subject:(single cell fluorescence microscopy)

Virginia Tech

1. Tavassoly, Iman. Dynamics of Cell Fate Decisions Mediated by the Interplay of Autophagy and Apoptosis in Cancer Cells: Mathematical Modeling and Experimental Observations .

Degree: PhD, Genetics, Bioinformatics, and Computational Biology, 2013, Virginia Tech

URL: http://hdl.handle.net/10919/79557

► Autophagy is a conserved biological stress response in mammalian cells that is responsible for clearing damaged proteins and organelles from the cytoplasm and recycling their… (more)

Subjects/Keywords: Apoptosis; Autophagy; Cancer; Cell Death; Dynamic Modeling; Live Cell Imaging; Quantitative Fluorescence Microscopy; Single-Cell

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APA (6^th Edition):

Tavassoly, I. (2013). Dynamics of Cell Fate Decisions Mediated by the Interplay of Autophagy and Apoptosis in Cancer Cells: Mathematical Modeling and Experimental Observations . (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/79557

Chicago Manual of Style (16^th Edition):

Tavassoly, Iman. “Dynamics of Cell Fate Decisions Mediated by the Interplay of Autophagy and Apoptosis in Cancer Cells: Mathematical Modeling and Experimental Observations .” 2013. Doctoral Dissertation, Virginia Tech. Accessed March 08, 2021. http://hdl.handle.net/10919/79557.

MLA Handbook (7^th Edition):

Tavassoly, Iman. “Dynamics of Cell Fate Decisions Mediated by the Interplay of Autophagy and Apoptosis in Cancer Cells: Mathematical Modeling and Experimental Observations .” 2013. Web. 08 Mar 2021.

Vancouver:

Tavassoly I. Dynamics of Cell Fate Decisions Mediated by the Interplay of Autophagy and Apoptosis in Cancer Cells: Mathematical Modeling and Experimental Observations . [Internet] [Doctoral dissertation]. Virginia Tech; 2013. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/10919/79557.

Council of Science Editors:

Tavassoly I. Dynamics of Cell Fate Decisions Mediated by the Interplay of Autophagy and Apoptosis in Cancer Cells: Mathematical Modeling and Experimental Observations . [Doctoral Dissertation]. Virginia Tech; 2013. Available from: http://hdl.handle.net/10919/79557

University of Utah

2. Cooper, Justin T. Single-molecule fluorescence microscopy of molecular interactions at reversed-phase chromatographic interfaces.

Degree: PhD, Chemistry, 2014, University of Utah

URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/3354/rec/2197

► The development of techniques to probe molecular transport and the dynamics of molecular interactions at interfaces is important for understanding and optimizingsurface-based technologies including surface-enhanced… (more)

▼ The development of techniques to probe molecular transport and the dynamics of molecular interactions at interfaces is important for understanding and optimizingsurface-based technologies including surface-enhanced spectroscopies, biological assays, sensors, catalysis, and chemical separations. In particular, the efficiency and resolution of separation via reversed-phase liquid chromatography is governed by the interaction ofanalytes with the solution/stationary phase interface. Most commonly, the stationary phase material consists of high surface area, micron-sized, mesoporous silica particles functionalized with n-alkane ligands. Understanding the timescales at which analytemolecules are transported through the interior of the particle, as well as adsorbed and desorbed from the particle surface, is of fundamental importance in the development of new, more efficient chromatographic materials.Probing chemical interactions at interfaces is difficult due to the selectivity needed to measure the small population of molecules at an interface versus bulk solution. Measuring interfacial chemical interactions within chromatographic particles has the added challenge that the majority of the surface area is contained within the particle making it difficult to measure interfacial processes directly.In this work, single-molecule spectroscopic techniques are used to measure the transport and adsorption/desorption kinetics of molecules at planar reversed-phase chromatographic interfaces and within reversed-phase chromatographic particles. Fluorescence imaging with single-molecule tracking is used to track the locations of fluorescent molecules during their retention within chromatographic particles. Thisyields information regarding their diffusion rates and their residence time within the particle. Statistical criteria based on the single-molecule localization resolution are also developed to characterize the population of strongly adsorbed molecules and their effect on intraparticle molecular residence times. Fluorescence imaging is also combined with fluorescence-correlation spectroscopy and used to measure fast interfacial transport and sorption kinetics at planar models of chromatographic interfaces. This technique has higher temporal resolutionrelative to imaging and is capable of measuring transport approaching free solution diffusion rates of small molecules.Finally, a comparison is made between interfacial transport rates and surface populations measured at planar chromatographic interfacial models versus within porous particles. It is found that n-alkyl modified planar interfaces are reasonable models for reversed-phase chromatographic particles with proper interpretation of measured parameters.

Subjects/Keywords: Fluorescence; Microscopy; Single-molecule imaging

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APA (6^th Edition):

Cooper, J. T. (2014). Single-molecule fluorescence microscopy of molecular interactions at reversed-phase chromatographic interfaces. (Doctoral Dissertation). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/3354/rec/2197

Chicago Manual of Style (16^th Edition):

Cooper, Justin T. “Single-molecule fluorescence microscopy of molecular interactions at reversed-phase chromatographic interfaces.” 2014. Doctoral Dissertation, University of Utah. Accessed March 08, 2021. http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/3354/rec/2197.

MLA Handbook (7^th Edition):

Cooper, Justin T. “Single-molecule fluorescence microscopy of molecular interactions at reversed-phase chromatographic interfaces.” 2014. Web. 08 Mar 2021.

Vancouver:

Cooper JT. Single-molecule fluorescence microscopy of molecular interactions at reversed-phase chromatographic interfaces. [Internet] [Doctoral dissertation]. University of Utah; 2014. [cited 2021 Mar 08]. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/3354/rec/2197.

Council of Science Editors:

Cooper JT. Single-molecule fluorescence microscopy of molecular interactions at reversed-phase chromatographic interfaces. [Doctoral Dissertation]. University of Utah; 2014. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/3354/rec/2197

University of Saskatchewan

3. Lu, Yin. Single-molecule fluorescence microscopy studies of fluorescent probes in thin films and on nanoparticle surfaces.

Degree: 2011, University of Saskatchewan

URL: http://hdl.handle.net/10388/etd-01312011-155230

► Single-molecule (SM) fluorescence spectroscopy has become a useful and important experimental approach for investigating the optical properties of chemical systems. In this thesis, four subprojects… (more)

▼ Single-molecule (SM) fluorescence spectroscopy has become a useful and important experimental approach for investigating the optical properties of chemical systems. In this thesis, four subprojects in the field of SM fluorescence spectroscopy are presented in which SM spectroscopy has provided invaluable experimental insight into the systems of interest. In the first project, the photophysical properties of Calcium-Green 1 (CG-1), a calcium-ion indicator, were studied at both the ensemble and SM levels. CG-1 is non-fluorescent in the absence of Ca2+ and becomes strongly fluorescent when bound to Ca2+. In the ensemble measurements, the absorption and fluorescence spectra were collected under various Ca2+ concentrations. In addition, the fluorescence lifetime of CG-2 was also studied as a function of [Ca2+]. From SM measurements, the photobleaching time and fluorescence intensity distributions of CG-1 were studied both in the presence and in absence of Ca2+. The results were compared with those obtained for the dual-fluorophoric variant, Calcium-Green 2 (CG-2), whose photophysical properties have been investigated by previous researchers. The experimental results reveal that CG-1 can exist in two different forms: a highly-quenched form due to the occurrence of photoinduced electron transfer (PET) in the absence of Ca2+, and a strongly fluorescent form when bound to Ca2+. The second project is a continuation of a previous study on CG-2. In the dual-chromophore CG-2 system, energy transfer between chromophores is controlled by the orientation and spatial separation between chromophores. Dual polarization fluorescence microscopy was used to determine the relative conformation of the two fluorophores in the emissive form of CG-2. Distributions of fluorescence polarization of individual CG-2 molecules were collected for both Ca2+-free and Ca2+-saturated conditions. The experimental polarization results were compared to those calculated from a simple geometric model based on randomly-orientated fluorescent dimers. The results show good agreement with previous calculations of the molecular conformation of CG-2. This indicates that the dual polarization imaging approach has significant potential as a general tool for characterizing chromophore orientation in coupled-fluorophore systems. In the third project, Nile Red (NR), a solvatochromic lipid stain, was incorporated into phase separated Langmuir-Blodgett (LB) films composed of arachidic acid (AA) and perfluorotetradecanoic acid (PA). According to previous studies by atomic force microscopy (AFM), two types of separated domains are formed in the LB films: micron-sized hexagonal discontinuous domains that are exclusively comprised of AA, and the surrounding continuous domains which are enriched in PA. The photophysical properties of NR were characterized in the two physically and chemically distinct domains via bulk and SM fluorescence measurements. In addition to fluorescence microscopy, fluorescence confocal spectromicroscopy was also applied in the ensemble… Advisors/Committee Members: Paige, Matthew F., Burgess, Ian, Steer, Ronald P., Baranski, Andrzej, Lee, Jeremy S., Loppnow, Glen R..

Subjects/Keywords: fluorescence; single-molecule; microscopy

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APA (6^th Edition):

Lu, Y. (2011). Single-molecule fluorescence microscopy studies of fluorescent probes in thin films and on nanoparticle surfaces. (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/etd-01312011-155230

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Lu, Yin. “Single-molecule fluorescence microscopy studies of fluorescent probes in thin films and on nanoparticle surfaces.” 2011. Thesis, University of Saskatchewan. Accessed March 08, 2021. http://hdl.handle.net/10388/etd-01312011-155230.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Lu, Yin. “Single-molecule fluorescence microscopy studies of fluorescent probes in thin films and on nanoparticle surfaces.” 2011. Web. 08 Mar 2021.

Vancouver:

Lu Y. Single-molecule fluorescence microscopy studies of fluorescent probes in thin films and on nanoparticle surfaces. [Internet] [Thesis]. University of Saskatchewan; 2011. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/10388/etd-01312011-155230.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Lu Y. Single-molecule fluorescence microscopy studies of fluorescent probes in thin films and on nanoparticle surfaces. [Thesis]. University of Saskatchewan; 2011. Available from: http://hdl.handle.net/10388/etd-01312011-155230

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universiteit Utrecht

4. Daniël, J.W. Kisspeptin in vitro: a concentration response study and testing of kisspeptin antagonist P271.

Degree: 2014, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/289058

► Kisspeptin is an important regulator of the hypothalamic-pituitary-gonadal axis in mammals. It acts on the GnRH neurons trough the GPR54 receptor initiating GnRH release. The… (more)

Subjects/Keywords: Kisspeptin; GPR54; Antagonist; P271; in vitro; single-cell fluorescence microscopy; fura-2-AM

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APA (6^th Edition):

Daniël, J. W. (2014). Kisspeptin in vitro: a concentration response study and testing of kisspeptin antagonist P271. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/289058

Chicago Manual of Style (16^th Edition):

Daniël, J W. “Kisspeptin in vitro: a concentration response study and testing of kisspeptin antagonist P271.” 2014. Masters Thesis, Universiteit Utrecht. Accessed March 08, 2021. http://dspace.library.uu.nl:8080/handle/1874/289058.

MLA Handbook (7^th Edition):

Daniël, J W. “Kisspeptin in vitro: a concentration response study and testing of kisspeptin antagonist P271.” 2014. Web. 08 Mar 2021.

Vancouver:

Daniël JW. Kisspeptin in vitro: a concentration response study and testing of kisspeptin antagonist P271. [Internet] [Masters thesis]. Universiteit Utrecht; 2014. [cited 2021 Mar 08]. Available from: http://dspace.library.uu.nl:8080/handle/1874/289058.

Council of Science Editors:

Daniël JW. Kisspeptin in vitro: a concentration response study and testing of kisspeptin antagonist P271. [Masters Thesis]. Universiteit Utrecht; 2014. Available from: http://dspace.library.uu.nl:8080/handle/1874/289058

University of California – Berkeley

5. Alfieri, Katherine Nell. Single Molecule Observations of Receptor:Ligand Binding at Live T Cell-Supported Membrane Interfaces.

Degree: Chemistry, 2015, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/5g43m7bz

► Recognition of antigen by T cells occurs at the junction between a T cell and an antigen-presenting cell. Within this highly constrained interface, the T… (more)

▼ Recognition of antigen by T cells occurs at the junction between a T cell and an antigen-presenting cell. Within this highly constrained interface, the T cell receptor (TCR) interacts with its cognate antigen peptide major histocompatibility complex (pMHC). Additional signaling and adhesion molecules present in this intercellular environment influence its overall topography and geometry, which can significantly impact receptor:ligand binding events. The work presented in this dissertation describes three studies aimed at making direct, in situ measurements of molecular interactions during T cell signal transduction. For all of these studies, I use a hybrid live T cell-supported membrane system to mimic the physiological juxtacrine signaling environment and single molecule fluorescence microscopy to monitor individual receptor:ligand binding events. The supported membrane is functionalized with fluorescently-tagged pMHC and the formation of individual pMHC:TCR complexes is observed via time-resolved single molecule techniques. Using these approaches, I report live cell, two-dimensional pMHC:TCR kinetics and affinity measurements in self-reactive human T cell clones and discuss discrepancies between my results and those determined via mechanical assays. I also describe a novel method for simultaneously monitoring pMHC:TCR binding and downstream cellular response in a single cell. This strategy allows the measurement of all pMHC:TCR interactions leading to T cell activation and reveals a cumulative dwell time threshold required for activation. In order to better understand the molecular interactions of the costimulatory protein CD80, I have developed a novel CD80-SNAP-tag reagent suitable for single molecule receptor:ligand binding studies. I discuss the design, characterization, and application of this reagent, which has been used to demonstrate global environmental changes in the membrane-membrane interface during T cell triggering. Together, these studies emphasize the importance of investigating ligand binding in a physiologically relevant context and will contribute to a better understanding of the early stages of T cell signaling.

Subjects/Keywords: Chemistry; Biophysics; Molecular biology; fluorescence microscopy; signal transduction; single molecule techniques; T cell receptor

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APA (6^th Edition):

Alfieri, K. N. (2015). Single Molecule Observations of Receptor:Ligand Binding at Live T Cell-Supported Membrane Interfaces. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/5g43m7bz

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Alfieri, Katherine Nell. “Single Molecule Observations of Receptor:Ligand Binding at Live T Cell-Supported Membrane Interfaces.” 2015. Thesis, University of California – Berkeley. Accessed March 08, 2021. http://www.escholarship.org/uc/item/5g43m7bz.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Alfieri, Katherine Nell. “Single Molecule Observations of Receptor:Ligand Binding at Live T Cell-Supported Membrane Interfaces.” 2015. Web. 08 Mar 2021.

Vancouver:

Alfieri KN. Single Molecule Observations of Receptor:Ligand Binding at Live T Cell-Supported Membrane Interfaces. [Internet] [Thesis]. University of California – Berkeley; 2015. [cited 2021 Mar 08]. Available from: http://www.escholarship.org/uc/item/5g43m7bz.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Alfieri KN. Single Molecule Observations of Receptor:Ligand Binding at Live T Cell-Supported Membrane Interfaces. [Thesis]. University of California – Berkeley; 2015. Available from: http://www.escholarship.org/uc/item/5g43m7bz

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

6. P. Bonaiuti. A FISTFUL OF MOLECULES: CELLS ESCAPE AN OPERATIONAL MITOTIC CHECKPOINT THROUGH A STOCHASTIC PROCESS.

Degree: 2018, Università degli Studi di Milano

URL: http://hdl.handle.net/2434/554699

► The cell cycle culminates with the segregation of sister chromatids, which is a fundamental step in ensuring the transmission of unaltered genetic material. Chromosome segregation… (more)

Subjects/Keywords: mitosis; single-cell microscopy; mathematical model; adaptation; fluorescence correlation spectroscopy; Settore BIO/11 - Biologia Molecolare

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APA (6^th Edition):

Bonaiuti, P. (2018). A FISTFUL OF MOLECULES: CELLS ESCAPE AN OPERATIONAL MITOTIC CHECKPOINT THROUGH A STOCHASTIC PROCESS. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/554699

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Bonaiuti, P.. “A FISTFUL OF MOLECULES: CELLS ESCAPE AN OPERATIONAL MITOTIC CHECKPOINT THROUGH A STOCHASTIC PROCESS.” 2018. Thesis, Università degli Studi di Milano. Accessed March 08, 2021. http://hdl.handle.net/2434/554699.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Bonaiuti, P.. “A FISTFUL OF MOLECULES: CELLS ESCAPE AN OPERATIONAL MITOTIC CHECKPOINT THROUGH A STOCHASTIC PROCESS.” 2018. Web. 08 Mar 2021.

Vancouver:

Bonaiuti P. A FISTFUL OF MOLECULES: CELLS ESCAPE AN OPERATIONAL MITOTIC CHECKPOINT THROUGH A STOCHASTIC PROCESS. [Internet] [Thesis]. Università degli Studi di Milano; 2018. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/2434/554699.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Bonaiuti P. A FISTFUL OF MOLECULES: CELLS ESCAPE AN OPERATIONAL MITOTIC CHECKPOINT THROUGH A STOCHASTIC PROCESS. [Thesis]. Università degli Studi di Milano; 2018. Available from: http://hdl.handle.net/2434/554699

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Pennsylvania

7. Levesque, Marshall. Measuring Transcription Directly From Our Chromosomes.

Degree: 2013, University of Pennsylvania

URL: https://repository.upenn.edu/edissertations/773

► 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… (more)

▼ 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.

Subjects/Keywords: Chromosomes; fluorescence microscopy; RNA FISH; Single nucleotide variants; Translocations; Biomedical; Cell Biology

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APA (6^th Edition):

Levesque, M. (2013). Measuring Transcription Directly From Our Chromosomes. (Thesis). University of Pennsylvania. Retrieved from https://repository.upenn.edu/edissertations/773

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Levesque, Marshall. “Measuring Transcription Directly From Our Chromosomes.” 2013. Thesis, University of Pennsylvania. Accessed March 08, 2021. https://repository.upenn.edu/edissertations/773.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Levesque, Marshall. “Measuring Transcription Directly From Our Chromosomes.” 2013. Web. 08 Mar 2021.

Vancouver:

Levesque M. Measuring Transcription Directly From Our Chromosomes. [Internet] [Thesis]. University of Pennsylvania; 2013. [cited 2021 Mar 08]. Available from: https://repository.upenn.edu/edissertations/773.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Levesque M. Measuring Transcription Directly From Our Chromosomes. [Thesis]. University of Pennsylvania; 2013. Available from: https://repository.upenn.edu/edissertations/773

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

King Abdullah University of Science and Technology

8. Al Alwan, Bader. Spatio-Temporal Characterization of Ligand-Receptor Interactions in Haematopoietic Stem Cell Rolling during Homing.

Degree: Biological and Environmental Sciences and Engineering (BESE) Division, 2018, King Abdullah University of Science and Technology

URL: http://hdl.handle.net/10754/629897

► Researches on Hematopoietic Stem Cell (HSC) have been expanding that leads to an increase in our understanding of HSC normal behaviors and abnormal alterations. One… (more)

▼ Researches on Hematopoietic Stem Cell (HSC) have been expanding that leads to an increase in our understanding of HSC normal behaviors and abnormal alterations. One of the most important issues in the research on HSCs is to understand the mechanism of the homing process of these cells to settle in their niche in the bone marrow and establish the production of various blood cell types after bone marrow transplantation. The cells first must come in contact with the endothelial cells. This contact is known as adhesion and occurs through a multi-step paradigm ending with transmigration to the bone marrow niche. The initial step of the homing, tethering and rolling of HSC, is mediated by P- and E-Selectins present on endothelial cell surface through their interactions with the ligands expressed on the surface of HSC. Thus, understanding the adhesion process and its contribution for efficient HSCs homing will have great impact on HSC therapy. The selectin – ligands interaction has been intensively studied using in vivo and in vitro approaches. However, the molecular mechanism involved by HSCs at single molecule level is poorly understood. Here in this study, a novel experimental method to unravel the molecular mechanisms of the Selectin-ligands interactions in vitro at the single molecule level is developed by combining microfluidics, epi-fluorescence microscopy and live cells. In this work, the new single-molecule imaging technique enabled us to directly visualize the nanoscale spatiotemporal dynamics of the membrane protein-ligand interactions under conditions of shear stress acting on the cells at the molecular level in real time. Using this method, we revealed that selectin ligands on membrane-tethers and slings show unique spatiotemporal dynamics that is distinct from those on the cell body. We demonstrated that the membrane tethers are formed from single microvilli on the cells, which provides a mechanism to spatially localize selectin ligands, PSGL-1 and CD44 on the tethers and slings. We also demonstrated that the selectin ligands show fast diffusional motion along the tethers and slings compared with that on the cell body due to the detachment of cell membranes from actin cytoskeleton during the formation of the tethers. Our results suggest that the spatial confinement of the selectin ligands together with the fast scanning of a large area by the selectin ligands increase the efficiency of selectin-ligands interaction during the rolling, resulting in slow and stable rolling of the cell on selectin. Our findings contribute significantly to molecular level understanding of the initial step of HSCs. This single-molecule imaging technique that we developed in this study will find wide applications in the molecular-level studies on cell-cell interactions including cancer cell metastasis. Advisors/Committee Members: Habuchi, Satoshi (advisor), Merzaban, Jasmeen (committee member), Mishra, Himanshu (committee member), Yeow, Edwin (committee member).

Subjects/Keywords: Haematopoietic Stem Cell; Bone marrow transplant; HSC homing; Fluorescence microscopy; Ligand-Receptor; Single-Molecule

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Al Alwan, B. (2018). Spatio-Temporal Characterization of Ligand-Receptor Interactions in Haematopoietic Stem Cell Rolling during Homing. (Thesis). King Abdullah University of Science and Technology. Retrieved from http://hdl.handle.net/10754/629897

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Al Alwan, Bader. “Spatio-Temporal Characterization of Ligand-Receptor Interactions in Haematopoietic Stem Cell Rolling during Homing.” 2018. Thesis, King Abdullah University of Science and Technology. Accessed March 08, 2021. http://hdl.handle.net/10754/629897.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Al Alwan, Bader. “Spatio-Temporal Characterization of Ligand-Receptor Interactions in Haematopoietic Stem Cell Rolling during Homing.” 2018. Web. 08 Mar 2021.

Vancouver:

Al Alwan B. Spatio-Temporal Characterization of Ligand-Receptor Interactions in Haematopoietic Stem Cell Rolling during Homing. [Internet] [Thesis]. King Abdullah University of Science and Technology; 2018. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/10754/629897.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Al Alwan B. Spatio-Temporal Characterization of Ligand-Receptor Interactions in Haematopoietic Stem Cell Rolling during Homing. [Thesis]. King Abdullah University of Science and Technology; 2018. Available from: http://hdl.handle.net/10754/629897

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of California – Irvine

9. Li, Xuan. Microfluidic Single-Cell Analysis from Phenotype to Genotype.

Degree: Biomedical Engineering, 2019, University of California – Irvine

URL: http://www.escholarship.org/uc/item/4x14p4mb

► Single-cell analysis is of critical importance in revealing population heterogeneity, identifying minority sub-populations of interest, as well as discovering unique characteristics of individual cells. Conventional… (more)

Subjects/Keywords: Biomedical engineering; Cell-Cell Interaction; Dielectrophoretic Nanotweezers; Fluorescence Lifetime Imaging Microscopy; Microfluidics; Single-Cell Analysis; Transfection

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Li, X. (2019). Microfluidic Single-Cell Analysis from Phenotype to Genotype. (Thesis). University of California – Irvine. Retrieved from http://www.escholarship.org/uc/item/4x14p4mb

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Li, Xuan. “Microfluidic Single-Cell Analysis from Phenotype to Genotype.” 2019. Thesis, University of California – Irvine. Accessed March 08, 2021. http://www.escholarship.org/uc/item/4x14p4mb.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Li, Xuan. “Microfluidic Single-Cell Analysis from Phenotype to Genotype.” 2019. Web. 08 Mar 2021.

Vancouver:

Li X. Microfluidic Single-Cell Analysis from Phenotype to Genotype. [Internet] [Thesis]. University of California – Irvine; 2019. [cited 2021 Mar 08]. Available from: http://www.escholarship.org/uc/item/4x14p4mb.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Li X. Microfluidic Single-Cell Analysis from Phenotype to Genotype. [Thesis]. University of California – Irvine; 2019. Available from: http://www.escholarship.org/uc/item/4x14p4mb

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Cambridge

10. Palayret, Matthieu Grégoire Simon. Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation.

Degree: PhD, 2015, University of Cambridge

► Single-molecule localisation microscopy (SMLM) allows imaging of fluorescently-tagged proteins in live cells with a precision well below that of the diffraction limit. As a single-molecule… (more)

▼ Single-molecule localisation microscopy (SMLM) allows imaging of fluorescently-tagged proteins in live cells with a precision well below that of the diffraction limit. As a single-molecule technique, it has also introduced a new quantitative approach to fluorescence microscopy. In the Part A of this thesis, the design and building of three SMLM instruments, the implementation of a custom-developed image analysis package and the characterisation of the photo-physical properties of the photo-activable fluorescent protein used in this thesis (mEos), are discussed. Then, a new post-processing method for SMLM analysis is characterised: axial optical sectioning of SMLM images is demonstrated by thresholding fitted localisations using their fitted width and amplitude to reject fluorophores that emit from above or below a virtual ‘light-sheet’, a thin volume centred on the focal plane of the microscope. This method provides qualitative and quantitative improvements to SMLM. In the Part B of this thesis, SMLM is applied to study T cell activation. Although the T cell receptor plays a key role in immunity, its stoichiometry in the membrane of resting T cells is still a matter of debate. Here, single-molecule counting methods are implemented to compare the stoichiometry of TCRs fused with mEos2 in resting T cells to monomeric and dimeric controls. However, because of the stochasticity of mEos2 photo-physics, results are inconclusive and new counting techniques based on structural imaging are discussed. In addition to TCR triggering, T cells require the co-stimulatory triggering of the CD28 transmembrane receptor to become fully activated. However, some immobilised anti-CD28 antibodies, referred to as super-agonists (SA), can directly activate T cells without triggering the TCR. In this thesis, single-molecule tracking techniques are used to investigate the molecular mechanism of CD28 super-agonism in live T cells. The results indicate that the diffusion of CD28 is slowed by SA binding. This effect is further discussed in light of the kinetic-segregation model proposed for TCR triggering. Quantitative SMLM as implemented and further developed in this work offers new tools to investigate the molecular mechanisms initiating T cell activation, ultimately facilitating the discovery of novel approaches to target these pathways for therapeutic purposes.

Subjects/Keywords: T-cell receptor; kinetic-segregation; CD28 super-agonist; single-molecule localisation microscopy; super-resolution fluorescence microscopy; virtual 'light-sheet'; optical sectioning

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APA (6^th Edition):

Palayret, M. G. S. (2015). Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/252696https://www.repository.cam.ac.uk/bitstream/1810/252696/2/Movie%20B-1.avi ; https://www.repository.cam.ac.uk/bitstream/1810/252696/3/Movie%20B-2.mp4 ; https://www.repository.cam.ac.uk/bitstream/1810/252696/4/Automation.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/5/virtual%20light-sheet.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/6/General%20Code.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/7/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/252696/8/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/252696/9/PhDThesis_MatthieuPalayret.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/252696/10/PhDThesis_MatthieuPalayret.pdf.jpg

Chicago Manual of Style (16^th Edition):

Palayret, Matthieu Grégoire Simon. “Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation.” 2015. Doctoral Dissertation, University of Cambridge. Accessed March 08, 2021. https://www.repository.cam.ac.uk/handle/1810/252696https://www.repository.cam.ac.uk/bitstream/1810/252696/2/Movie%20B-1.avi ; https://www.repository.cam.ac.uk/bitstream/1810/252696/3/Movie%20B-2.mp4 ; https://www.repository.cam.ac.uk/bitstream/1810/252696/4/Automation.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/5/virtual%20light-sheet.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/6/General%20Code.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/7/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/252696/8/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/252696/9/PhDThesis_MatthieuPalayret.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/252696/10/PhDThesis_MatthieuPalayret.pdf.jpg.

MLA Handbook (7^th Edition):

Palayret, Matthieu Grégoire Simon. “Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation.” 2015. Web. 08 Mar 2021.

Vancouver:

Palayret MGS. Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation. [Internet] [Doctoral dissertation]. University of Cambridge; 2015. [cited 2021 Mar 08]. Available from: https://www.repository.cam.ac.uk/handle/1810/252696https://www.repository.cam.ac.uk/bitstream/1810/252696/2/Movie%20B-1.avi ; https://www.repository.cam.ac.uk/bitstream/1810/252696/3/Movie%20B-2.mp4 ; https://www.repository.cam.ac.uk/bitstream/1810/252696/4/Automation.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/5/virtual%20light-sheet.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/6/General%20Code.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/7/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/252696/8/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/252696/9/PhDThesis_MatthieuPalayret.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/252696/10/PhDThesis_MatthieuPalayret.pdf.jpg.

Council of Science Editors:

Palayret MGS. Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation. [Doctoral Dissertation]. University of Cambridge; 2015. Available from: https://www.repository.cam.ac.uk/handle/1810/252696https://www.repository.cam.ac.uk/bitstream/1810/252696/2/Movie%20B-1.avi ; https://www.repository.cam.ac.uk/bitstream/1810/252696/3/Movie%20B-2.mp4 ; https://www.repository.cam.ac.uk/bitstream/1810/252696/4/Automation.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/5/virtual%20light-sheet.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/6/General%20Code.zip ; https://www.repository.cam.ac.uk/bitstream/1810/252696/7/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/252696/8/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/252696/9/PhDThesis_MatthieuPalayret.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/252696/10/PhDThesis_MatthieuPalayret.pdf.jpg

University of New Mexico

11. Schwartz, Samantha. Visualizing Mast Cell Activation: Single Molecule Dynamics of Early Events in FceRI Signaling.

Degree: Nanoscience and Microsystems, 2016, University of New Mexico

URL: http://hdl.handle.net/1928/32334

► Healthy immune cell behavior requires sensitive and robust control over the processes that regulate signal transduction. In this work we employ single molecule fluorescence… (more)

▼ Healthy immune cell behavior requires sensitive and robust control over the processes that regulate signal transduction. In this work we employ single molecule fluorescence imaging techniques to quantify adapter protein recruitment, lateral mobility, receptor aggregation, and cytoskeletal organization to create a better understanding of many key processes in immune cell regulation. We focus on understanding the initiating events in FceRI signaling in mast cells. Mast cell signaling encompassing a wide array of cellular outcomes including calcium flux, release of pre-formed inflammatory mediators and the production of cytokines. Careful control over appropriate reactions to external antigens is necessary for mast cells to properly function within the context of an immune response. The antigen binding and signaling domains of FceRI are carried on different subunits. Because no studies to date have thoroughly investigated the integrity of the FceRI complex, it remains unclear how antigen binding regulates the dynamics and spatio-temporal distribution of the intracellular signaling ITAM domains. We address this by quantifying the dynamics and localization of the of the FceRI-gamma subunit relative to the FceRI-alpha subunit. We utilize a Fluorogen Activating Protein (FAP) tag to fluorescently label the FceRI-gamma subunit, and demonstrate its versatility as a novel probe for single particle tracking. Direct labeling of the FceRI-gamma also allows us to address long standing questions regarding the influence of IgE binding on receptor behavior. Given our understanding for how antigen addition regulates FceRI signaling domains, we next explore how FceRI aggregation regulates its association with the intracellular tyrosine kinase Syk. Proper initiation of tyrosine kinase activity is absolutely necessary for all receptor dependent signaling, yet it is not completely understood how Syk function is regulated. In this work we use single molecule imaging to follow individual Syk molecules at the plasma membrane and investigate how FceRI distribution influences its spatial and temporal behavior. We combine these findings with biochemical readouts to correlate the behavior of Syk with functional consequences.\\\\\\\ In addition to investigating FceRI signaling, we also demonstrate how localization based super-resolution imaging can provide new insights into immune cell biology. First, we report on the development of FAP as a novel probe for super-resolution imaging and live cell super-resolution imaging of intracellular structures (specifically the actin cytoskeleton). Second, we use super-resolution imaging to quantify the nanoscale aggregation of FcgRI and assess the influence of cytokine stimulation on FcgRI distribution. Third, we use super-resolution imaging to explore the nanoscale architecture of the podosome mechano-sensory assembly in dendritic cells. Advisors/Committee Members: Lidke, Diane, Wilson, Bridget, Wandinger-Ness, Angela, Lidke, Keith.

Subjects/Keywords: IgE Signaling; Single Molecule Flourescence Microscopy; Super-resolution Fluorescence Microscopy; Mast cell Signaling; Nanoscience and Nanotechnology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Schwartz, S. (2016). Visualizing Mast Cell Activation: Single Molecule Dynamics of Early Events in FceRI Signaling. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/32334

Chicago Manual of Style (16^th Edition):

Schwartz, Samantha. “Visualizing Mast Cell Activation: Single Molecule Dynamics of Early Events in FceRI Signaling.” 2016. Doctoral Dissertation, University of New Mexico. Accessed March 08, 2021. http://hdl.handle.net/1928/32334.

MLA Handbook (7^th Edition):

Schwartz, Samantha. “Visualizing Mast Cell Activation: Single Molecule Dynamics of Early Events in FceRI Signaling.” 2016. Web. 08 Mar 2021.

Vancouver:

Schwartz S. Visualizing Mast Cell Activation: Single Molecule Dynamics of Early Events in FceRI Signaling. [Internet] [Doctoral dissertation]. University of New Mexico; 2016. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/1928/32334.

Council of Science Editors:

Schwartz S. Visualizing Mast Cell Activation: Single Molecule Dynamics of Early Events in FceRI Signaling. [Doctoral Dissertation]. University of New Mexico; 2016. Available from: http://hdl.handle.net/1928/32334

University of Oxford

12. Sustarsic, Marko. In vitro, in silico and in vivo studies of the structure and conformational dynamics of DNA polymerase I.

Degree: PhD, 2016, University of Oxford

URL: http://ora.ox.ac.uk/objects/uuid:ea317d58-00f7-4fc4-b71b-866b4becf0f7 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.690133

► DNA polymerases are a family of molecular machines involved in high-fidelity DNA replication and repair, of which DNA polymerase I (Pol) is one the best-characterized… (more)

▼ DNA polymerases are a family of molecular machines involved in high-fidelity DNA replication and repair, of which DNA polymerase I (Pol) is one the best-characterized members. Pol is a strand-displacing polymerase responsible for Okazaki fragment synthesis and base-excision repair in bacteria; it consists of three protein domains, which harbour its 5’-3' polymerase, 3’-5’ exonuclease and 5’ endonuclease activities. In the first part of the thesis, we use a combination of single-molecule Förster resonance energy transfer (smFRET) and rigid-body docking to probe the structure of Pol bound to its gapped-DNA substrate. We show that the DNA substrate is highly bent in the complex, and that the downstream portion of the DNA is partly unwound. Using all-atom molecular dynamics (MD) simulations, we identify residues in the polymerase important for strand displacement and for downstream DNA binding. Moreover, we use coarse-grained simulations to investigate the dynamics of the gapped-DNA substrate alone, allowing us to propose a model for specific recognition and binding of gapped DNA by Pol. In the second part of the thesis, we focus on the catalytically important conformational change in Pol that involves the closing of the ‘fingers’ subdomain of the protein around an incoming nucleotide. We make use of the energy decomposition method (EDM) to predict the stability-determining residues for the closed and open conformations of Pol, and test their relevance by site-directed mutagenesis. We apply the unnatural amino acid approach and a single-molecule FRET assay of Pol fingers-closing, to show that substitutions in the stability-determining residues significantly affect the conformational equilibrium of Pol. In the final part of the thesis, we attempt to study Pol in its native environment of the living cell. We make use of the recently developed method of internalization by electroporation, and optimize it for organically labelled proteins. We demonstrate the internalization and single-molecule tracking of Pol, and provide preliminary data of intra-molecular FRET in Pol, both at the single-cell and single-molecule levels. Finally, by measuring smFRET within an internalized gapped-DNA construct, we observe DNA binding and bending by endogenous Pol, confirming the physiological relevance of our in vitro Pol-DNA structure.

Subjects/Keywords: 572.8; DNA polymerases; Electroporation; Biochemistry; Fluorescence microscopy; Molecular dynamics; Biophysics; Single-molecule spectroscopy; In-cell FRET; Single-molecule FRET

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sustarsic, M. (2016). In vitro, in silico and in vivo studies of the structure and conformational dynamics of DNA polymerase I. (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:ea317d58-00f7-4fc4-b71b-866b4becf0f7 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.690133

Chicago Manual of Style (16^th Edition):

Sustarsic, Marko. “In vitro, in silico and in vivo studies of the structure and conformational dynamics of DNA polymerase I.” 2016. Doctoral Dissertation, University of Oxford. Accessed March 08, 2021. http://ora.ox.ac.uk/objects/uuid:ea317d58-00f7-4fc4-b71b-866b4becf0f7 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.690133.

MLA Handbook (7^th Edition):

Sustarsic, Marko. “In vitro, in silico and in vivo studies of the structure and conformational dynamics of DNA polymerase I.” 2016. Web. 08 Mar 2021.

Vancouver:

Sustarsic M. In vitro, in silico and in vivo studies of the structure and conformational dynamics of DNA polymerase I. [Internet] [Doctoral dissertation]. University of Oxford; 2016. [cited 2021 Mar 08]. Available from: http://ora.ox.ac.uk/objects/uuid:ea317d58-00f7-4fc4-b71b-866b4becf0f7 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.690133.

Council of Science Editors:

Sustarsic M. In vitro, in silico and in vivo studies of the structure and conformational dynamics of DNA polymerase I. [Doctoral Dissertation]. University of Oxford; 2016. Available from: http://ora.ox.ac.uk/objects/uuid:ea317d58-00f7-4fc4-b71b-866b4becf0f7 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.690133

Texas A&M University

13. Kim, Dongyoung. Imaging Three-Dimensional Single Molecule Dynamics in its Cellular Context.

Degree: PhD, Biomedical Engineering, 2016, Texas A&M University

URL: http://hdl.handle.net/1969.1/187328

► Three-dimensional single molecule microscopy enables the study of dynamic processes in living cells at the level of individual molecules. Multifocal plane microscopy (MUM) is an… (more)

Subjects/Keywords: Microscopy; Fluorescence microscopy; Single molecule microscopy; Single molecule tracking; Electron microscopy; Prostate cancer

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kim, D. (2016). Imaging Three-Dimensional Single Molecule Dynamics in its Cellular Context. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/187328

Chicago Manual of Style (16^th Edition):

Kim, Dongyoung. “Imaging Three-Dimensional Single Molecule Dynamics in its Cellular Context.” 2016. Doctoral Dissertation, Texas A&M University. Accessed March 08, 2021. http://hdl.handle.net/1969.1/187328.

MLA Handbook (7^th Edition):

Kim, Dongyoung. “Imaging Three-Dimensional Single Molecule Dynamics in its Cellular Context.” 2016. Web. 08 Mar 2021.

Vancouver:

Kim D. Imaging Three-Dimensional Single Molecule Dynamics in its Cellular Context. [Internet] [Doctoral dissertation]. Texas A&M University; 2016. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/1969.1/187328.

Council of Science Editors:

Kim D. Imaging Three-Dimensional Single Molecule Dynamics in its Cellular Context. [Doctoral Dissertation]. Texas A&M University; 2016. Available from: http://hdl.handle.net/1969.1/187328

University of Utah

14. Myers, Grant Aaron. Characterizing the interactions of molecules with phospholipid vesicles and bilayers by confocal raman and single-molecule fluorescence microscopy.

Degree: PhD, Chemistry, 2012, University of Utah

URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/1922/rec/447

► Molecular interactions with phospholipid bilayers are investigated using two types of laser-based microscopies. In optical-trapping confocal Raman microscopy, individual phospholipid vesicles are held in place… (more)

▼ Molecular interactions with phospholipid bilayers are investigated using two types of laser-based microscopies. In optical-trapping confocal Raman microscopy, individual phospholipid vesicles are held in place in situ with laser tweezers while Raman scattering spectra are collected to report the preconcentration of analyte molecules via pH-gradient loading. A theory of accumulation is developed to account for source-depletion and vesicle buffering, factors that can significantly reduce the total accumulation. The system of 10 equations including 10 unknowns, five equilibrium constants and five experimental parameters was solved with symbolic-based mathematics software to yield a sixth-order polynomial having a single physically-meaningful, positive, real root. Utilizing this theory, an experiment is designed in which a single vesicle is manipulated by optical tweezers into isolation from other interfering vesicles and subjected to a variety of solution conditions. Raman spectra are analyzed quantitatively with a classical least squares method to determine the concentrations of compounds inside of the vesicle. When the pH gradient is 6.5 units and the citric-acid buffer inside of vesicles is 0.5 M, a 104-fold preconcentration factor of a model compound benzyl-dimethyl amine is observed, where accumulation into a 600-nm diameter vesicle is complete in less than 20 min.Total-internal-reflection fluorescence (TIRF) microscopy is a technique with the dynamic range, spatial and temporal resolution capable of characterizing the interactionsivof single fluorescently labeled peptides with a planar supported lipid bilayer. TIRF images are analyzed with an adjacent pixel criterion to discriminate between molecular events and random noise exceeding the threshold. The bi-exponential distribution of event durations is interpreted with respect to a consecutive reversible three-state kinetics model, where unfolded peptides from solution first interact weakly with the bilayer then fold to persist for a longer time. Application of this model is shown to be capable of transforming the measured event times into the microscopic rates of the system including the rates of peptide folding and unfolding. The Gibb’s free energy of the folding reaction from these measured rates, 1.7 kJ⋅mol-1 is comparable to that of other helix-forming membrane active peptides measured by isothermal titration calorimetry.

Subjects/Keywords: Fluorescence; Microscopy; Raman; Single-molecule; Spectroscopy

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APA (6^th Edition):

Myers, G. A. (2012). Characterizing the interactions of molecules with phospholipid vesicles and bilayers by confocal raman and single-molecule fluorescence microscopy. (Doctoral Dissertation). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/1922/rec/447

Chicago Manual of Style (16^th Edition):

Myers, Grant Aaron. “Characterizing the interactions of molecules with phospholipid vesicles and bilayers by confocal raman and single-molecule fluorescence microscopy.” 2012. Doctoral Dissertation, University of Utah. Accessed March 08, 2021. http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/1922/rec/447.

MLA Handbook (7^th Edition):

Myers, Grant Aaron. “Characterizing the interactions of molecules with phospholipid vesicles and bilayers by confocal raman and single-molecule fluorescence microscopy.” 2012. Web. 08 Mar 2021.

Vancouver:

Myers GA. Characterizing the interactions of molecules with phospholipid vesicles and bilayers by confocal raman and single-molecule fluorescence microscopy. [Internet] [Doctoral dissertation]. University of Utah; 2012. [cited 2021 Mar 08]. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/1922/rec/447.

Council of Science Editors:

Myers GA. Characterizing the interactions of molecules with phospholipid vesicles and bilayers by confocal raman and single-molecule fluorescence microscopy. [Doctoral Dissertation]. University of Utah; 2012. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/1922/rec/447

Cornell University

15. Van Slyke, Alexander LeRoy. DEVELOPMENT OF NOVEL METHODS FOR IMAGING MEMBRANE PROTEIN STOICHIOMETRY AT THE SINGLE MOLECULE LEVEL AND FOR FABRICATION OF A SINGLE MOLECULE PROTEIN-DNA IMAGING DEVICE.

Degree: PhD, Biophysics, 2019, Cornell University

URL: http://hdl.handle.net/1813/67625

► Single molecule fluorescence imaging techniques have revolutionized the way we study biology by offering methods to examine the behavior and arrangement of individual molecules and… (more)

▼ Single molecule fluorescence imaging techniques have revolutionized the way we study biology by offering methods to examine the behavior and arrangement of individual molecules and the molecular mechanisms underlying biological processes. These techniques permit the investigation of transient states and critical heterogeneities undetectable by ensemble measurements and genome-wide assays. In this dissertation, I detail a series of projects, performed as a member of the laboratory of Warren Zipfel, in which new single molecule methods were created and applied to address important biological questions. A technique designed to study protein-DNA interactions at the single molecule level in a high-throughput fashion is called “DNA curtains.” The nanopatterned microfluidic devices necessary for these experiments have previously been fabricated using electron-beam lithography. We developed a simplified, cost effective, and more accessible method of fabricating these devices. Due to their modular DNA binding domain, transcription activator-like effectors (TALEs) have potential to be used in the study of gene function and gene editing with medical and agricultural applications. Understanding the target search mechanism of TALEs is important to developing more efficient and accurate ways to design and deliver TALE proteins. In my first project, we investigated TALEs using “DNA curtains” in an effort to elucidate the details of this search mechanism. Many single molecule techniques require the sample to be observed in vitro in order to isolate the biomolecule of interest. As a result, physiological behavior may not be preserved. In my second project, we developed a method named Single Protein Recovery After Dilution (SPReAD) that addresses this limitation by enabling protein stoichiometry and function to be studied in vivo. My final project is an investigation of the functional composition of metabotropic glutamate receptors (mGluRs). Glutamate acts as both a neurotransmitter and neuromodulator in the central nervous system. These neuromodulatory effects are mediated by mGluRs and their improper function has been linked to schizophrenia and Fragile X Syndrome. Understanding the stoichiometry of mGluR complexes is necessary to the development of pharmacological compounds which modulate their signaling. We investigated the interaction between Group I mGluRs at the single molecule level in vivo utilizing our SPReAD technique. Advisors/Committee Members: Zipfel, Warren R. (chair), Pollack, Lois (committee member), Lis, John T. (committee member).

Subjects/Keywords: Single Molecule; Microscopy; Fluorescence; Optical Spectroscopy; Biophysics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Van Slyke, A. L. (2019). DEVELOPMENT OF NOVEL METHODS FOR IMAGING MEMBRANE PROTEIN STOICHIOMETRY AT THE SINGLE MOLECULE LEVEL AND FOR FABRICATION OF A SINGLE MOLECULE PROTEIN-DNA IMAGING DEVICE. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/67625

Chicago Manual of Style (16^th Edition):

Van Slyke, Alexander LeRoy. “DEVELOPMENT OF NOVEL METHODS FOR IMAGING MEMBRANE PROTEIN STOICHIOMETRY AT THE SINGLE MOLECULE LEVEL AND FOR FABRICATION OF A SINGLE MOLECULE PROTEIN-DNA IMAGING DEVICE.” 2019. Doctoral Dissertation, Cornell University. Accessed March 08, 2021. http://hdl.handle.net/1813/67625.

MLA Handbook (7^th Edition):

Van Slyke, Alexander LeRoy. “DEVELOPMENT OF NOVEL METHODS FOR IMAGING MEMBRANE PROTEIN STOICHIOMETRY AT THE SINGLE MOLECULE LEVEL AND FOR FABRICATION OF A SINGLE MOLECULE PROTEIN-DNA IMAGING DEVICE.” 2019. Web. 08 Mar 2021.

Vancouver:

Van Slyke AL. DEVELOPMENT OF NOVEL METHODS FOR IMAGING MEMBRANE PROTEIN STOICHIOMETRY AT THE SINGLE MOLECULE LEVEL AND FOR FABRICATION OF A SINGLE MOLECULE PROTEIN-DNA IMAGING DEVICE. [Internet] [Doctoral dissertation]. Cornell University; 2019. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/1813/67625.

Council of Science Editors:

Van Slyke AL. DEVELOPMENT OF NOVEL METHODS FOR IMAGING MEMBRANE PROTEIN STOICHIOMETRY AT THE SINGLE MOLECULE LEVEL AND FOR FABRICATION OF A SINGLE MOLECULE PROTEIN-DNA IMAGING DEVICE. [Doctoral Dissertation]. Cornell University; 2019. Available from: http://hdl.handle.net/1813/67625

University of Illinois – Urbana-Champaign

16. Jain, Ankur. Probing cellular protein complexes using single-molecule pull-down.

Degree: PhD, 0319, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/46887

► Cellular processes result from dynamic interactions between biomolecules. The gold standard method for investigating interaction between biomolecules is the pull-down assay. We have extended the… (more)

▼ Cellular processes result from dynamic interactions between biomolecules. The gold standard method for investigating interaction between biomolecules is the pull-down assay. We have extended the conventional pull-down assay to its ultimate limit: the analysis of single biomolecular complexes. We achieve this goal by performing the pull-downs directly on to the surface of microscope slides and visualizing the captured biomolecules at single-molecule resolution using total internal reflection fluorescence (TIRF) microscopy. We name this technology single-molecule pull-down or SiMPull. In one reification biotinylated antibody against the protein of interest is immobilized on a flow chamber. The flow chambers are passivated using a polymer coating such that the cellular components do not bind, and the immobilized antibody specifically captures the target protein. Cell lysates are diluted to obtain isolated molecules suitable for single-molecule imaging. The target molecules are fluorescently labeled either using a genetically encoded fluorescent protein tag or using antibodies, and imaged using a single-molecule TIRF microscope. Using SiMPull we are able to discriminate between multiple association states of a protein as well as determine the stoichiometry of interaction. This technology is widely applicable to an array of biological contexts, and is suitable to analysis of endogenous protein complexes from animal tissue. In particular, we have used SiMPull to investigate the architecture and assembly of mechanistic target of rapamycin complexes. The complexes captured from cell extracts on to our imaging chambers retain their functional activities: thus SiMPull can be used as a preparatory tool for single-molecule biochemical analysis on proteins that cannot be readily purified or reconstituted. Finally, we have extended this approach to the analysis of lipid-protein interactions. Advisors/Committee Members: Ha, Taekjip (advisor), Ha, Taekjip (Committee Chair), Chen, Jie (committee member), Gruebele, Martin (committee member), Myong, Su-A (committee member), Prasanth, Supriya G. (committee member).

Subjects/Keywords: single-molecule; fluorescence microscopy; protein interactions

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Jain, A. (2014). Probing cellular protein complexes using single-molecule pull-down. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/46887

Chicago Manual of Style (16^th Edition):

Jain, Ankur. “Probing cellular protein complexes using single-molecule pull-down.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 08, 2021. http://hdl.handle.net/2142/46887.

MLA Handbook (7^th Edition):

Jain, Ankur. “Probing cellular protein complexes using single-molecule pull-down.” 2014. Web. 08 Mar 2021.

Vancouver:

Jain A. Probing cellular protein complexes using single-molecule pull-down. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/2142/46887.

Council of Science Editors:

Jain A. Probing cellular protein complexes using single-molecule pull-down. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/46887

University of Illinois – Urbana-Champaign

17. Zhou, Ruobo. Fluorescence-force spectroscopy at the single molecule level.

Degree: PhD, 0240, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/31921

► During the past decade, various powerful single-molecule techniques have evolved and helped to address important questions in life sciences. As the single molecule techniques become… (more)

▼ During the past decade, various powerful single-molecule techniques have evolved and helped to address important questions in life sciences. As the single molecule techniques become mature, there is increasingly pressing need to maximize the information content of the analysis in order to be able to study more complex systems that better approximate in-vivo conditions. Here, we develop a fluorescence-force spectroscopy method to combine single-molecule fluorescence spectroscopy with optical tweezers. Optical tweezers are used to manipulate and observe mechanical properties on the nanometer scale and piconewton force range. However, once the force range is in the low piconewton range or less, the spatial resolution of optical tweezers decreases significantly. In combination with fluorescence spectroscopy, like single molecule Förster (or fluorescence) resonance energy transfer (FRET) whose detectable distance range is approximately 3-10 nm, we are able to observe nanometer fluctuations and internal conformational changes in a low-force regime. The possibility to place fluorescent labels at nearly any desired position and a sophisticated design of the experiment increases the amount of information that can be extracted in contrast to pure mechanical or fluorescence experiments. We demonstrate the applications of this method to various biological systems including: 1) to measure the effect of very low forces on the nanometer scale conformational transitions of the DNA four-way (Holliday) junction; 2) to dissect protein diffusion and dissociation mechanisms on single stranded DNA, 3) to calibrate FRET-based in-vivo force sensors and 4) to study mechanical unfolding of single proteins. The results could not have been obtained with fluorescence or force measurement alone, and clearly demonstrates the power and generality of our approach. Finally, we show that self-quenching of two identical fluorophores can be used to detect small conformational dynamics corresponding to sub-nanometer distance changes of single molecules in a FRET-insensitive short range (< 3 nm), extending the detectable distance range of our fluorescence-force spectroscopy method. Advisors/Committee Members: Ha, Taekjip (advisor), Aksimentiev, Aleksei (Committee Chair), Ha, Taekjip (committee member), Selvin, Paul R. (committee member), Stack, John D. (committee member).

Subjects/Keywords: single molecule detection; fluorescence microscopy; optical tweezers

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APA (6^th Edition):

Zhou, R. (2012). Fluorescence-force spectroscopy at the single molecule level. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/31921

Chicago Manual of Style (16^th Edition):

Zhou, Ruobo. “Fluorescence-force spectroscopy at the single molecule level.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 08, 2021. http://hdl.handle.net/2142/31921.

MLA Handbook (7^th Edition):

Zhou, Ruobo. “Fluorescence-force spectroscopy at the single molecule level.” 2012. Web. 08 Mar 2021.

Vancouver:

Zhou R. Fluorescence-force spectroscopy at the single molecule level. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/2142/31921.

Council of Science Editors:

Zhou R. Fluorescence-force spectroscopy at the single molecule level. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/31921

Penn State University

18. Son, Seoyoung. THE ROLE OF THE MEMBRANE IN INTEGRIN-MEDIATED ADHESION OF CELLS TO SURFACES.

Degree: 2018, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/15230szs328

► The adhesion of cells to an extracellular matrix is a dynamic process involving structural and signaling proteins, that, in turn, regulate key cellular processes, including… (more)

▼ The adhesion of cells to an extracellular matrix is a dynamic process involving structural and signaling proteins, that, in turn, regulate key cellular processes, including migration, gene expression, differentiation, and signaling. Integrins play important roles as primary adhesion receptors, and integrin-mediated cell adhesion sites can be differentiated, based on size and location, into nascent adhesions, focal complexes, focal adhesions, and fibrillar adhesions. The formation of nascent adhesions to a surface requires the bending of the membrane toward a surface, diffusion of integrins to the area of close contact, and molecular adhesion. Each of these processes is sensitive to the lipid makeup of the membrane. Therefore, the lipid bilayer may exert significant control over the dynamics of nascent adhesion formation. Because integrin-mediated adhesion is a central feature of cellular adhesion, locomotion, and endothelial cell mechanobiology, we investigated how membrane properties of thickness, compressibility, and bending rigidity modulate the formation of nascent cell adhesions via membrane curvature, redistribution of integrins and bond formation. Although integrins are known to be transmembrane proteins, little is known about the role of membrane biophysics and dynamics in integrin adhesion. We treated human aortic endothelial cells (HAECs) with exogenous amphiphiles shown previously in model membranes and computationally to affect bilayer thickness and lipid phase separation and subsequently measured single integrin molecule adhesion kinetics using an optical trap, and diffusion using fluorescence correlation spectroscopy (FCS). Benzyl alcohol (BA) partitions to liquid-disordered (Ld) domains, thins them, and causes the greatest increase in the hydrophobic mismatch between liquid-ordered (Lo) and Ld domains among the three amphiphiles, leading to domain separation. In HAECs, BA increased β1-integrin-RGD affinity by 18% with a transition from single to double valency, consistent with a doubling of the molecular brightness of mCherry-tagged β1-integrins measured using FCS. Accordingly, BA caused an increase in the size of FAK/paxillin positive peripheral adhesions and reduced migration speeds as measured using wound healing assays. Vitamin E (VE), which partitions to domain boundaries and disperses them by lowering edge energy, left integrin affinity unchanged, but reduced binding probability, leading to smaller focal adhesions, and equivalent migration speed relative to untreated cells. VE reversed the BA-induced decrease in migration speed. Triton X also thickens Lo domains but partitions to both lipid phases and left unchanged binding kinetics, focal adhesion sizes, and migration speed. These results demonstrate that only the amphiphile that thinned Ld lipid-domains increased β1-integrin-RGD affinity and valency thus implicating Ld domains in modulating integrin adhesion, nascent adhesion formation, and cell migration. To study the membrane mechanical properties, we developed a method for measuring, in… Advisors/Committee Members: Peter J Butler, Dissertation Advisor/Co-Advisor, Peter J Butler, Committee Chair/Co-Chair, William O Hancock, Committee Member, Justin Lee Brown, Committee Member, Tae-Hee Lee, Outside Member, Esther Winter Gomez, Committee Member.

Subjects/Keywords: Integrin; Membrane mechanical Properties; Time-correlated single photon microscopy; Cell adhesion; Fluorescence correlation spectroscopy; Optical trap

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APA (6^th Edition):

Son, S. (2018). THE ROLE OF THE MEMBRANE IN INTEGRIN-MEDIATED ADHESION OF CELLS TO SURFACES. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/15230szs328

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Son, Seoyoung. “THE ROLE OF THE MEMBRANE IN INTEGRIN-MEDIATED ADHESION OF CELLS TO SURFACES.” 2018. Thesis, Penn State University. Accessed March 08, 2021. https://submit-etda.libraries.psu.edu/catalog/15230szs328.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Son, Seoyoung. “THE ROLE OF THE MEMBRANE IN INTEGRIN-MEDIATED ADHESION OF CELLS TO SURFACES.” 2018. Web. 08 Mar 2021.

Vancouver:

Son S. THE ROLE OF THE MEMBRANE IN INTEGRIN-MEDIATED ADHESION OF CELLS TO SURFACES. [Internet] [Thesis]. Penn State University; 2018. [cited 2021 Mar 08]. Available from: https://submit-etda.libraries.psu.edu/catalog/15230szs328.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Son S. THE ROLE OF THE MEMBRANE IN INTEGRIN-MEDIATED ADHESION OF CELLS TO SURFACES. [Thesis]. Penn State University; 2018. Available from: https://submit-etda.libraries.psu.edu/catalog/15230szs328

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vrije Universiteit Amsterdam

19. Wildenberg, S.H.J.L. van den. Single-protein motion on microtubules and in cell membranes .

Degree: 2011, Vrije Universiteit Amsterdam

URL: http://hdl.handle.net/1871/18728

Subjects/Keywords: Single-protein; dyanmics; motion; microtubules; cell membrane; fluorescence microscopy

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APA (6^th Edition):

Wildenberg, S. H. J. L. v. d. (2011). Single-protein motion on microtubules and in cell membranes . (Doctoral Dissertation). Vrije Universiteit Amsterdam. Retrieved from http://hdl.handle.net/1871/18728

Chicago Manual of Style (16^th Edition):

Wildenberg, S H J L van den. “Single-protein motion on microtubules and in cell membranes .” 2011. Doctoral Dissertation, Vrije Universiteit Amsterdam. Accessed March 08, 2021. http://hdl.handle.net/1871/18728.

MLA Handbook (7^th Edition):

Wildenberg, S H J L van den. “Single-protein motion on microtubules and in cell membranes .” 2011. Web. 08 Mar 2021.

Vancouver:

Wildenberg SHJLvd. Single-protein motion on microtubules and in cell membranes . [Internet] [Doctoral dissertation]. Vrije Universiteit Amsterdam; 2011. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/1871/18728.

Council of Science Editors:

Wildenberg SHJLvd. Single-protein motion on microtubules and in cell membranes . [Doctoral Dissertation]. Vrije Universiteit Amsterdam; 2011. Available from: http://hdl.handle.net/1871/18728

20. Carr, Alexander Roy. Development of three-dimensional super-resolution imaging using a double-helix point spread function.

Degree: PhD, 2018, University of Cambridge

URL: https://doi.org/10.17863/CAM.26413 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.753476

► Single-molecule localisation microscopy (SMLM), has allowed for optical microscopy to probe biological systems beyond the diffraction limit. The intrinsic 3D nature of biology has motivated… (more)

Subjects/Keywords: 572.028; DHPSF; 3D-SMLM; SMLM; Super-resolution; SPT; Single-molecule; Double-Helix; PSF; Fluorescence; Microscopy; T-cell; KS model

2 more images…

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APA (6^th Edition):

Carr, A. R. (2018). Development of three-dimensional super-resolution imaging using a double-helix point spread function. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.26413 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.753476

Chicago Manual of Style (16^th Edition):

Carr, Alexander Roy. “Development of three-dimensional super-resolution imaging using a double-helix point spread function.” 2018. Doctoral Dissertation, University of Cambridge. Accessed March 08, 2021. https://doi.org/10.17863/CAM.26413 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.753476.

MLA Handbook (7^th Edition):

Carr, Alexander Roy. “Development of three-dimensional super-resolution imaging using a double-helix point spread function.” 2018. Web. 08 Mar 2021.

Vancouver:

Carr AR. Development of three-dimensional super-resolution imaging using a double-helix point spread function. [Internet] [Doctoral dissertation]. University of Cambridge; 2018. [cited 2021 Mar 08]. Available from: https://doi.org/10.17863/CAM.26413 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.753476.

Council of Science Editors:

Carr AR. Development of three-dimensional super-resolution imaging using a double-helix point spread function. [Doctoral Dissertation]. University of Cambridge; 2018. Available from: https://doi.org/10.17863/CAM.26413 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.753476

University of Akron

21. Ray, Lucille Alexandria. Live single cell fluorescence microscopy; from antibiotic resistance detection to mitochondrial dysfunction.

Degree: PhD, Chemistry, 2020, University of Akron

URL: http://rave.ohiolink.edu/etdc/view?acc_num=akron1597342775751888

► Single-cell fluorescence microscopy is a powerful tool which can be used to investigate the nature of cellular responses to external stimuli. The application of single-cell… (more)

▼ Single-cell fluorescence microscopy is a powerful tool which can be used to investigate the nature of cellular responses to external stimuli. The application of single-cell fluorescence microscopy to the growing problem of antimicrobial susceptibility detection stands to improve and refine our ability to address bacterial resistance in human infections. In cases of severe bacterial infection, determining the correct antibiotic to use to combat an infection is a race against the patient’s dwindling lifespan. By combining the RedoxSensor™ Green fluorescent dye with live single-cell imaging, we have developed a method for antimicrobial susceptibility testing which can identify susceptibility to a given antibiotic within 100 minutes of treatment. We show that this method is reproducible and can identify susceptibility to several bacterial cell wall targets and bacterial cell membrane targeted antibiotics. Our methodology has considerable applicability within the sphere of rational antibiotic drug design as well in its ability to identify antibiotic efficacy as a function of time instead of antibiotic concentration. We use our method to compare the efficacy of 4 recently synthesized polyurethane antimicrobials. Our work lays the framework for expansion upon our method into microfluidics systems and use in screening candidate antimicrobial drugs.Mitochondrial morphological analysis within living eukaryotic cells represents another challenge which requires careful application of single-cell fluorescence microscopy. The cuprizone mouse treatment model for multiple sclerosis is known to generate enlarged mitochondria within oligodendrocytes, but much remains unknown about the dynamics of their formation. Cultured MO3.13 oligodendrocyte cells treated with cuprizone are shown to undergo mitochondrial enlargement within 8 hours of direct cuprizone exposure via single-cell mitochondrial size determination with MitoTracker Red fluorescent dye. Cuprizone treatment is also shown to increase oxygen consumption rapidly following oligodendrocyte exposure using porphyrin-based fluorescence lifetime oxygen consumption measurement. Advisors/Committee Members: Konopka, Michael (Advisor).

Subjects/Keywords: Biochemistry; Chemistry; Microbiology; microscopy; single-cell; antibiotic resistance; fluorescence; mitochondria; cuprizone; antibacterial susceptibility testing; antimicrobial polymer

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ray, L. A. (2020). Live single cell fluorescence microscopy; from antibiotic resistance detection to mitochondrial dysfunction. (Doctoral Dissertation). University of Akron. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=akron1597342775751888

Chicago Manual of Style (16^th Edition):

Ray, Lucille Alexandria. “Live single cell fluorescence microscopy; from antibiotic resistance detection to mitochondrial dysfunction.” 2020. Doctoral Dissertation, University of Akron. Accessed March 08, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=akron1597342775751888.

MLA Handbook (7^th Edition):

Ray, Lucille Alexandria. “Live single cell fluorescence microscopy; from antibiotic resistance detection to mitochondrial dysfunction.” 2020. Web. 08 Mar 2021.

Vancouver:

Ray LA. Live single cell fluorescence microscopy; from antibiotic resistance detection to mitochondrial dysfunction. [Internet] [Doctoral dissertation]. University of Akron; 2020. [cited 2021 Mar 08]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=akron1597342775751888.

Council of Science Editors:

Ray LA. Live single cell fluorescence microscopy; from antibiotic resistance detection to mitochondrial dysfunction. [Doctoral Dissertation]. University of Akron; 2020. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=akron1597342775751888

22. Syed, Aleem. Spatial and temporal dynamics of receptor for advanced glycation endproducts, integrins, and actin cytoskeleton as probed with fluorescence-based imaging techniques.

Degree: 2016, Iowa State University

URL: https://lib.dr.iastate.edu/etd/16026

► Systematic spatial and temporal fluctuations are a fundamental part of any biological process. For example, lateral diffusion of membrane proteins is one of the key… (more)

▼ Systematic spatial and temporal fluctuations are a fundamental part of any biological process. For example, lateral diffusion of membrane proteins is one of the key mechanisms in their cellular function. Lateral diffusion governs how membrane proteins interact with intracellular, transmembrane, and extracellular components to achieve their function. Herein, fluorescence-based techniques are used to elucidate the dynamics of receptor for advanced glycation end-products (RAGE) and integrin membrane proteins. RAGE is a transmembrane protein that is being used as a biomarker for various diseases. RAGE dependent signaling in numerous pathological conditions is well studied. However, RAGE lateral diffusion in the cell membrane is poorly understood. For this purpose, effect of cholesterol, cytoskeleton dynamics, and presence of ligand on RAGE lateral diffusion is investigated. RAGE diffusion in the cell membrane is probed with fluorescence recovery after photobleaching (FRAP) and single particle tracking (SPT). The ensemble diffusion measurement of RAGE with FRAP indicated that RAGE diffuses freely in the cell membrane with a large mobile fraction. Also, a decrease in the mobile fraction is observed when the actin cytoskeleton dynamics are altered with cytoskeletal drugs cytochalasin-D and Jasplakinolide. Further, RAGE signaling is observed to be dependent on an intact actin cytoskeleton in cells. On the other hand, confined diffusion of RAGE is measured when the lateral diffusion is probed one protein at a time with SPT. Methylglyoxal modified-bovine serum albumin (MGO-BSA) is used as a RAGE ligand to study how the presence of ligand affects RAGE lateral diffusion. RAGE’s affinity for ligand increases linearly with the net negative surface charge on the MGO-BSA. Although incubation of MGO-BSA with different percent primary amine modification changes the diffusion properties of RAGE, no correlation is measured in the magnitude of the change in the diffusion properties with the ligand binding affinity and the net negative surface charge. Ligand induced changes are not present when cholesterol is depleted from the cell membrane, indicating that cholesterol plays a role in ligand induced changes on RAGE lateral diffusion. The work advances our understanding of factors that affect RAGE lateral diffusion and signaling and also the connection between RAGE lateral diffusion and signaling. The effect of a highly conserved membrane proximal cysteine (Cys1368) residue on the diffusion properties of integrins in Drosophila S2 cells is elucidated using FRAP and SPT. Mutating Cys1368 to Val1368 altered the lateral diffusion properties of this receptor. Both FRAP and SPT indicate larger mobile population for the Val1368 integrins compared to wild-type integrins. Tandem mass spectrometry results and protein sequence analysis show that Cys1368 is a potential palmitoylation or redox post-translational modification site. Finally, a method for imaging protein distribution and for probing local environment around fluorophore in cells at…

Subjects/Keywords: Cell membrane biophysics; Fluorescence Lifetime Imaging; Fluorescence Recovery after Photobleaching; Single Particle Tracking; Stimulated Emission Depletion Microscopy; Visible light Photocages; Analytical Chemistry; Biophysics; Cell Biology

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APA (6^th Edition):

Syed, A. (2016). Spatial and temporal dynamics of receptor for advanced glycation endproducts, integrins, and actin cytoskeleton as probed with fluorescence-based imaging techniques. (Thesis). Iowa State University. Retrieved from https://lib.dr.iastate.edu/etd/16026

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Syed, Aleem. “Spatial and temporal dynamics of receptor for advanced glycation endproducts, integrins, and actin cytoskeleton as probed with fluorescence-based imaging techniques.” 2016. Thesis, Iowa State University. Accessed March 08, 2021. https://lib.dr.iastate.edu/etd/16026.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Syed, Aleem. “Spatial and temporal dynamics of receptor for advanced glycation endproducts, integrins, and actin cytoskeleton as probed with fluorescence-based imaging techniques.” 2016. Web. 08 Mar 2021.

Vancouver:

Syed A. Spatial and temporal dynamics of receptor for advanced glycation endproducts, integrins, and actin cytoskeleton as probed with fluorescence-based imaging techniques. [Internet] [Thesis]. Iowa State University; 2016. [cited 2021 Mar 08]. Available from: https://lib.dr.iastate.edu/etd/16026.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Syed A. Spatial and temporal dynamics of receptor for advanced glycation endproducts, integrins, and actin cytoskeleton as probed with fluorescence-based imaging techniques. [Thesis]. Iowa State University; 2016. Available from: https://lib.dr.iastate.edu/etd/16026

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Edinburgh

23. Taylor, Daniel. Bacterial confinement in micro fluidic micro-environments.

Degree: PhD, 2019, University of Edinburgh

URL: http://hdl.handle.net/1842/36528

► Microfluidic droplet systems have shown great promise in the study of biological systems. In this thesis I explore the application of a microfluidic droplet system… (more)

▼ Microfluidic droplet systems have shown great promise in the study of biological systems. In this thesis I explore the application of a microfluidic droplet system to the study of small bacterial populations and their growth response to antibiotics. This thesis comprises of three primary results sections. The first section details the development and fabrication of a custom microfluidic system. This microfluidic system is designed to study the growth dynamics of small Escherichia coli (E. coli ) bacterial communities. The second section presents an image processing and analysis workflow that is designed to be used in conjunction with the microfluidic device to extract quantitative growth data of confined bacterial communities with single cell precision. The third section details a study that uses the microfluidic system to measure the growth dynamics of E. coli communities encapsulated within microfluidic droplets whilst uninhibited and under the effect of the antibiotic streptomycin. In the first section, I present the development, design and fabrication of a two-part microfluidic device that is later used to study the growth dynamics of E. coli bacteria. The first part of the microfluidic device consists of droplet generating microfluidic geometry that is designed to encapsulate small communities of E. coli bacteria (typically 1-5 cells in size) within microfluidic droplets around 30μm in diameter. The second part of the microfluidic device is composed of a micro fluidic reservoir that is designed to store microfluidic droplets. By imaging the droplets in the storage reservoir with a combination of brightfield and fluorescence microscopy, the growth dynamics of the encapsulated bacterial communities can be described. In the second section of the thesis, I present the development and operating principles of my image processing and analysis workflow. This workflow automatically extracts quantitative bacterial growth data from a gridded array of brightfield and fluorescence microscopy images taken across the microfluidic device during experimentation. The analysis algorithm is capable of processing upwards of 200 fields of view across 80 time frames. This makes it possible to detect, track and measure the size of upwards of 1000 encapsulated bacterial communities with single cell precision. Droplet boundaries are detected using brightfield microscopy images and each droplet is tracked from one time step to the next using a modified particle tracking algorithm. Bacterial community sizes are measured by counting individual bacteria in thresholded fluorescence microscopy images. In the final section of this thesis, a study of E. coli bacteria was conducted using the microfluidic device. Small communities of bacteria, typically 1-5 cells in size, were confined in microfluidic droplets and observed for 8 hours. The bacteria were grown in the absence of antibiotic, as well as in the presence of the antibiotic streptomycin at various concentrations. A number of metrics of the growth dynamics are extracted from the study and…

Subjects/Keywords: bacteria; microfluidics; antibiotics; fluorescence microscopy; microscopy; image processing; E. coli; population dynamics; statistical analysis; minimum inhibitory concentration; single cell variability; cell heterogeneity

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Taylor, D. (2019). Bacterial confinement in micro fluidic micro-environments. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/36528

Chicago Manual of Style (16^th Edition):

Taylor, Daniel. “Bacterial confinement in micro fluidic micro-environments.” 2019. Doctoral Dissertation, University of Edinburgh. Accessed March 08, 2021. http://hdl.handle.net/1842/36528.

MLA Handbook (7^th Edition):

Taylor, Daniel. “Bacterial confinement in micro fluidic micro-environments.” 2019. Web. 08 Mar 2021.

Vancouver:

Taylor D. Bacterial confinement in micro fluidic micro-environments. [Internet] [Doctoral dissertation]. University of Edinburgh; 2019. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/1842/36528.

Council of Science Editors:

Taylor D. Bacterial confinement in micro fluidic micro-environments. [Doctoral Dissertation]. University of Edinburgh; 2019. Available from: http://hdl.handle.net/1842/36528

University of Cambridge

24. Palayret, Matthieu Grégoire Simon. Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation.

Degree: PhD, 2015, University of Cambridge

URL: https://doi.org/10.17863/CAM.16306 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.675901

► Single-molecule localisation microscopy (SMLM) allows imaging of fluorescently-tagged proteins in live cells with a precision well below that of the diffraction limit. As a single-molecule… (more)

▼ Single-molecule localisation microscopy (SMLM) allows imaging of fluorescently-tagged proteins in live cells with a precision well below that of the diffraction limit. As a single-molecule technique, it has also introduced a new quantitative approach to fluorescence microscopy. In the Part A of this thesis, the design and building of three SMLM instruments, the implementation of a custom-developed image analysis package and the characterisation of the photo-physical properties of the photo-activable fluorescent protein used in this thesis (mEos), are discussed. Then, a new post-processing method for SMLM analysis is characterised: axial optical sectioning of SMLM images is demonstrated by thresholding fitted localisations using their fitted width and amplitude to reject fluorophores that emit from above or below a virtual ?light-sheet?, a thin volume centred on the focal plane of the microscope. This method provides qualitative and quantitative improvements to SMLM. In the Part B of this thesis, SMLM is applied to study T cell activation. Although the T cell receptor plays a key role in immunity, its stoichiometry in the membrane of resting T cells is still a matter of debate. Here, single-molecule counting methods are implemented to compare the stoichiometry of TCRs fused with mEos2 in resting T cells to monomeric and dimeric controls. However, because of the stochasticity of mEos2 photo-physics, results are inconclusive and new counting techniques based on structural imaging are discussed. In addition to TCR triggering, T cells require the co-stimulatory triggering of the CD28 transmembrane receptor to become fully activated. However, some immobilised anti-CD28 antibodies, referred to as super-agonists (SA), can directly activate T cells without triggering the TCR. In this thesis, single-molecule tracking techniques are used to investigate the molecular mechanism of CD28 super-agonism in live T cells. The results indicate that the diffusion of CD28 is slowed by SA binding. This effect is further discussed in light of the kinetic-segregation model proposed for TCR triggering. Quantitative SMLM as implemented and further developed in this work offers new tools to investigate the molecular mechanisms initiating T cell activation, ultimately facilitating the discovery of novel approaches to target these pathways for therapeutic purposes.

Subjects/Keywords: 540; T-cell receptor; kinetic-segregation; CD28 super-agonist; single-molecule localisation microscopy; super-resolution fluorescence microscopy; virtual 'light-sheet'; optical sectioning

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APA (6^th Edition):

Palayret, M. G. S. (2015). Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.16306 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.675901

Chicago Manual of Style (16^th Edition):

Palayret, Matthieu Grégoire Simon. “Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation.” 2015. Doctoral Dissertation, University of Cambridge. Accessed March 08, 2021. https://doi.org/10.17863/CAM.16306 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.675901.

MLA Handbook (7^th Edition):

Palayret, Matthieu Grégoire Simon. “Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation.” 2015. Web. 08 Mar 2021.

Vancouver:

Palayret MGS. Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation. [Internet] [Doctoral dissertation]. University of Cambridge; 2015. [cited 2021 Mar 08]. Available from: https://doi.org/10.17863/CAM.16306 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.675901.

Council of Science Editors:

Palayret MGS. Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation. [Doctoral Dissertation]. University of Cambridge; 2015. Available from: https://doi.org/10.17863/CAM.16306 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.675901

University of Toronto

25. Downie, Kelsey Jean. Live Cell Imaging of CEACAM1 Dynamics and Self-association during Bacterial Binding.

Degree: 2013, University of Toronto

URL: http://hdl.handle.net/1807/42829

►

The carcinoembryonic antigen-related cellular adhesion molecule 1 (CEACAM1) is a human receptor that facilitates adhesion with neighbouring cells, as well as with certain pathogens. CEACAM1… (more)

Subjects/Keywords: fluorescence microscopy; CEACAM; live cell imaging; 0541

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APA (6^th Edition):

Downie, K. J. (2013). Live Cell Imaging of CEACAM1 Dynamics and Self-association during Bacterial Binding. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/42829

Chicago Manual of Style (16^th Edition):

Downie, Kelsey Jean. “Live Cell Imaging of CEACAM1 Dynamics and Self-association during Bacterial Binding.” 2013. Masters Thesis, University of Toronto. Accessed March 08, 2021. http://hdl.handle.net/1807/42829.

MLA Handbook (7^th Edition):

Downie, Kelsey Jean. “Live Cell Imaging of CEACAM1 Dynamics and Self-association during Bacterial Binding.” 2013. Web. 08 Mar 2021.

Vancouver:

Downie KJ. Live Cell Imaging of CEACAM1 Dynamics and Self-association during Bacterial Binding. [Internet] [Masters thesis]. University of Toronto; 2013. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/1807/42829.

Council of Science Editors:

Downie KJ. Live Cell Imaging of CEACAM1 Dynamics and Self-association during Bacterial Binding. [Masters Thesis]. University of Toronto; 2013. Available from: http://hdl.handle.net/1807/42829

Virginia Tech

26. Khanduja, Nimisha. Processive Acceleration of Actin Barbed End Assembly by N-WASP.

Degree: PhD, Biological Sciences, 2014, Virginia Tech

URL: http://hdl.handle.net/10919/54933

► Actin-based cell motility plays crucial roles throughout the lifetime of an organism. The dynamic rearrangement of the actin cytoskeleton triggers a plethora of cellular processes… (more)

▼ Actin-based cell motility plays crucial roles throughout the lifetime of an organism. The dynamic rearrangement of the actin cytoskeleton triggers a plethora of cellular processes including cellular migration. Neural Wiskott Aldrich syndrome protein (N-WASP) is involved in transduction of signals from receptors on the cell surface to the actin cytoskeleton. N-WASP activated actin polymerization drives extension of invadopodia and podosomes into the basement layer. In addition to activating Arp2/3 complex, N-WASP binds actin filament barbed ends, and both N-WASP and barbed ends are tightly clustered in these invasive structures. We used nanofibers coated with N-WASP WWCA domains as model cell surfaces and single actin filament imaging to determine how clustered N-WASP affects Arp2/3-independent barbed end assembly. Individual barbed ends captured by WWCA domains of N-WASP grew at or below their diffusion limited assembly rate. At high filament densities, overlapping filaments formed buckles between their nanofiber tethers and myosin attachment points. These buckles grew 3.4-fold faster than the diffusion-limited rate of unattached barbed ends. N-WASP constructs with and without the native poly-proline (PP) region showed similar rate enhancements. Increasing polycationic Mg2+ or Spermine to enhance filament bundling increased the frequency of filament buckle formation, consistent with a requirement of accelerated assembly on barbed end bundling. Our preliminary data shows that tethered N-WASP construct containing one WH2 domain does not generate processive bundles or filament loops leading us to believe that tandem WH2 is required for processivity. We propose that this novel N-WASP assembly activity provides an Arp2/3-independent force that drives nascent filament bundles into the basement layer during cell invasion. Discovery of this bundle mediated unique pathway involved in invasion and metastasis will provide new targets for therapeutic development. Advisors/Committee Members: Cimini, Daniela (committeechair), Nain, Amrinder (committee member), Huckle, William Rupert (committee member), Winkel, Brenda S. J. (committee member), Kuhn, Jeffrey R. (committee member).

Subjects/Keywords: Cell Movement; Actin Motility; Microscopy; Fluorescence; TIRF

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APA (6^th Edition):

Khanduja, N. (2014). Processive Acceleration of Actin Barbed End Assembly by N-WASP. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/54933

Chicago Manual of Style (16^th Edition):

Khanduja, Nimisha. “Processive Acceleration of Actin Barbed End Assembly by N-WASP.” 2014. Doctoral Dissertation, Virginia Tech. Accessed March 08, 2021. http://hdl.handle.net/10919/54933.

MLA Handbook (7^th Edition):

Khanduja, Nimisha. “Processive Acceleration of Actin Barbed End Assembly by N-WASP.” 2014. Web. 08 Mar 2021.

Vancouver:

Khanduja N. Processive Acceleration of Actin Barbed End Assembly by N-WASP. [Internet] [Doctoral dissertation]. Virginia Tech; 2014. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/10919/54933.

Council of Science Editors:

Khanduja N. Processive Acceleration of Actin Barbed End Assembly by N-WASP. [Doctoral Dissertation]. Virginia Tech; 2014. Available from: http://hdl.handle.net/10919/54933

Kansas State University

27. Sun, Xiaojiao. Single molecule studies of acidity in heterogeneous catalysts.

Degree: PhD, Department of Chemical Engineering, 2013, Kansas State University

URL: http://hdl.handle.net/2097/16423

► Amorphous silica-alumina is widely used as a solid acid catalyst for various reactions in oil refining and the petrochemical industry. The strength and the number… (more)

▼ Amorphous silica-alumina is widely used as a solid acid catalyst for various reactions in oil refining and the petrochemical industry. The strength and the number of the acid sites in the material are most often believed to arise from the alumina atoms inserted into the silica lattice. The existence of the acidity distribution across the framework is a result of the local composition or the short-range interactions on the silica-alumina surface. Conventional techniques used to characterize silica-alumina provide effective information on the average acidity, but may not reflect the heterogeneity of surface acidity within the material. Recently, it is possible to study individual catalytic sites on solid catalysts by single molecule fluorescence microscopy with high time and space resolution. Fluorophores can be chosen that emit at different wavelengths depending on the properties of the local environment. By doping these fluorophores into a solid matrix at nanomolar concentrations, individual probe molecules can be imaged. Valuable information can be extracted by analyzing changes in the fluorescence spectrum of the guest molecules within a host matrix. In this research, silica-alumina thin films were studied with single molecule fluorescence microscopy. The samples were prepared by a sol-gel method and a wide-field fluorescence microscope was used to locate and characterize the fluorescent behaviors of pH sensitive probes. In mesoporous thin films, the ratio of the dye emission at two wavelengths provides an effective means to sense the effective pH of the microenvironment in which each molecule resides. The goal of this work was to develop methods to quantify the acidity of individual micro-environments in heterogeneous networks. Pure silica films treated with external phosphate solutions of different pH values were used to provide references of the fluorescence signals from individual dye molecules. SM emission data were obtained from mesoporous Al-Si films as a function of Al content in films ranging from 0% to 20% alumina. Histograms of the emission ratio revealed that films became more acidic with increasing Al content. The acidity on interior surfaces in zeolite pores was also of interest in this work. A microfluidic device was built to isolate the interior surface from the exterior surface. Some preliminary results showed the potential of using SM fluorescence method to study the acidic properties inside the pores of zeolite crystals. Advisors/Committee Members: Keith L. Hohn.

Subjects/Keywords: Catalyst characterization, Single molecule fluorescence microscopy; Single molecule fluorescence microscopy; Chemical Engineering (0542); Chemistry (0485); Engineering (0537)

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APA (6^th Edition):

Sun, X. (2013). Single molecule studies of acidity in heterogeneous catalysts. (Doctoral Dissertation). Kansas State University. Retrieved from http://hdl.handle.net/2097/16423

Chicago Manual of Style (16^th Edition):

Sun, Xiaojiao. “Single molecule studies of acidity in heterogeneous catalysts.” 2013. Doctoral Dissertation, Kansas State University. Accessed March 08, 2021. http://hdl.handle.net/2097/16423.

MLA Handbook (7^th Edition):

Sun, Xiaojiao. “Single molecule studies of acidity in heterogeneous catalysts.” 2013. Web. 08 Mar 2021.

Vancouver:

Sun X. Single molecule studies of acidity in heterogeneous catalysts. [Internet] [Doctoral dissertation]. Kansas State University; 2013. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/2097/16423.

Council of Science Editors:

Sun X. Single molecule studies of acidity in heterogeneous catalysts. [Doctoral Dissertation]. Kansas State University; 2013. Available from: http://hdl.handle.net/2097/16423

28. Abdul Rehman, Sohaib. Super-resolution microscopy : novel developments and optimisations.

Degree: PhD, 2019, University of Cambridge

URL: https://doi.org/10.17863/CAM.43503 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.787773

► This thesis describes the design, development and optimisation of a multifunctional localisation based super-resolution microscope at Cambridge Advanced Imaging Centre. The microscope is optimised to… (more)

Subjects/Keywords: Fluorescence Microscopy; Super-resolution Microscopy; Localisation Microscopy; Three-dimensional Microscopy; Lightfield Microscopy; Single Molecule Tracking; Clustering; Notch Pathway; Chromatin Architecture; Optics

10 more images…

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APA (6^th Edition):

Abdul Rehman, S. (2019). Super-resolution microscopy : novel developments and optimisations. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.43503 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.787773

Chicago Manual of Style (16^th Edition):

Abdul Rehman, Sohaib. “Super-resolution microscopy : novel developments and optimisations.” 2019. Doctoral Dissertation, University of Cambridge. Accessed March 08, 2021. https://doi.org/10.17863/CAM.43503 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.787773.

MLA Handbook (7^th Edition):

Abdul Rehman, Sohaib. “Super-resolution microscopy : novel developments and optimisations.” 2019. Web. 08 Mar 2021.

Vancouver:

Abdul Rehman S. Super-resolution microscopy : novel developments and optimisations. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Mar 08]. Available from: https://doi.org/10.17863/CAM.43503 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.787773.

Council of Science Editors:

Abdul Rehman S. Super-resolution microscopy : novel developments and optimisations. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://doi.org/10.17863/CAM.43503 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.787773

University of Cambridge

29. Abdul Rehman, Sohaib. Super-resolution Microscopy: Novel Developments and Optimisations.

Degree: PhD, 2019, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/296453

► This thesis describes the design, development and optimisation of a multifunctional localisation based super-resolution microscope at Cambridge Advanced Imaging Centre. The microscope is optimised to… (more)

Subjects/Keywords: Fluorescence Microscopy; Super-resolution Microscopy; Localisation Microscopy; Three-dimensional Microscopy; Lightfield Microscopy; Single Molecule Tracking; Clustering; Notch Pathway; Chromatin Architecture; Optics

Record Details Similar Records Cite « Share

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Abdul Rehman, S. (2019). Super-resolution Microscopy: Novel Developments and Optimisations. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/296453

Chicago Manual of Style (16^th Edition):

Abdul Rehman, Sohaib. “Super-resolution Microscopy: Novel Developments and Optimisations.” 2019. Doctoral Dissertation, University of Cambridge. Accessed March 08, 2021. https://www.repository.cam.ac.uk/handle/1810/296453.

MLA Handbook (7^th Edition):

Abdul Rehman, Sohaib. “Super-resolution Microscopy: Novel Developments and Optimisations.” 2019. Web. 08 Mar 2021.

Vancouver:

Abdul Rehman S. Super-resolution Microscopy: Novel Developments and Optimisations. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Mar 08]. Available from: https://www.repository.cam.ac.uk/handle/1810/296453.

Council of Science Editors:

Abdul Rehman S. Super-resolution Microscopy: Novel Developments and Optimisations. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://www.repository.cam.ac.uk/handle/1810/296453

Colorado School of Mines

30. Cannataro, Frank. Development of single molecule total internal reflection fluorescence microscope.

Degree: MS(M.S.), Mechanical Engineering, 2015, Colorado School of Mines

URL: http://hdl.handle.net/11124/17142

► We mostly think and communicate science at the single-molecule level, but do experiments at the ensemble level. This gap between our thinking and experiments has… (more)

Subjects/Keywords: total internal reflection fluorescence; fluorescence; single molecule; optomechanical; microscopy; spectroscopy; Total internal reflection (Optics); Molecules; Fluorescence; Microscopy; Spectrum analysis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cannataro, F. (2015). Development of single molecule total internal reflection fluorescence microscope. (Masters Thesis). Colorado School of Mines. Retrieved from http://hdl.handle.net/11124/17142

Chicago Manual of Style (16^th Edition):

Cannataro, Frank. “Development of single molecule total internal reflection fluorescence microscope.” 2015. Masters Thesis, Colorado School of Mines. Accessed March 08, 2021. http://hdl.handle.net/11124/17142.

MLA Handbook (7^th Edition):

Cannataro, Frank. “Development of single molecule total internal reflection fluorescence microscope.” 2015. Web. 08 Mar 2021.

Vancouver:

Cannataro F. Development of single molecule total internal reflection fluorescence microscope. [Internet] [Masters thesis]. Colorado School of Mines; 2015. [cited 2021 Mar 08]. Available from: http://hdl.handle.net/11124/17142.

Council of Science Editors:

Cannataro F. Development of single molecule total internal reflection fluorescence microscope. [Masters Thesis]. Colorado School of Mines; 2015. Available from: http://hdl.handle.net/11124/17142

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