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Open Access Publications from the University of California

Scholarly Works (7 results)

  • Thesis
  • Peer Reviewed
UC Irvine Electronic Theses and Dissertations (2016)

Routine surveillance for infectious diseases results in earlier detection and better prognosis. However, current diagnostic measures for infectious diseases are not directly translatable to low-resource settings as they are expensive, time-consuming, and require heavy medical infrastructure and trained personnel. The need for effective point-of-care (POC) diagnostics is critically important: the vast majority of deaths from infectious diseases occur in developing countries.

Here, a platform for producing enhanced fluorescence signals with applications in POC technology is presented. Dense multi-scale silica (SiO2) structures are fabricated on pre-stressed polyolefin (PO) film and characterized. Linkage of fluorescent biomolecules on the SiO2 structures results in far-field fluorescence signal enhancements (~116-fold with respect to a planar glass control and ~50-fold with respect to a flat unshrunk fluorescently conjugated polymer film) with increased signal-to-noise ratio (SNR) that are robust and reproducible. Optical characterization of the SiO2 structures point to the concentration effect and optical scattering as the underlying mechanisms responsible for the far-field fluorescence signal enhancements.

Using the biotin-streptavidin hybridization as a model system, improved limits of detection (LOD) of the model target streptavidin were achieved on the SiO2 structures relative to a flat glass control. Disease detection applications are demonstrated using the SiO2 structures. Sandwich immunoassays for TNF-α and p24 antigen are performed on the SiO2 structures and lower LODs are achieved (550 pg mL-1 and 30 pg mL-1 for TNF-α and p24 antigen, respectively). The SiO2 structures demonstrate potential for POC applications as enhanced signal correlates to increased sensitivity.

    Cover page: Shrink-Induced Silica Structures for Improved Biological Detection
    • Article
    • Peer Reviewed
    UCI Open Access Publishing Fund (2013)
    Dense multiscale silica (SiO2) micro- and nanostructures are fabricated on a pre-stressed polymer fi lm. This novel SiO 2 substrate serves as a robust platform to enhance the fl uorescence signal of bound biomolecules. Through a combination of surface concentration, light scattering, and changes in the photophysical properties of the confi ned dye molecules, dramatic fl uorescence signal enhancements (average = 116 times greater than on planar glass) and increased signal-to-noise ratio (76:1) are demonstrated with tetramethylrhodamine isothiocyanate (TRITC)-conjugated streptavidin (STRITC) on SiO 2 structures. Enhanced detection sensitivity of STRITC over glass on the SiO 2 structures is achieved down to a detection limit of 11 ng mL −1 . Such signifi cant fl uorescence signal enhancements have importance in practical applications such disease diagnostics and surface sensing.
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    Cover page: Shrink-Induced Silica Structures for Far-field Fluorescence EnhancementsCreative Commons 'BY' version 4.0 license
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2014)
    The field of micro- and nanofabrication has developed extensively in the past several decades with rising interest in alternative fabrication techniques. Growth of these areas has been driven by needs that remain unaddressed by traditional lithographical methods: inexpensive, upscalable, biocompatible, and easily integrated into complete lab-on-a-chip (LOC) systems. Shape memory polymers (SMPs) have been explored as an alternative substrate. This review first focuses on structure fabrication at the micron and nanoscale using specifically heat-shrinkable SMPs and highlights the innovative improvements to this technology in the past several years. The second part of the review illustrates demonstrated applications of these micro- and nanostructures fabricated from heat-shrinkable SMP films. The review concludes with a discussion about future prospects of heat-shrinkable SMP structures for integration into LOC systems.
      Cover page: Thermally-induced miniaturization for micro- and nanofabrication: progress and updates.
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2001)
      Retroviruses in nondividing cells and yeast retrotransposons must transit the nuclear membrane in order for integration to occur. Mutations in a bipartite basic motif in the carboxyl-terminal domain of the Ty3 integrase (IN) protein were previously shown to block transposition at a step subsequent to 3'-end processing of Ty3 extrachromosomal DNA. In this work, the Ty3 IN was shown to be sufficient to target green fluorescent protein to the nucleolus. Mutations in the bipartite basic motif abrogated this localization. The region containing the motif was shown to be sufficient for nuclear but not subnuclear localization of a heterologous protein. Viruslike particles (VLPs) from cells expressing a Ty3 element defective for nuclear localization were inactive in an in vitro integration assay, suggesting that nuclear entry is required to form active VLPs or that this motif is required for post-nuclear entry steps. Ty3 inserts at transcription initiation sites of genomic tRNA genes and plasmid-borne 5S and U6 RNA genes transcribed by RNA polymerase III. In situ hybridization with Ty3- and Ty3 long terminal repeat-specific probes showed that these elements which are associated with tRNA genes do not colocalize with the ribosomal DNA (rDNA). However, a PCR assay of cells undergoing transposition showed that Ty3 insertion does occur into the 5S genes, which, in yeast, are interspersed with the rDNA and therefore, like Ty3 IN, associated with the nucleolus.
        Cover page: Integrase Mediates Nuclear Localization of Ty3Creative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2014)
        We describe a manufacturable and scalable method for fabrication of multiscale wrinkled silica (SiO2) structures on shrink-wrap film to enhance fluorescence signals in DNA fluorescence microarrays. We are able to enhance the fluorescence signal of hybridized DNA by more than 120 fold relative to a planar glass slide. Notably, our substrate has improved detection sensitivity (280 pM) relative to planar glass slide (11 nM). Furthermore, this is accompanied by a 30-45 times improvement in the signal-to-noise ratio (SNR). Unlike metal enhanced fluorescence (MEF) based enhancements, this is a far-field and uniform effect based on surface concentration and photophysical effects from the nano- to microscale SiO2 structures. Notably, the photophysical effects contribute an almost 2.5 fold enhancement over the concentration effects alone. Therefore, this simple and robust method offers an efficient technique to enhance the detection capabilities of fluorescence based DNA microarrays.
          Cover page: Shrink-Induced Silica Multiscale Structures for Enhanced Fluorescence from DNA Microarrays
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2016)
          Silica (SiO2) micro- and nanostructures fabricated with pre-stressed thermoplastic shrink wrap film have been shown to yield far-field fluorescence signal enhancements over their planar or wrinkled counterparts. The SiO2 structures have previously been used for improved detection of fluorescently labelled proteins and DNA. In this work, we probe the mechanism responsible for the dramatic increases in fluorescence signal intensity. Optical characterization studies attribute the fluorescence signal enhancements to increased surface density and light scattering from the rough SiO2 structures. Using this information, we come up with a theoretical approximation for the enhancement factor based off the scattering effects alone. We show that increased deposition thickness of SiO2 yields improved fluorescence signal enhancements, with an optimal SiO2 thin layer achieved at 20 nm. Finally, we show that the SiO2 substrates serve as a suitable platform for disease diagnostics, and show improved limits of detection (LOD) for the human immunodeficiency virus type 1 (HIV-1) p24 antigen.
            Cover page: Multi-scale silica structures for improved HIV-1 Capsid (p24) antigen detectionCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2024)
            Intracellular calcium (Ca2+) is ubiquitous to cell signaling across biology. While existing fluorescent sensors and reporters can detect activated cells with elevated Ca2+ levels, these approaches require implants to deliver light to deep tissue, precluding their noninvasive use in freely behaving animals. Here we engineered an enzyme-catalyzed approach that rapidly and biochemically tags cells with elevated Ca2+ in vivo. Ca2+-activated split-TurboID (CaST) labels activated cells within 10 min with an exogenously delivered biotin molecule. The enzymatic signal increases with Ca2+ concentration and biotin labeling time, demonstrating that CaST is a time-gated integrator of total Ca2+ activity. Furthermore, the CaST readout can be performed immediately after activity labeling, in contrast to transcriptional reporters that require hours to produce signal. These capabilities allowed us to apply CaST to tag prefrontal cortex neurons activated by psilocybin, and to correlate the CaST signal with psilocybin-induced head-twitch responses in untethered mice.
              Cover page: Rapid, biochemical tagging of cellular activity history in vivo
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