Dissertations / Theses on the topic 'Single organ'

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2019
Cataloged from PDF version of thesis.
Includes bibliographical references.
The biological processes that sustain a complex organism require the orchestrated dynamics of complex cellular ensembles. Several vital systems - such as the immune system, the digestive system and more - must process internal and external signals to maintain functional homeostasis in response to perturbations at the systems-level. To further understand how groups of cells collectively respond to perturbations, we have applied single-cell RNA-sequencing and complementary techniques to explore cellular behaviors within complex systems at multiple relevant biological scales: from within a single organ, to an organ system, to across several human individuals with differing genetic backgrounds linked by a shared phenotype. More specifically, at the level of the organ, we have explored acute injury responses in the liver. We have identified and described a new compensatory phase of the liver response to injury, in which surviving hepatocytes upregulate their expression of critical liver function genes to maintain overall organ function. Next, we extended our approach from a focus on an acute injury targeting a single organ to exploring chronic damage resulting from a long-term high fat diet across multiple gastrointestinal and immune compartments. Our analysis revealed molecular pathways and changes in stem gene expression which may contribute to obesity-related disease. Finally, we characterized shared features across multiple unique human donors with a common phenotype, elite control of HIV-1. We identified and validated a subset of highly functional dendritic cells, and developed broadly applicable computational approaches to identify reproducible responses across donors and to nominate candidate targets for rationally modulating the system. Overall, our work demonstrates the utility of single-cell RNA-sequencing for uncovering important cellular phenotypes that inform systems-level responses at any biological scale.
by Kellie Elizabeth Kolb.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Chemistry

Improving treatment and prevention of pelvic organ prolapse, a disorder affecting up to half of parous women, requires thorough mechanical analysis of the vagina and other endopelvic structures at the cellular level. In this study, we tested single vaginal smooth muscle cells (SMCs) to quantify their elastic moduli. Cells were enzymatically isolated from vaginal walls of freshly sacrificed, virgin Long Evans rats and cultured using well-established methods. A custom-built experimental setup was used to perform tensile tests. Micropipettes were fabricated to serve as cantilever-type load cells, which were coated in cellular adhesive. Two pipettes applied tension to SMCs until adhesion between the cell and a pipette failed. During mechanical testing, images of SMCs were collected and translated into strain and stress. Specifically, force/stress data were calculated using Euler-Bernoulli Beam Theory and by making simplifying geometric assumptions. The average initial and total elastic moduli (mean ± SEM) for single vaginal SMCs were 6.06 ± 0.26 kPa and 5.4 ± 0.24 kPa, respectively, which is within the range reported for other types of SMCs, mainly airway and vascular, of various species. This protocol can and will be applied to further investigate mechanics of single cells from the pelvic region with independent variables such as parity, age, body mass index, and various stages of POP. Results of these experiments will provide critical information for improving current treatments like drug therapies, surgical procedures, medical grafts and implants, and preventative practices like stretching and exercise techniques.
Master of Science

Septic shock (sepsis accompanied by cardiovascular failure) is an extreme manifestation of the host inflammatory response to severe infection. Tumor necrosis factor alpha (TNFα) super family induced nuclear factor kappa B (NF-κB) signaling pathways play a critical role in the pathophysiology of the disease. A better understanding of how TNFα induced NF-κB signaling influences the pathogenesis of septic shock is imperative. NF-κB signaling is activated by a canonical pathway or a non-canonical pathway. The canonical NF-κB pathway requires the IκB kinase (IKK) complex comprised of IKKα/β/γ. Activation of the IKK complex in response to inflammatory stimuli, such as TNFα, results in ubiquitin-dependent degradation of IκBα or IκBβ, releasing p50 related dimers to the nucleus. In response to TNFα superfamily induced inflammation in the non-canonical pathway, NF-κB inducing kinase (NIK), a docking molecule, recruits IΚΚα to p100 thus activating IΚΚα. This phosphorylates p100, which is then degraded, releasing p52 containing RelB heterodimers to the nucleus. It has been shown that genetic variation in key inflammatory genes contributes to outcome in sepsis. We hypothesized that genetic variation in genes of TNFα super family induced NF- κB signaling would be associated with mortality in septic shock. Specifically, we first tested the hypothesis that genetic variation within the cytosolic members of the canonical and noncanonical pathway may be associated with mortality in septic shock. We found that the CC genotype of NIK rs7222094 is associated with increased mortality and organ dysfunction in septic shock patients. This is perhaps due to altered regulation of NF-κB pathway genes, including CXCL10. We then tested the hypothesis that genetic variation in genes upregulated by these pathways may be associated with mortality in septic shock. We showed that the G allele of TNFAIP2 rs8126 is associated with increased mortality and organ dysfunction in septic shock patients. We then elucidated a novel biological mechanism whereby TNFAIP2 is a novel inhibitor of Ras, CREB and NF-κB; TNFAIP2 levels are controlled by rs8126; and these by allele differences are reflected in the inhibiton of Ras, CREB and NF-κB.

Die Geräte, durch die Musik im Zeitalter der technischen (Re-)Produktion gehört wird, haben sich immer wieder gewandelt. Solche Geräte müssen überhört werden. Nur so kann Musik gehört werden. Trotzdem – so die These der Arbeit – organisieren diese Geräte das Hören und sind Agenturen einer Bewirtschaftung und Technisierung der Wahrnehmung. In der Arbeit wird anhand von zwei Fallstudien aus der Geschichte der Rock- und Popmusik gezeigt, wie solche Geräte sowohl den Hörer als auch die gehörte Musik formieren. Durch Hörtechnologien bilden sich neue Hörpraktiken heraus und die Körperlichkeit des Hörers wird neu bestimmt. Die Anpassung von Klanggeschehen an spezifische Hörtechnologien wird im Mastering – dem letzten Schritt der technischen Musikproduktion – untersuchbar. Die Geräte, durch die Musik gehört wird, sind also weder schlichte Wiedergabetechnologien noch bloße elektrotechnische Artefakte. Vielmehr sind sie Gefüge aus Klanglichkeit, Körperlichkeit und Technologie. Diese werden in der Arbeit als Hörgeräte auf den Begriff gebracht. Die Hörgeräte der Rock- und Popmusik zielen – wie ihre medizintechnischen Verwandten – auf die Materialität der Wahrnehmung. Im Gegensatz zu diesen funktionieren sie jedoch nicht als Prothesen, die an einer gattungsweit postulierten Norm ausgerichtet sind. Statt Normen bergen sie Exzesse – an Serialität und Wiederholung – sowie Eskalationen – von Lautstärke und von hohen und tiefen Frequenzen. Die Arbeit ist in drei Kapiteln gegliedert. Im ersten Kapitel wird die These der Arbeit in Bezug auf theoretische Diskurse der Musik-, Kultur- und Medienwissenschaft verortet und eine begriffliche Systematik entwickelt. Kapitel zwei und drei sind Fallstudien gewidmet. In der ersten wird das Jukeboxhören der Rock’n’Roll-Kultur der 1950er Jahre untersucht, in der zweiten das Soundsystemhören der Disco- und Clubkultur der 1970er bis 1990er Jahre. Die im ersten Kapitel entwickelte begriffliche Systematik macht die Fallstudien vergleichbar.
The devices by which music is listened to in the age of technological (re-)production have changed over and over again. These devices must be imperceptible to the ear. Only then can music be heard. Nonetheless – this is the claim of the thesis – these devices organize hearing and are agents of a cultivation and technization of perception. Based on two case studies from the history of rock and pop music, this thesis reveals how such devices constitute not only the listener but also the music which is listened to. Through listening technologies new listening practices emerge and the corporality of the listener is newly defined. The adaptation of sound to specific listening technologies can be analysed during the mastering process, the last step in technological music production. The devices by which music is listened to are thus neither simple technologies of reproduction nor mere electrotechnical artefacts. Rather, they are assemblages of sound, corporality, and technology. In this thesis these assemblages are called “Hörgeräte” (listening devices). The listening devices of rock and pop music target – like medical-technical “Hörgeräte” (hearing aids) – the materiality of perception. Contrary to medical technologies, however, listening devices do not function as prostheses, which are calibrated according to medical industry standards. Instead, they contain excesses – of seriality and repetition – and escalations – of amplitude and high and low frequencies. The thesis is arranged in three chapters. In the first chapter I situate the main argument of the thesis within discourses of musicology, media and cultural studies, and develop my own terminology. Chapters two and three deal with case studies. In chapter two I investigate jukebox listening in 1950s rock’n’roll culture, whilst in chapter three I explore sound system listening in disco and club culture from the 1970s to the 1990s. The terminology developed in chapter one enables a comparison of the case studies.

Plasma pretreatments are environmentally benign and energy efficient processes for modifying the surface chemistry of materials. In an effort to improve the strength of the titanium alloy/FM-5 polyimide adhesive joint for aerospace applications, oxygen plasma pretreatments and novel thin plasma polymerized (PP) films were investigated as adhesion promoters. Plasma treatments were carried out using custom-built, low pressure, radio frequency, inductively coupled plasma reactors. Ti-6Al-4V coupons were plasma treated and used to prepare miniature single lap shear (SLS) joints. The effects of plasma pretreatments on surface chemistry were studied using x-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), Fourier transform infrared analysis (FTIR), and contact angle measurements. Relationships between composition, mechanical properties, and adhesion of PP films on Ti-6Al-4V and silicon wafers were investigated. The nanomechanical properties (modulus, hardness and adhesion) were studied using atomic force microscopy (AFM) nanoindentation and nanoscratch testing. A design of experiments (DOE) three factorial model was used to optimize the parameters for oxygen plasma treatments. Oxygen plasma pretreatments enhanced joint strength by cleaning the titanium surface and creating an extended oxide layer. Nanoindentation of oxygen plasma treated substrates showed no change in the surface mechanical properties due to the oxygen plasma treatment. This suggested that the improved SLS strength of the oxygen plasma pretreated substrates was due to the cleaning of the substrate and the removal of carbonaceous contaminants, rather than any changes in the morphology of the oxide layer. PP acetylene films were predominantly carbon, with oxygen as the other main constituent (incorporated mostly as C-O and C=O). For all SLS specimens tested, the adhesion between PP acetylene and FM-5 adhesive was adequate. However, the strength of SLS joints was limited by the adhesion of the PP acetylene to the Ti-6Al-4V substrate. The effects of a large number of plasma parameters, such as substrate pretreatment, carrier gas, input power, flow rate and film thickness were investigated. All samples failed at the PP film/Ti-6Al-4V interface or within the PP acetylene film, and thicker PP films yielded lower SLS strengths. PP films deposited at lower power exhibited higher hardness and reduced modulus than films deposited at higher power. Overall, thinner films exhibited higher hardness and reduced Young's modulus than thicker films. PP films of higher hardness yielded higher critical loads at debond (thickness normalized) during the nanoscratch test. Thin films were developed via the vapor plasma polymerization of titanium(IV) isobutoxide (TiiB). XPS results suggested that titanium was incorporated into the film as TiO2 clusters dispersed in an organic matrix. No evidence for Ti-C was obtained from the XPS spectra. PP films of TiiB were much more compliant than PP acetylene films. This behavior was attributed to decreased fragmentation and lower crosslinking that occurred during PP TiiB film deposition. These PP films did not exhibit sol-gel-like qualities, and because of the way titanium was incorporated into the films, a more appropriate name for these films might be "titanium dioxide-doped plasma polymerized films."
Ph. D.

碩士
國立臺灣海洋大學
海洋法律研究所
96
Corruption is the biggest barrier for the development of a country and the main reason of causing party transition in the government as well. Taiwan’s annual rating of corruptive image made by “Transparency International ” has been gradually drawn back from the 25th place in 1995 to the 34th place in 2007. Which indicates that domestic corruption is serious. There are domestic institutions in charge of anti-corruption, such as The Control Yuan, The Procuratorate, Investigation Bureau in Ministry of Justice, Department of Government Employee Ethics in Ministry of Justice. Why did they fail to bring about the desired effect? Referring to efficient results of anti-corruption in Hong Kong, Singapore and Japan, we found reasons. Besides, the determination from the authority, reformation and promotion of Investigation Bureau, which is mainly responsible for anti-corruption, are strongly needed. By integrating Investigation Bureau, Department of Government Employee Ethics and Central Office in Ministry of Justice, “Investigation Incorruption Administration” is established under the Executive Yuan with independent financial budget and as a second-class institution with guarantee term of office for the director. With higher position in the government, the anti-corruption institute could integrate resources, avoid interfering from other departments and investigate corruptions of executive officers in order to meet the goal that the inferiors imitate the superiors. In order to establish an independent commission against corruption, laws implemented for anti-corruption should be reviewed. Under the spirit of the human rights and justice, staff in Independent Commission Against Corruption is given power to investigate, prevent and execute anti-corruption work and eventually to build up an incorrupt and developed country.

A central question in biology is how different cell types interact with each other and their native environment to form complex functional systems and networks. Although our ability to investigate this question has considerably expanded from the development of genetically encoded tools, some limitations still persist. For instance, we are limited in our ability to visualize the native three dimensional environments of whole organs. Additionally, it is challenging to efficiently deliver transgenes into difficult-to-target areas through direct-injections, such as the cardiac ganglia, or broadly distributed networks, such as the myenteric nervous system, which limits our ability to extensively study these areas. Therefore, tools and methods that overcome these limitations are needed. Towards this end, my thesis work has been focused on developing tools for single-cell resolution phenotyping in whole organs. I have been developing tissue clearing technologies to render whole organs transparent for optical interrogation and characterizing viral capsids and engineering viral vectors for noninvasive widespread gene delivery to the central and peripheral nervous system.

Tissue clearing techniques for three dimensional optical interrogation were invented over a century ago. However, these earlier methods used harsh organic chemicals and failed to retain the tissue’s native fluorescence or epitopes. These earlier methods eventually became incompatible to the hundreds of newly generated transgenic mouse lines that allowed for cell type-specific expression of fluorescent transgenes or to fluorescent labeling techniques, such as immunohistochemistry (IHC). The first part of my dissertation is aimed at addressing these limitations by further developing and standardizing a tissue clearing method that utilizes the vasculature to perfuse clearing reagents. This technique, called perfusion assisted agent release in situ (PARS) enables (i) whole organ clearing of soft tissue, (ii) preservation of native fluorescence, and (iii) preservation of epitopes compatible with IHC.

Although PARS allows us to optically investigate whole soft tissue organs, it is unsuitable for clearing bone tissue. The clearing of bone is important as it may provide optical access to delicate environments, such as the lymphatic vessels lining the dural sinuses beneath the skull that would otherwise be damaged through traditional methods. However, clearing bone tissue is challenging since it is composed of both soft (bone marrow) and hard (mineral) tissue. To overcome this challenge, I developed a clearing method that rendered intact bone tissue transparent by using EDTA to decalcify bones and by constructing a convective flow chamber to efficiently clear bones. This method, called Bone CLARITY, is able to preserve native fluorescence and epitopes. In order to demonstrate the utility of Bone CLARITY, I collaborated with colleagues to quantitatively access a rare and non-uniformly distributed population of osteoprogenitor cells in their native three dimensional environment. Bone CLARITY in conjunction with light-sheet microscope enabled the early detection of an increase to this osteoprogenitor population after administration of a novel anabolic drug, which may have been undetected with traditional techniques.

Towards my second goal, I have been working on characterizing adeno-associated viruses (AAVs) for non-invasive widespread gene delivery across the central or peripheral nervous system. Through systemic delivery, these novel AAVs are able to efficiently deliver transgenes to (i) difficult-to-target areas, such as the dorsal root ganglia; (ii) cellular populations that are widely distributed across the mouse body, such as neurons in the myenteric nervous system, and (iii) through highly selective barriers, such as the blood-brain barrier. These viruses enable rapid expression of transgenes for perturbing and monitoring cellular circuits, or for potentially treating neurological diseases. In addition, I worked on engineering or validating several different gene regulatory elements to achieve cell type restricted expression in transgenic and non-transgenic animals with AAVs. These viral vectors may prove useful in rapidly testing newly developed genetic tools. Finally, I developed and characterized two different two-component viral vector systems to control the density of labeling when systemically delivering genes with our novel engineered viruses. I utilized this two-component system to perform single-cell morphology studies in the CNS and PNS. Collectively, these capsids and vectors expand the AAV toolbox and enable efficient and versatile gene delivery into the CNS and PNS of transgenic and non-transgenic animals.

This work describes, for the first time, the electrochemical and electrocatalytic properties of self-assembled layers of single-walled carbon nanotubes (SWCNTs) intergrated with selected organo-iron complexes and Cysteamine (Cys) forming a base on gold electrodes. The organo-iron complexes selected for this study were octa(hydroxyethylthio)phthalocyaninatoiron(II) (FeOHETPc), tetraaminophthalocyninatoiron(II) (FeTAPc), tetraaminophthalocyninatocobalt(II) (CoTAPc), ferrocene monocarboxylic acid (FMCA), ferrocene dicarboxylic acid (FDCA) or a mixture of SWCNT and FMCA or FDCA. The successful fabrication of these electrodes were established using atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and electrochemical techniques such as cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), square wave voltammetry (SWV) and chronoamperometry (CA) The Au-Cys-SWCNT-FeOHETPc electrode exhibited strong dependence on the reaction of the head groups and the pH of the working electrolytes. The high electron transfer capability of the Au-Cys-SWCNT-FeOHETPc electrode over other electrodes as the Au-Cys-SWCNT or the Au-Cys-FeOHETPc or the Au-FeOHETPc suggests that SWCNT greatly improves the electronic communication between FeOHETPc and the bare gold electrode. The electron transfer rate constant (kapp) of Au-Cys-SWCNT-FeOHETPc in pH 4.8 conditions (~1.7 x 10-2 cm s-1) over that of the electrode obtained from SWCNT integrated with tetraaminophthalocyninatocobalt(II) (Au-Cys-SWCNT-CoTAPc) (5.1 x 10-3 cm s-1) is attributed to the possible effect of both the central metal on the phthalocyanine core and subsituents on the peripheral positions of the phthalocyanine rings. This work clearly proved that the aligned SWCNTs arrays exhibit much faster electron transfer kinetics to redox-active species in solutions compared to the randomly dispersed (drop-dried) SWCNTs. The advantageous electron transfer properties of the aligned Au-Cys-SWCNT-FeOHETPc electrode, coupled with its ease of fabrication and electrochemical stability, could be found useful in electrochemical sensing and catalysis. Thiocyanate ion was used as an analytical probe to examine the electrocatalytic properties of these modified gold electrodes. This work shows that SWCNT-FeOHETPc hybrid exhibits excellent sensitivity towards the detection of thiocyanate compared to electrodes containing SWCNT or FeTAPc or FeOHETPc only, indicating the ability of the SWCNTs to function as effective conductive nanowires for the detection of this important analyte. The electrochemical response of the FeOHETPc based electrodes was greater than their FeTAPc-based electrode counterparts, indicative of the impact of peripheral substituents on the phthalocyanine core towards electrocatalytic behaviour of these types of hybrids. Nevertheless, the exchange of the central metal as seen with the case of CoTAPc (see chapter 3), provide useful comparative electrochemical activity of this complexes versus FeTAPc with the same chemical environment with an indication of iron being the best as metal centre. FMCA or FDCA were covalently attached to the base Cysteamine monolayer to form the Au-Cys-FMCA and Au-Cys-FDCA, respectively. The same covalent attachment strategy was used to form the mixed SWCNTs and ferrocene-terminated layers (i.e., Au-Cys-SWCNT/FMCA and Au-Cys-SWCNT/FDCA). The impact of neighbouring SWCNTs on the electron transfer dynamics of the ferrocene molecular assemblies in acidic medium (0.5 M H2SO4) and in a solution (pH 7.2) of an outer-sphere redox probe ([Fe(CN)6]4-/ [Fe(CN) 6]3-) was explored. The electron transfer rate constants in both solution media essentially decrease as Au-Cys-FMCA > Au-Cys-SWCNT/FDCA > Au-Cys-FDCA > Au-Cys-SWCNT/FMCA. This trend has been interpreted in terms of several factors such as the locations of the ferrocene species in a range of environments with a range of potentials, the proximity /interactions of the ferrocenes with one another, and electrostatic interaction or repulsion existing between the negatively-charged redox probe and the modified electrodes. Square wave voltammetry was used to examine the catalytic behaviour of the electrodes. Au-Cys-SWCNT/FDCA proved to be the best electrode, possibly due to the repulsive interactions between the negatively charged SCN- and high number of surface –COOH species at the SWCNT/FDCA. This novel study has provided some useful insights as to how CNTs co-assembled with ferrocene-terminated thiols could impact on the heterogeneous electron transfer kinetics as well as the electrocatalytic detection of the self-assembled ferrocene layers.
Thesis (PhD)--University of Pretoria, 2010.
Chemistry
unrestricted

1 Abstract This work deals with the performance of supervision over the financial market and the entities operating in the financial market. Part of the work is devoted to consumer protection in the financial market and compensation systems. Because of the fact that the Czech Republic became a member of the European Union in 2004, this work includes also legislation of regulation and supervision of this level, as this treatment significantly predetermines Czech adjustment. Following questions were examined as an example of protecting the interests of clients of supervised entities: - whether there are any tools to protect the client's interests at the level of supervised entities, - what kind of role the supervisory authority has or may have in relation between a supervised entity and its client, - how are the client's financial interests protected in the event of failure of the supervised entity and whether this protection is de lege lata sufficient. The theoretical part of the work briefly describes the institute of supervision, its assorting and forms. The authority of supervisor is discussed in the next part together with the regulations under which the supervision is conducted. Owing to the fact that the scope of supervisory activity of the Czech National Bank is quite extensive, and the objective of...