature, a pairwise force expression that follows Newton's third law can be found without referring to any partition of the potential. Based on this force formula, a stress applicable for periodic systems can be unambiguously defined. The force formula can then be used to derive the heat current formulas using a natural potential partitioning. Our heat current formulation is found to be equivalent to most of the seemingly different heat current formulas used in the literature, but to deviate from the stress-based formula derived from two-body potential. We validate our formulation numerically on various systems described by the Tersoff potential, namely three-dimensional silicon and diamond, two-dimensional graphene, and quasi-one-dimensional carbon nanotube. The effects of cell size and production time used in the simulation are examined.
      Cover page: Force and heat current formulas for many-body potentials in molecular dynamics simulations with applications to thermal conductivity calculations
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2023)
      The naringin extraction process was optimised using response surface methodology (RSM). A central component design was adopted, which included four parameters: extraction temperature (X1), material-liquid ratio (X2), extraction time (X3), and ultrasonic frequency (X4) of 74.79 °C, 1.58 h, 1:56.51 g/mL, and 28.05 KHz, respectively. Based on these optimal extraction conditions, naringin was tested to verify the model's accuracy. Naringin yield was 36.2502 mg/g, which was equivalent to the predicted yield of 36.0124 mg/g. DM101 macroporous adsorption resin was used to purify naringin. The effects of loading concentration, loading flow rate, and sample pH on the adsorption rate of naringin and the effect of ethanol concentration on the desorption rate of naringin were investigated. The optimum conditions for naringin purification using macroporous resins were determined. The optimal loading concentration, sample solution pH, and loading flow rate were 0.075 mg/mL, 3.5, and 1.5 mL/min, respectively. Three parallel tests were conducted under these conditions, and the average naringin yield was 77.5643%. Naringin's structure was identified using infrared spectroscopy and nuclear magnetic resonance. In vitro determination of the lipid-lowering activity of naringin was also conducted. These results showed that naringin has potential applications as a functional food for lowering blood lipid levels.
        Cover page: Optimisation of the Extraction Process of Naringin and Its Effect on Reducing Blood Lipid Levels In Vitro
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2019)
        The catalytic activity of low-dimensional electrocatalysts is highly dependent on their local atomic structures, particularly those less-coordinated sites found at edges and corners; therefore, a direct probe of the electrocatalytic current at specified local sites with true nanoscopic resolution has become critically important. Despite the growing availability of operando imaging tools, to date it has not been possible to measure the electrocatalytic activities from individual material edges and directly correlate those with the local structural defects. Herein, we show the possibility of using feedback and generation/collection modes of operation of the scanning electrochemical microscope (SECM) to independently image the topography and local electrocatalytic activity with 15-nm spatial resolution. We employed this operando microscopy technique to map out the oxygen evolution activity of a semi-2D nickel oxide nanosheet. The improved resolution and sensitivity enables us to distinguish the higher activities of the materials' edges from that of the fully coordinated surfaces in operando The combination of spatially resolved electrochemical information with state-of-the-art electron tomography, that unravels the 3D complexity of the edges, and ab initio calculations allows us to reveal the intricate coordination dependent activity along individual edges of the semi-2D material that is not achievable by other methods. The comparison of the simulated line scans to the experimental data suggests that the catalytic current density at the nanosheet edge is ∼200 times higher than that at the NiO basal plane.
          Cover page: Direct high-resolution mapping of electrocatalytic activity of semi-two-dimensional catalysts with single-edge sensitivity
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2016)
          A new series of 20 brominated chalcone derivatives were designed, synthesized, and investigated for their effects against the growth of four cancer cell lines (EC109, SKNSH, HepG2, MGC803). Among them, compound 19 which given chemical name of H72, was the most potent one on gastric cancer cell lines (i.e. MGC803, HGC27, SGC7901) with IC50s ranged from 3.57 to 5.61μM. H72 exhibited less cytotoxicity to non-malignant gastric epithelial cells GES-1. H72 treatment of MGC803 and HGC27 induced generation of reactive oxygen species (ROS) leading to activation of caspase 9/3 cascade and mitochondria mediated apoptosis. H72 also up-regulated the expression of DR5, DR4 and BimEL, and down-regulated the expression of Bid, Bcl-xL, and XIAP. N-acetyl cysteine (NAC), a ROS scavenger completely blocked these effects of H72 in MGC803 cells. Intraperitoneal administration of H72 significantly inhibited the growth of MGC803 cells in vivo in a xenograft mouse model without observed toxicity. These results indicated that H72 is a lead brominated chalcone derivate and deserves further investigation for prevention and treatment of gastric cancer.
            Cover page: A new brominated chalcone derivative suppresses the growth of gastric cancer cells in vitro and in vivo involving ROS mediated up-regulation of DR5 and 4 expression and apoptosis
            • Article
            • Peer Reviewed
            Lawrence Berkeley National Laboratory (2004)

            The atomic scale structure of the 5-fold symmetric surface of an AlPdMn quasicrystal is investigated quantitatively by comparing x-ray photoelectron diffraction (XPD) simulations to experiment. The observed 5-fold symmetry of the diffraction patterns indicates that the surface is quasicrystalline with no hint of a reconstruction from the bulk structure. In analyzing the experimental data, many possible bulk terminations have been tested. Those few that fit best to the data have in common that they contain an Al-rich surface layer followed by a dense mixed Al/Pd/Mn layer. These best terminations, while not identical to each other, are suggested to form terraces coexisting on a real surface. Structural relaxations of the quasicrystal surface are also analyzed: mixing several best-fit terminations gives average best-fit interlayer spacing changes of Dd12 = -0.057 Angstrom, Dd24 = +0.159 Angstrom. These results are in good agreement with a prior structure determination by LEED on a sample that was prepared in a different manner.

              Cover page: Atomic scale structure of the 5-fold surface of an AlPdMn quasicrystal: A quantitative X-Ray photoelectron diffraction analysis
              • Article
              • Peer Reviewed
              UC Irvine Previously Published Works (2017)
              A new series of etherification chalcone derivatives were designed and synthesized through Willimison etherification and Claisen-Schmidt condensation. Among them, compound 2-c which was given chemical name of S17, has been successfully screened out as the most potent one on gastric cancer cell line(MGC803) through the investigation for their effects against the growth of five cancer cell lines (EC109, HepG2, MCF7, MGC803, SKNSH). S17 exhibited strong anti-proliferative activity on other two gastric cancer cells (HGC27 and SGC7901), but less cytotoxicity to non-malignant gastric epithelial cells GES1. S17 potently killed gastric cancer cells with causing modulation of Bcl-2 family proteins and activation of caspase 9/3 cascade. S17 also up-regulated DR5 expression and DR5 knockdown partially reversed S17-induced apoptosis, caspase activation and MMP decrease. S17 robustly induced generation of ROS with Keap/Nrf2 pathway activated and the application of ROS scavenger N-acetyl cysteine (NAC) completely blocked these effects by S17 in MGC803 cells. Intraperitoneal administration of S17 significantly inhibited the growth of MGC803 cells in vivo in a xenograft mouse model without observed toxicity. These results indicated that S17 is a leadbrominated chalcone derivate and deserves further investigation for prevention and treatment of gastric cancer.
                Cover page: A novel chalcone derivative S17 induces apoptosis through ROS dependent DR5 up-regulation in gastric cancer cells
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2019)
                Despite the importance of studying the instability of delithiated cathode materials, it remains difficult to underpin the degradation mechanism of lithium-rich cathode materials due to the complication of combined chemical and structural evolutions. Herein, we use state-of-the-art electron microscopy tools, in conjunction with synchrotron X-ray techniques and first-principle calculations to study a 4d-element-containing compound, Li2Ru0.5Mn0.5O3. We find surprisingly, after cycling, ruthenium segregates out as metallic nanoclusters on the reconstructed surface. Our calculations show that the unexpected ruthenium metal segregation is due to its thermodynamic insolubility in the oxygen deprived surface. This insolubility can disrupt the reconstructed surface, which explains the formation of a porous structure in this material. This work reveals the importance of studying the thermodynamic stability of the reconstructed film on the cathode materials and offers a theoretical guidance for choosing manganese substituting elements in lithium-rich as well as stoichiometric layer-layer compounds for stabilizing the cathode surface.
                  Cover page: Anomalous metal segregation in lithium-rich material provides design rules for stable cathode in lithium-ion batteryCreative Commons 'BY' version 4.0 license
                  • Article
                  • Peer Reviewed
                  ICTS Publications (2017)

                  A series of novel formononetin-dithiocarbamate derivatives were designed, synthesized and evaluated for antiproliferative activity against three selected cancer cell line (MGC-803, EC-109, PC-3). The first structure-activity relationship (SAR) for this formononetin-dithiocarbamate scaffold is explored in this report with evaluation of 14 variants of the structural class. Among these analogues, tert-butyl 4-(((3-((3-(4-methoxyphenyl)-4-oxo-4H-chromen-7-yl)oxy)propyl)thio)carbonothioyl)piperazine-1-carboxylate (8i) showed the best inhibitory activity against PC-3 cells (IC50 = 1.97 μM). Cellular mechanism studies elucidated 8i arrests cell cycle at G1 phase and regulates the expression of G1 checkpoint-related proteins in concentration-dependent manners. Furthermore, 8i could inhibit cell growth via MAPK signaling pathway and inhibit migration via Wnt pathway in PC-3 cells.

                    Cover page: Design and synthesis of formononetin-dithiocarbamate hybrids that inhibit growth and migration of PC-3 cells via MAPK/Wnt signaling pathways.Creative Commons 'BY' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2016)
                      Cover page: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)Creative Commons 'BY-NC-ND' version 4.0 license
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