Doctor of Philosophy

dissertationIn this work, single molecule fluorescence microscopy techniques are used to investigate the role of electrostatics in deoxyribonucleic acid (DNA) hybridization, and in the interactions of DNA and colloidal particles with charged surfaces. Single molecule total internal reflection fluorescence (TIRF) microscopy provides the sensitivity and interfacial specificity needed to probe electrostatic interactions in the microscopic electrical double-layer region between charged molecules and surfaces. Image analysis has been developed to quantitatively detect single molecule spots in TIRF images by sampling their diffraction-limited point-spread function by multiple pixels on the imaging sensor. By detecting spots with multiple pixels above an intensity threshold, single molecules can be located with signal-to-noise ratios as low as 2.5, minimizing false positive and false negative probabilities. Single molecule imaging was used to monitor the time-course of individual complementary strand DNA hybridization events. Target single stranded DNA (ssDNA) was immobilized at an interface, and its absolute surface density and association constant were determined from the binding isotherm of fluorescently labeled complimentary strand probe ssDNA. Dissociation rate constants of the DNA duplex were determined from the dissociation times, and association rates were calculated from the association constant and the dissociation rate assuming a two-state binding model. From the dependence of association constants, association rates, and dissociation rates on ionic strength, an Eyring model was used to determine the electrostatic contribution to the free energy of the transition state and the fully hybridized double-helix. The electrostatic interactions between large DNA plasmids and a potential-controlled indium tin oxide (ITO) semiconductor surface were investigated by measuring DNA populations and diffusion near the semiconductor surface as a function of applied potential. DNA populations increased exponentially with positive applied potentials, while maintaining free-solution-like diffusion coefficients and no surface adsorption. A Boltzmann model indicates that interfacial DNA has a net charge less than one electron equivalent, suggesting that much of its charge is screened by counterions. Similar accumulation with increasing positive applied potential was observed with 100 nm carboxylate-polystyrene colloidal particles. These colloidal particles were used to investigate shifts in surface charge of the ITO-aqueous interface induced by photoexcitation of charge carriers in the semiconductor

Measuring Transcription Directly From Our Chromosomes

Our genome is organized into DNA segments called chromosomes. Alterations to the typically invariant number and composition of chromosomes are hallmarks of serious disease like cancer. Understanding how rearranging chromosomes affects chromosomal behavior and ultimately leads to disease requires chromosome-specific gene expression measurements, but current tools are insufficient. This thesis describes tools for measuring transcription while discriminating which copy of a gene the RNA comes from. The ability to take these measurements in single cells enabled us to measure changes in transcription on translocated chromosomes or from the maternal vs. paternal chromosomes. Firstly, we introduce intron chromosomal expression FISH (iceFISH), a multiplex imaging method for measuring transcription and chromosome structure simultaneously on single chromosomes. We find substantial differences in transcriptional frequency between genes on a translocated chromosome and the same genes in their normal chromosomal context in the same cell. Correlations between genes on a single chromosome pointed toward a cis chromosome-level transcriptional interaction spanning 14.3 megabases. Chromosomes also come in nearly identical pairs and gene expression is a mixture of RNA transcribed from the maternal or paternal copies. The infrequent sequence differences between parental copies can have serious implications for the viability of cell or organism but detecting single nucleotide differences is difficult, making these behaviors nearly impossible to study in detail. We present a high efficiency fluorescence in situ hybridization method for detecting single nucleotide variants (SNVs) on individual RNA transcripts, both exonic and intronic. We used this method to quantify allelic expression at the population and single cell level, and also to distinguish maternal from paternal chromosomes in single cells. The findings we present in this thesis have far-reaching implications for understanding the transcriptional effects of translocations, and the tools described in this thesis are widely applicable to studying gene regulation and developing in vitro diagnostics

Quantitative mRNA detection with advanced nonlinear microscopy

Cell-specific information on quantity and localization of key mRNA transcripts in single-cell level are critical to the assessment of cancer risk, therapy efficacy, and effective prevention strategies. While current techniques are not capable to visualize single mRNA transcript beyond the diffraction limit. In this thesis, two nonlinear technologies, second harmonic super-resolution microscopy (SHaSM) and transient absorption microscopy (TAM), are developed to detect and quantify single Human edimer receptor 2 (Her2) mRNA transcripts. The SHaSM is used to detect single mRNA transcript beyond the diffraction limit, while the TAM is employed to detect mRNA without the interference of fluorescence background. The thesis presents the fundamental study on the probes used in SHaSM, the concept and instrumental layout of the two technologies, and the detection as well as quantification of mRNA transcript in cells and tissues by super resolution microscopy and background-free detection microscopy. The first part of my dissertation focuses on the introduction of available mRNA detection methods and nonlinear imaging techniques. In chapter 2, I mainly characterize the SHG emission behavior of individual BTO nanocrystals via time-resolved single molecule spectroscopy, correlation spectroscopy, and confocal microscopy. High-intensity stable emission is collected from individual BTO nanocrystals with a high signal-to-noise ratio; the polar-dependent emission behavior of individual BTO NCs was also investigated theoretically and experimentally; and the dynamics of individual BTO in turbid medium is studied by an improved autocorrelation spectroscopy. The third chapter develops a novel second harmonic super-resolution microscopy (SHaSM), which is capable of detecting individual BTO nanocrystals with the lateral resolution as high as 30 nm. Motivated by the capability of SHaSM to visualize single BTO nanocrystals beyond the diffraction limit, we develop a dimer configuration of BTO nanocrystals for detecting single mRNA transcript beyond the diffraction limit. We validate our SHaSM to resolve single mRNA transcript first in vitro. Preformed BTO dimers are detected and differentiated by the SHaSM and by the SEM as the control. Expression level and localization patterns of Her2 mRNA transcript in single SKBR3, MCF7, and HeLa cell are investigated with the SHaSM. SHaSM can successfully differentiate the Her2 mRNA from the nonspecific BTO monomers, and identify more than one transcript in a diffraction-limited spot for SKBR3 cells. Quantification results agree well with the theoretical estimation and the RNA FISH results, and in addition it shows that the SHaSM has more accurate quantification when detecting over-expressed mRNA transcript. Furthermore we applied the SHG probes and SHaSM to study the heterogeneity of Her2 mRNA transcript in breast cancer tissues. High-specific binding of the SHG probes is observed and high penetration detection can be realized. In addition to the SHaSM, I also develop a background-free method to detect and quantify mRNA transcript. A femto-second transient absorption microscopy (TAM) is developed in the lab. It starts with the theoretical description of the TAM process, and then introduce the fundamental optical properties of the gold nanoparticles in TAM. By chemically treating the gold nanoparticles and conjugating with ODN probes, the gold nanoparticles hybridize to the mRNA molecules and are visualized in the TAM, together with label-free images of cells obtained in the SRS microscopy. mRNA is quantified with single copy sensitivity and is validated by the FISH approach. Super resolution microscopy of Her2 mRNA transcript in single cells will provide more accurate quantification in single cells; what\u27s more, it can be potentially employed to investigate the dynamics of single mRNA transcript beyond the diffraction limit, which is extremely significant in basic biology. TAM microscopy promotes the detection of mRNA transcript at a high speed without fluorescence background, which can be further utilized to investigate the dynamics of RNA regulation. Both these two methods will promote our understandings of the expression level and localization patterns of mRNA transcript in single cells, provide a route to employ mRNA transcript as a marker or indicator for cancer diagnosis and therapy

Single-cell western blotting.

To measure cell-to-cell variation in protein-mediated functions, we developed an approach to conduct ∼10(3) concurrent single-cell western blots (scWesterns) in ∼4 h. A microscope slide supporting a 30-μm-thick photoactive polyacrylamide gel enables western blotting: settling of single cells into microwells, lysis in situ, gel electrophoresis, photoinitiated blotting to immobilize proteins and antibody probing. We applied this scWestern method to monitor single-cell differentiation of rat neural stem cells and responses to mitogen stimulation. The scWestern quantified target proteins even with off-target antibody binding, multiplexed to 11 protein targets per single cell with detection thresholds of <30,000 molecules, and supported analyses of low starting cell numbers (∼200) when integrated with FACS. The scWestern overcomes limitations of antibody fidelity and sensitivity in other single-cell protein analysis methods and constitutes a versatile tool for the study of complex cell populations at single-cell resolution

Specialized astrocytes mediate glutamatergic gliotransmission in the CNS

Multimodal astrocyte–neuron communications govern brain circuitry assembly and function1. For example, through rapid glutamate release, astrocytes can control excitability, plasticity and synchronous activity2,3 of synaptic networks, while also contributing to their dysregulation in neuropsychiatric conditions4–7. For astrocytes to communicate through fast focal glutamate release, they should possess an apparatus for Ca2+-dependent exocytosis similar to neurons8–10. However, the existence of this mechanism has been questioned11–13 owing to inconsistent data14–17 and a lack of direct supporting evidence. Here we revisited the astrocyte glutamate exocytosis hypothesis by considering the emerging molecular heterogeneity of astrocytes18–21 and using molecular, bioinformatic and imaging approaches, together with cell-specific genetic tools that interfere with glutamate exocytosis in vivo. By analysing existing single-cell RNA-sequencing databases and our patch-seq data, we identified nine molecularly distinct clusters of hippocampal astrocytes, among which we found a notable subpopulation that selectively expressed synaptic-like glutamate-release machinery and localized to discrete hippocampal sites. Using GluSnFR-based glutamate imaging22 in situ and in vivo, we identified a corresponding astrocyte subgroup that responds reliably to astrocyte-selective stimulations with subsecond glutamate release events at spatially precise hotspots, which were suppressed by astrocyte-targeted deletion of vesicular glutamate transporter 1 (VGLUT1). Furthermore, deletion of this transporter or its isoform VGLUT2 revealed specific contributions of glutamatergic astrocytes in cortico-hippocampal and nigrostriatal circuits during normal behaviour and pathological processes. By uncovering this atypical subpopulation of specialized astrocytes in the adult brain, we provide insights into the complex roles of astrocytes in central nervous system (CNS) physiology and diseases, and identify a potential therapeutic target

Characterising Chinese Hamster Ovary Cell Line Stability in Bioproduction of Therapeutic Proteins

No abstract

Microfluidics-Based Single-Cell Functional Proteomics Microchip for Portraying Protein Signal Transduction Networks within the Framework of Physicochemical Principles, with Applications in Fundamental and Translational Cancer Research

Single-cell functional proteomics assays can connect genomic information to biological function through quantitative and multiplex protein measurements. Tools for single-cell proteomics have developed rapidly over the past 5 years and are providing unique opportunities. This thesis describes an emerging microfluidics-based toolkit for single cell functional proteomics, focusing on the development of the single cell barcode chips (SCBCs) with applications in fundamental and translational cancer research. The microchip designed to simultaneously quantify a panel of secreted, cytoplasmic and membrane proteins from single cells will be discussed at the beginning, which is the prototype for subsequent proteomic microchips with more sophisticated design in preclinical cancer research or clinical applications. The SCBCs are a highly versatile and information rich tool for single-cell functional proteomics. They are based upon isolating individual cells, or defined number of cells, within microchambers, each of which is equipped with a large antibody microarray (the barcode), with between a few hundred to ten thousand microchambers included within a single microchip. Functional proteomics assays at single-cell resolution yield unique pieces of information that significantly shape the way of thinking on cancer research. An in-depth discussion about analysis and interpretation of the unique information such as functional protein fluctuations and protein-protein correlative interactions will follow. The SCBC is a powerful tool to resolve the functional heterogeneity of cancer cells. It has the capacity to extract a comprehensive picture of the signal transduction network from single tumor cells and thus provides insight into the effect of targeted therapies on protein signaling networks. We will demonstrate this point through applying the SCBCs to investigate three isogenic cell lines of glioblastoma multiforme (GBM). The cancer cell population is highly heterogeneous with high-amplitude fluctuation at the single cell level, which in turn grants the robustness of the entire population. The concept that a stable population existing in the presence of random fluctuations is reminiscent of many physical systems that are successfully understood using statistical physics. Thus, tools derived from that field can probably be applied to using fluctuations to determine the nature of signaling networks. In the second part of the thesis, we will focus on such a case to use thermodynamics-motivated principles to understand cancer cell hypoxia, where single cell proteomics assays coupled with a quantitative version of Le Chatelier's principle derived from statistical mechanics yield detailed and surprising predictions, which were found to be correct in both cell line and primary tumor model. The third part of the thesis demonstrates the application of this technology in the preclinical cancer research to study the GBM cancer cell resistance to molecular targeted therapy. Physical approaches to anticipate therapy resistance and to identify effective therapy combinations will be discussed in detail. Our approach is based upon elucidating the signaling coordination within the phosphoprotein signaling pathways that are hyperactivated in human GBMs, and interrogating how that coordination responds to the perturbation of targeted inhibitor. Strongly coupled protein-protein interactions constitute most signaling cascades. A physical analogy of such a system is the strongly coupled atom-atom interactions in a crystal lattice. Similar to decomposing the atomic interactions into a series of independent normal vibrational modes, a simplified picture of signaling network coordination can also be achieved by diagonalizing protein-protein correlation or covariance matrices to decompose the pairwise correlative interactions into a set of distinct linear combinations of signaling proteins (i.e. independent signaling modes). By doing so, two independent signaling modes – one associated with mTOR signaling and a second associated with ERK/Src signaling have been resolved, which in turn allow us to anticipate resistance, and to design combination therapies that are effective, as well as identify those therapies and therapy combinations that will be ineffective. We validated our predictions in mouse tumor models and all predictions were borne out. In the last part, some preliminary results about the clinical translation of single-cell proteomics chips will be presented. The successful demonstration of our work on human-derived xenografts provides the rationale to extend our current work into the clinic. It will enable us to interrogate GBM tumor samples in a way that could potentially yield a straightforward, rapid interpretation so that we can give therapeutic guidance to the attending physicians within a clinical relevant time scale. The technical challenges of the clinical translation will be presented and our solutions to address the challenges will be discussed as well. A clinical case study will then follow, where some preliminary data collected from a pediatric GBM patient bearing an EGFR amplified tumor will be presented to demonstrate the general protocol and the workflow of the proposed clinical studies.</p

Dielectrophoretic (DEP) Tweezers: New Tool for Molecular Force Spectroscopy

Many recent advances in DNA sequencing technology have taken advantage of single-molecule techniques using fluorescently-labeled oligonucleotides as the principle mode of detection. In spite of the successes of fluorescent-based sequencers, avoidance of labeled nucleotides could substantially reduce the costs of sequencing. This dissertation will describe the development of an alternative sequencing method, in which unlabeled DNA can be manipulated directly on a massively parallel scale using single molecule force spectroscopy. We demonstrated that a combination of a wide-field optical detection technique (evanescent field excitation) with dielectrophoretic (DEP) tweezers could determine the amount of the double-stranded character of DNA. This thesis discusses all aspects of the implementation of DEP tweezers, including the principle of operation, making of polymer force probes, numerical modeling of various designs, fabrication of electrode and disposable chip, force calibration, and the assembly of the device. The feasibility of this technique was demonstrated by conducting force spectroscopy on single DNA molecules using DEP tweezers. The development of such a single molecule force spectroscopy technique shows great potential for genome sequencing and other analytical applications that employ direct manipulation of biomolecules

A stochastic view on surface inhomogeneity of nanoparticles

The interactions between and with nanostructures can only be fully understood when the functional group distribution on their surfaces can be quantified accurately. Here we apply a combination of direct stochastic optical reconstruction microscopy (dSTORM) imaging and probabilistic modelling to analyse molecular distributions on spherical nanoparticles. The properties of individual fluorophores are assessed and incorporated into a model for the dSTORM imaging process. Using this tailored model, overcounting artefacts are greatly reduced and the locations of dye labels can be accurately estimated, revealing their spatial distribution. We show that standard chemical protocols for dye attachment lead to inhomogeneous functionalization in the case of ubiquitous polystyrene nanoparticles. Moreover, we demonstrate that stochastic fluctuations result in large variability of the local group density between particles. These results cast doubt on the uniform surface coverage commonly assumed in the creation of amorphous functional nanoparticles and expose a striking difference between the average population and individual nanoparticle coverage