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Open Access Publications from the University of California

Scholarly Works (23 results)

  • Article
  • Peer Reviewed
UC Irvine Previously Published Works (1998)
Predictions from a gyrokinetic toroidal plasma model reproduce for the first time the evolution of Alfvén eigenmode (AE) dampings over a range of discharges. The coupling between shear-and kinetic-Alfvén waves is responsible for the main source of damping through Landau interactions and can be an order of magnitude larger than fluid predictions neglecting global kinetic effects. Strong stabilization occurs when the wave field gets localized radially by a rise in the edge magnetic shear, explaining why global AEs have never been detected in the Joint European Torus [Rebut, Bickerton, and Keen, Nucl. Fusion 25, 1011 (1985)] in the presence of an X point and suggesting how global Alfvén instabilities could be avoided in future reactors. © 1998 American Institute of Physics.
    Cover page: Prediction of Alfvén eigenmode dampings in the Joint European TorusCreative Commons 'BY' version 4.0 license
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (1997)
    An external antenna excites stable eigenmodes in elongated Ohmically heated plasmas in the Joint European Torus (JET) [P.-H. Rebut, R. J. Bickerton, and B. E. Keen, Nucl. Fusion 25, 1011 (1985)]. The frequency of the modes (240-290 kHz) falls in the gap in the magnetohydrodynamic (MHD) continuum that is produced by ellipticity. Some modes are very weakly damped (γ/ω<10-3). © 1997 American Institute of Physics.
      Cover page: Stable ellipticity-induced Alfvén eigenmodes in the Joint European TorusCreative Commons 'BY' version 4.0 license
      • Thesis
      • Peer Reviewed
      UC Irvine Electronic Theses and Dissertations (2015)

      This work presents several high throughput imaging and analysis techniques performed by fluorescence detection and surface plasmon resonance biosensing. The microarray fabrication methods introduced in this thesis, as well as the DNA functionalization on planar and nanoparticle surfaces, enable and facilitate the real-time study of adsorption events via DNA- DNA hybridization and protein-DNA interaction.

      Silica deposited on polyolefin film serves as the base for the development of DNA microarray. Fabrication process involves poly(L-glutamic acid) monolayer to react with amine functional groups functionalized on both the silica surface and the probe DNA strands. Covalently surface-bound probes then hybridize with fluorophore-labeled target DNA. Shrinking the microarray with heat significantly enhances the sensitivity of detection via fluorescence signal amplification.

      Polydopamine, a biomimetic polymer, easily and rapidly grows an adhesive layer to link amine-terminated, single-stranded DNA to gold surface. Self-polymerization of polydopamine simply requires mild reagents and reaction condition. The microarray formed with polydopamine attachment technique reserves its stability and specificity to detect DNA and protein targets by surface plasmon resonance imaging. This one-step microarray fabrication approach, when coupled with signal amplification from DNA-modified gold nanoparticles, empowers the detection limit capable of seeing down to 10 pM target concentration.

      Electrochemical deposition of polydopamine demonstrates strong control over film localization and thickness. This meticulous polymerization on gold surface at the microscale proves the high toposelectivity of this deposition technique. Amine-modified DNA bound on this polydopamine thin flim hybridizes with fluorophore-tagged DNA to generate fluorescent DNA micropatterns. This electordeposition also forms DNA microarrays used in surface plasmon resonance imaging for DNA-DNA hybridization and DNA-coated gold nanoparticle adsorption measurements.

      A 814 nm, near-infrared surface plasmon resonance microscope exemplifies a novel, objective-coupled sensing and imaging system at single-nanoparticle scale. This microscope visualizes individual binding occurrence of gold nanoparticles and polystyrene beads. Adsorption analysis presents the calculated surface plasmon resonance signal (Δ%R) as it varies with particle size. For initial biosensing measurements, the surface plasmon resonance microscopy examines each hybridization-adsorption of DNA-decorated gold nanoparticle on gold surface functionalized with either completely or partially complementary DNA monolayer.

        Cover page: Surface Functionalization for Enhanced Fluorescence Detection, Surface Plasmon Resonance Imaging and Microscopy
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2015)
        The sensitivity and selectivity of surface plasmon resonance imaging (SPRI) biosensing with nucleic acid microarrays can be greatly enhanced by exploiting various nucleic acid ligases, nucleases, and polymerases that manipulate the surface-bound DNA and RNA. We describe here various examples from each of these different classes of surface enzyme chemistries that have been incorporated into novel detection strategies that either drastically enhance the sensitivity of or create uniquely selective methods for the SPRI biosensing of proteins and nucleic acids. A dual-element generator-detector microarray approach that couples a bioaffinity adsorption event on one microarray element to nanoparticle-enhanced SPRI measurements of nucleic acid hybridization adsorption on a different microarray element is used to quantitatively detect DNA, RNA, and proteins at femtomolar concentrations. Additionally, this dual-element format can be combined with the transcription and translation of RNA from surface-bound double-stranded DNA (dsDNA) templates for the on-chip multiplexed biosynthesis of aptamer and protein microarrays in a microfluidic format; these microarrays can be immediately used for real-time SPRI bioaffinity sensing measurements.
          Cover page: Surface Enzyme Chemistries for Ultrasensitive Microarray Biosensing with SPR Imaging
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2022)
          Spikes are said to exhibit "memory" in that they can be altered by spikes that precede them. In retinal ganglion cell axons, for example, rapid spiking can slow the propagation of subsequent spikes. This increases inter-spike interval and, thus, low-pass filters instantaneous spike frequency. Similarly, a K+ ion channel blocker (4-aminopyridine, 4AP) increases the time-to-peak of compound action potentials recorded from optic nerve, and we recently found that reducing autophosphorylation of calcium/calmodulin-dependent protein kinase II (CaMKII) does too. These results would be expected if CaMKII modulates spike propagation by regulating 4AP-sensitive K+ channels. As steps toward identifying a possible substrate, we test whether (i) 4AP alters optic nerve spike shape in ways consistent with reducing K+ current, (ii) 4AP alters spike propagation consistent with effects of reducing CaMKII activation, (iii) antibodies directed against 4AP-sensitive and CaMKII-regulated K+ channels bind to optic nerve axons, and (iv) optic nerve CaMKII co-immunoprecipitates with 4AP-sensitive K+ channels. We find that, in adult rat optic nerve, (i) 4AP selectively slows spike repolarization, (ii) 4AP slows spike propagation, (iii) immunogen-blockable staining is achieved with anti-Kv4.3 antibodies but not with antibodies directed against Kv1.4 or Kv4.2, and (iv) CaMKII associates with Kv4.3. Kv4.3 may thus be a substrate that underlies activity-dependent spike regulation in adult visual system pathways.
            Cover page: Calcium/calmodulin-dependent protein kinase II associates with the K+ channel isoform Kv4.3 in adult rat optic nerve
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2017)
            Dopamine- and tyrosine hydroxylase-immunopositive cells (TH cells) modulate visually driven signals as they flow through retinal photoreceptor, bipolar, and ganglion cells. Previous studies suggested that TH cells release dopamine from varicose axons arborizing in the inner and outer plexiform layers after glutamatergic synapses depolarize TH cell dendrites in the inner plexiform layer and these depolarizations propagate to the varicosities. Although it has been proposed that these excitatory synapses are formed onto appendages resembling dendritic spines, spines have not been found on TH cells of most species examined to date or on TH cell somata that release dopamine when exposed to glutamate receptor agonists. By use of protocols that preserve proximal retinal neuron morphology, we have examined the shape, distribution, and synapse-related immunoreactivity of adult rat TH cells. We report here that TH cell somata, tapering and varicose inner plexiform layer neurites, and varicose outer plexiform layer neurites all bear spines, that some of these spines are immunopositive for glutamate receptor and postsynaptic density proteins (viz., GluR1, GluR4, NR1, PSD-95, and PSD-93), that TH cell somata and tapering neurites are also immunopositive for a γ-aminobutyric acid (GABA) receptor subunit (GABAA Rα1 ), and that a synaptic ribbon-specific protein (RIBEYE) is found adjacent to some colocalizations of GluR1 and TH in the inner plexiform layer. These results identify previously undescribed sites at which glutamatergic and GABAergic inputs may stimulate and inhibit dopamine release, especially at somata and along varicose neurites that emerge from these somata and arborize in various levels of the retina. J. Comp. Neurol. 525:1707-1730, 2017. © 2016 Wiley Periodicals, Inc.
              Cover page: Somatic and neuritic spines on tyrosine hydroxylase–immunopositive cells of rat retina
              • Article
              • Peer Reviewed
              UC Riverside Previously Published Works (2023)
                Cover page: Towards hyperlocal source identification of pollutants in cities by combining mobile measurements with atmospheric modeling
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2015)
                This paper describes how changes in the refractive index of single hydrogel nanoparticles (HNPs) detected with near-infrared surface plasmon resonance microscopy (SPRM) can be used to monitor the uptake of therapeutic compounds for potential drug delivery applications. As a first example, SPRM is used to measure the specific uptake of the bioactive peptide melittin into N-isopropylacrylamide (NIPAm)-based HNPs. Point diffraction patterns in sequential real-time SPRM differential reflectivity images are counted to create digital adsorption binding curves of single 220 nm HNPs from picomolar nanoparticle solutions onto hydrophobic alkanethiol-modified gold surfaces. For each digital adsorption binding curve, the average single nanoparticle SPRM reflectivity response, ⟨Δ%RNP⟩, was measured. The value of ⟨Δ%RNP⟩ increased linearly from 1.04 ± 0.04 to 2.10 ± 0.10% when the melittin concentration in the HNP solution varied from zero to 2.5 μM. No change in the average HNP size in the presence of melittin is observed with dynamic light scattering measurements, and no increase in ⟨Δ%RNP⟩ is observed in the presence of either FLAG octapeptide or bovine serum albumin. Additional bulk fluorescence measurements of melittin uptake into HNPs are used to estimate that a 1% increase in ⟨Δ%RNP⟩ observed in SPRM corresponds to the incorporation of approximately 65000 molecules into each 220 nm HNP, corresponding to roughly 4% of its volume. The lowest detected amount of melittin loading into the 220 nm HNPs was an increase in ⟨Δ%RNP⟩ of 0.15%, corresponding to the absorption of 10000 molecules.
                  Cover page: Measuring Melittin Uptake into Hydrogel Nanoparticles with Near-Infrared Single Nanoparticle Surface Plasmon Resonance Microscopy
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2017)
                  Dopamine- and tyrosine hydroxylase-immunopositive cells (TH cells) modulate visually driven signals as they flow through retinal photoreceptor, bipolar, and ganglion cells. Previous studies suggested that TH cells release dopamine from varicose axons arborizing in the inner and outer plexiform layers after glutamatergic synapses depolarize TH cell dendrites in the inner plexiform layer and these depolarizations propagate to the varicosities. Although it has been proposed that these excitatory synapses are formed onto appendages resembling dendritic spines, spines have not been found on TH cells of most species examined to date or on TH cell somata that release dopamine when exposed to glutamate receptor agonists. By use of protocols that preserve proximal retinal neuron morphology, we have examined the shape, distribution, and synapse-related immunoreactivity of adult rat TH cells. We report here that TH cell somata, tapering and varicose inner plexiform layer neurites, and varicose outer plexiform layer neurites all bear spines, that some of these spines are immunopositive for glutamate receptor and postsynaptic density proteins (viz., GluR1, GluR4, NR1, PSD-95, and PSD-93), that TH cell somata and tapering neurites are also immunopositive for a γ-aminobutyric acid (GABA) receptor subunit (GABAA Rα1 ), and that a synaptic ribbon-specific protein (RIBEYE) is found adjacent to some colocalizations of GluR1 and TH in the inner plexiform layer. These results identify previously undescribed sites at which glutamatergic and GABAergic inputs may stimulate and inhibit dopamine release, especially at somata and along varicose neurites that emerge from these somata and arborize in various levels of the retina. J. Comp. Neurol. 525:1707-1730, 2017. © 2016 Wiley Periodicals, Inc.
                    Cover page: Somatic and neuritic spines on tyrosine hydroxylase-immunopositive cells of rat retina.
                    • Article
                    • Peer Reviewed
                    UC Irvine Previously Published Works (2006)
                    A specific experimental apparatus consisting of an ion source and a detector for the investigation of the interaction between suprathermal ions and drift-wave turbulence is developed on the toroidal plasma experiment. Due to the low plasma temperature (∼5 eV), a spatially localized, small-size ion source (∼4 cm) mounted inside the vacuum vessel with relatively low ion energy (∼100 eV-1 keV) can be used. The source consists of an aluminosilicate Li-6 ion emitter (6 mm diameter, 10-30 μA current) installed on a two-dimensional (2D) poloidally moving system. The location, energy, and current density profile of the ion beam will be measured using a 2D movable gridded energy analyzer. © 2006 American Institute of Physics.
                      Cover page: Fast ion source and detector for investigating the interaction of turbulence with suprathermal ions in a low temperature toroidal plasmaCreative Commons 'BY' version 4.0 license
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