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Open Access Publications from the University of California

Scholarly Works (8 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2019)

X-ray and electron microscopy are crucial tools that are widely used in basic and translational sciences to detect, understand, and treat diseases. Operating at length scales between molecular machineries and individual cells, those mesoscale imaging techniques enable studies into macromolecular assembly, biomechanics, biomaterials, and cellular engineering, among many others. As X-ray and electron techniques become more advanced, however, we have reached a point at which single modal imaging is asymptotically approaching its usefulness for solving challenging scientific and engineering problems.

Since most natural systems comprise hierarchical organizations with heterogeneous compositions, individual imaging methods do not have the scope to understand the comprehensive set of rules governing a system's mesoscale self-organization and to make predictions of its macroscopic behaviors. This necessitates the development of a hybrid imaging approach that integrates X-ray and electron microscopy, and presents an opportunity to leverage both modalities in a complementary fashion. The four studies presented in this dissertation demonstrates the use of intra- or intermodal X-ray and electron microscopy to study a variety of organic and inorganic samples with heterogeneous compositions and mesoscale morphologies. This hybrid microscopy approach reveals multidimensional and multiscale insights into the structural, chemical, and dynamic properties of the samples.

Study 1 integrates X-ray fluorescence microscopy and ptychography for 3D imaging of frozen hydrated green algae; it highlights the potential of such an intramodal method for non-destructive correlative imaging with nanometer spatial resolution and elemental specificity. Study 2 combines X-ray and electron microscopy in 2D and 3D to study highly heterogeneous meteoric grains with elemental and chemical identification; it is used to reveal the meteorite's mineralogical properties, and at the same time showcases the power of multimodal X-ray and electron imaging.

Study 3 leverages linearly polarized X-rays and electron scanning nanodiffraction to reveal crystal orientations in dichroic coral particles. This demonstration suggests the possibility of combining X-ray and electron methods to study optically anisotropic materials across multiple length scales. Finally, Study 4 presents a novel lensless in situ coherent diffractive imaging technique for generating high spatiotemporal resolution movies of ultrafast dynamics. This technique may be integrated into existing X-ray diffractive imaging microscopes to add a temporal dimension to the multimodal imaging paradigm.

Taken together, this dissertation promotes multidisciplinary thinking in hybrid X-ray and electron imaging---one that seeks to integrate the strengths of each microscopy technique into a comprehensive correlative imaging paradigm that can help solve today's most challenging problems.

    Cover page: Developments in Mesoscale Correlative Multimodal X-ray Microscopy
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2018)
    Coherent diffractive imaging (CDI) has been widely applied in the physical and biological sciences using synchrotron radiation, X-ray free-electron laser, high harmonic generation, electrons, and optical lasers. One of CDI's important applications is to probe dynamic phenomena with high spatiotemporal resolution. Here, we report the development of a general in situ CDI method for real-time imaging of dynamic processes in solution. By introducing a time-invariant overlapping region as real-space constraint, we simultaneously reconstructed a time series of complex exit wave of dynamic processes with robust and fast convergence. We validated this method using optical laser experiments and numerical simulations with coherent X-rays. Our numerical simulations further indicated that in situ CDI can potentially reduce radiation dose by more than an order of magnitude relative to conventional CDI. With further development, we envision in situ CDI could be applied to probe a range of dynamic phenomena in the future.
      Cover page: In situ coherent diffractive imaging
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2017)
      Precise localization of nanoparticles within a cell is crucial to the understanding of cell-particle interactions and has broad applications in nanomedicine. Here, we report a proof-of-principle experiment for imaging individual functionalized nanoparticles within a mammalian cell by correlative microscopy. Using a chemically-fixed HeLa cell labeled with fluorescent core-shell nanoparticles as a model system, we implemented a graphene-oxide layer as a substrate to significantly reduce background scattering. We identified cellular features of interest by fluorescence microscopy, followed by scanning transmission X-ray tomography to localize the particles in 3D, and ptychographic coherent diffractive imaging of the fine features in the region at high resolution. By tuning the X-ray energy to the Fe L-edge, we demonstrated sensitive detection of nanoparticles composed of a 22 nm magnetic Fe3O4 core encased by a 25-nm-thick fluorescent silica (SiO2) shell. These fluorescent core-shell nanoparticles act as landmarks and offer clarity in a cellular context. Our correlative microscopy results confirmed a subset of particles to be fully internalized, and high-contrast ptychographic images showed two oxidation states of individual nanoparticles with a resolution of ~16.5 nm. The ability to precisely localize individual fluorescent nanoparticles within mammalian cells will expand our understanding of the structure/function relationships for functionalized nanoparticles.
        Cover page: Correlative cellular ptychography with functionalized nanoparticles at the Fe L-edge
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2017)
        Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iterates between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.
          Cover page: GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2018)
          Intestinal stem cells (ISCs) maintain and repair the intestinal epithelium. While regeneration after ISC-targeted damage is increasingly understood, injury-repair mechanisms that direct regeneration following injuries to differentiated cells remain uncharacterized. The enteric pathogen, rotavirus, infects and damages differentiated cells while sparing all ISC populations, thus allowing the unique examination of the response of intact ISC compartments during injury-repair. Upon rotavirus infection in mice, ISC compartments robustly expand and proliferating cells rapidly migrate. Infection results specifically in stimulation of the active crypt-based columnar ISCs, but not alternative reserve ISC populations, as is observed after ISC-targeted damage. Conditional ablation of epithelial WNT secretion diminishes crypt expansion and ISC activation, demonstrating a previously unknown function of epithelial-secreted WNT during injury-repair. These findings indicate a hierarchical preference of crypt-based columnar cells (CBCs) over other potential ISC populations during epithelial restitution and the importance of epithelial-derived signals in regulating ISC behavior.
            Cover page: Epithelial WNT Ligands Are Essential Drivers of Intestinal Stem Cell Activation
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2021)
            Biominerals such as seashells, coral skeletons, bone, and tooth enamel are optically anisotropic crystalline materials with unique nanoscale and microscale organization that translates into exceptional macroscopic mechanical properties, providing inspiration for engineering new and superior biomimetic structures. Using Seriatopora aculeata coral skeleton as a model, here, we experimentally demonstrate X-ray linear dichroic ptychography and map the c-axis orientations of the aragonite (CaCO3) crystals. Linear dichroic phase imaging at the oxygen K-edge energy shows strong polarization-dependent contrast and reveals the presence of both narrow (<35°) and wide (>35°) c-axis angular spread in the coral samples. These X-ray ptychography results are corroborated by four-dimensional (4D) scanning transmission electron microscopy (STEM) on the same samples. Evidence of co-oriented, but disconnected, corallite subdomains indicates jagged crystal boundaries consistent with formation by amorphous nanoparticle attachment. We expect that the combination of X-ray linear dichroic ptychography and 4D STEM could be an important multimodal tool to study nano-crystallites, interfaces, nucleation, and mineral growth of optically anisotropic materials at multiple length scales.
              Cover page: X-ray linear dichroic ptychography
              • Article
              • Peer Reviewed
              LBL Publications (2019)
              Multimodal microscopy that combines complementary nanoscale imaging techniques is critical for extracting comprehensive chemical, structural, and functional information, particularly for heterogeneous samples. X-ray microscopy can achieve high-resolution imaging of bulk materials with chemical, magnetic, electronic, and bond orientation contrast, while electron microscopy provides atomic-scale spatial resolution with quantitative elemental composition. Here, we combine x-ray ptychography and scanning transmission x-ray spectromicroscopy with three-dimensional energy-dispersive spectroscopy and electron tomography to perform structural and chemical mapping of an Allende meteorite particle with 15-nm spatial resolution. We use textural and quantitative elemental information to infer the mineral composition and discuss potential processes that occurred before or after accretion. We anticipate that correlative x-ray and electron microscopy overcome the limitations of individual imaging modalities and open up a route to future multiscale nondestructive microscopies of complex functional materials and biological systems.
                Cover page: Multimodal x-ray and electron microscopy of the Allende meteorite
                • Article
                • Peer Reviewed
                UC San Diego Previously Published Works (2021)
                The characterization of cancer genomes has provided insight into somatically altered genes across tumors, transformed our understanding of cancer biology, and enabled tailoring of therapeutic strategies. However, the function of most cancer alleles remains mysterious, and many cancer features transcend their genomes. Consequently, tumor genomic characterization does not influence therapy for most patients. Approaches to understand the function and circuitry of cancer genes provide complementary approaches to elucidate both oncogene and non-oncogene dependencies. Emerging work indicates that the diversity of therapeutic targets engendered by non-oncogene dependencies is much larger than the list of recurrently mutated genes. Here we describe a framework for this expanded list of cancer targets, providing novel opportunities for clinical translation.
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