VictorJuiz/thesis huggingface dataset:
Mechanism of an epigenetic switch that mediates neural development [electronic resource]

During the development of the vertebrate nervous system neural progenitors divide, generate progeny that exit mitosis and then migrate to sites where they elaborate specific morphologies and synaptic connections. Mitotic exit in neurons is accompanied by an essential switch in the Mammalian SWI/SNF (also called BAF) ATP-dependent chromatin regulatory complexes from the neural progenitor npBAF to neuron-specific nBAF complexes. We elucidated the mechanism of a microRNA/chromatin switch underlying the switch of the npBAF subunit, BAF53a for the nBAF subunit BAF53b. Recapitulating this microRNA/chromatin switch in fibroblasts leads to their direct conversion to neurons. We have defined the kinetics of nBAF complex assembly in the formation of induced neurons from ES cells or fibroblasts as well as normal neural differentiation and using proteomic analysis find that this switch also includes the removal of SS18 and its replacement by CREST at mitotic exit. We find that switching of chromatin remodeling mechanisms is highly correlated with a broad switch in the use of neurogenic transcription factors. Knockdown of SS18 in neural stem cells causes cell-cycle exit and failure to self-renew, while continued expression of SS18 in neurons blocks dendritic outgrowth underlining the importance of subunit switching. Recent whole genome sequencing studies show that dominant mutations in BAF subunits underlie widely different human neurologic diseases including mental retardation, microcephally, schizophrenia, sporadic mutations in autism as well as the neurodegenerative disease, amyotrophic lateral sclerosis (ALS) also known as Lou Gehrig's disease. Using whole exome analysis of ALS trios (trio=two unaffected parents and affected child), we identified and functionally characterized two de novo mutations in CREST that function in a dominant negative mode to inhibit dendrite outgrowth in cortical and motor neurons. As the aforementioned neurological diseases arise in different neuronal types, our studies suggest that the characteristics of these diseases must be interpreted in the context of the different BAF assemblies in neurons rather than a singular mSWI/SNF complex.

Keywords: Developmental Biology.
Advisor: Crabtree Gerald R. primary advisor. Thesis advisor
McConnell Susan K. advisor. Thesis advisor
Nusse Roel
Scott Matthew P. advisor. Thesis advisor
A mechanistic study of the Swedish NGF mutation (NGFR100W) [electronic resource] : trophic signaling versus nociception

Nerve growth factor (NGF) exerts multiple functions, e.g. trophic or nociceptive, on target neurons throughout development. The recent discovery of a point mutation in NGF [beta] (NGFR100W) in patients with hereditary sensory and autonomic neuropathy, type V (HSAN V) made it possible to distinguish the signaling mechanisms that lead to the two different functional outcomes of NGF. We recently the developed novel method to produce mono-biotinylated NGF that can be used for single molecule studies using a mammalian expression system. We confirmed that the mono-biotinylated NGF is mature and biologically active comparably to purified NGF from mice maxillary glands. We produced and purified the mutant NGF (NGFR100W) along with its wild type counterpart (wtNGF) using this mammalian expression system. We performed extensive biochemical, cellular, and live imaging experiments to examine the binding and signaling properties of NGFR100W. Our results showed that, similar to wtNGF, NGFR100W bound and activated TrkA receptor and its downstream signaling pathways to support neuronal survival and differentiation. However, NGFR100W failed to bind and stimulate p75NTR mediated signaling cascades. Furthermore, NGFR100W no longer had the ability to induce hyper-potentiation of dorsal root ganglion (DRG) neurons as detected by single cell patching clamp assay. Intraplantar injection of NGFR100W into adult rats induced neither thermal nor mechanical hyperalgesia. Taken together, our results demonstrate that, NGFR100W retains trophic support capability through TrkA, but no longer is involved in mediating pain functions through the p75NTR signaling pathways. These results may explain the increase in pain threshold and loss of pain perception in HSAN V patients.

Advisor: Doniach S. primary advisor. Thesis advisor
Mobley William C.
Smith Stephen J.
Mechanochemical coupling and structural dynamics in DNA gyrase [electronic resource]

DNA gyrase is a molecular motor that directionally introduces negative supercoils into DNA, serving a function that is critical to most bacterial life. This thesis addresses the question of how gyrase transduces chemical energy stored in ATP into mechanical energy stored in supercoiled DNA. I have investigated how substeps in the ATPase cycle -- ATP binding, hydrolysis and product release -- coordinate structural transitions of the nucleoprotein complex during the course of the supercoiling reaction. Using single-molecule real-time tracking of DNA compaction and rotation, I have characterized the geometry and interconversion dynamics of DNA configurations under different nucleotide conditions. A critical step in the reaction cycle of DNA gyrase involves the formation and manipulation of a chiral wrap in the path of DNA on a scale of ~ 150 base pairs. I show that chiral wrapping is a multistep process that dominates the overall kinetics and is modulated by ATP. My results identify new roles for ATP binding, hydrolysis and product release, and show that nucleotide states in gyrase cannot be uniquely identified with structural intermediates. The work reveals a sophisticated molecular motor in which a conformational landscape of loosely coupled transitions funnels the enzyme toward productive energy transduction.

Keywords: Applied Physics.
Advisor: Bryant Zev David primary advisor. Thesis advisor
Fisher Daniel S. primary advisor. Thesis advisor
Puglisi Joseph D. advisor. Thesis advisor
Methods for high dimensional uncertainty quantification [electronic resource] : regularization, sensitivity analysis, and derivative enhancement

Surrogates are used to mitigate the aggregate cost of simulation needed to perform a comprehensive uncertainty quantification (UQ) analysis. A realistic uncertainty analysis of any engineering system involves a large number of uncertainties, and as a result, the surrogates take inputs in a high dimensional space. We investigate surrogates that take the form of a truncated Legendre polynomial series, from which the coefficients associated to each polynomial basis function must be estimated. High dimensional estimation is a known instance of the curse of dimensionality, and for sufficiently "complex'" functions, an unsolved problem. In order to break the curse, we assume the function to be approximated is sparse in the Legendre polynomials and employ the machinery of l-1-regularized regression. We make three contributions under this theme. Firstly, we present a novel approach to choosing sample (design) points and show that it yields lower estimation error over a broad range of functions compared to existing sampling approaches. Secondly, we give a novel sparse estimator that effectively uses (partial) derivative information for estimation and show empirically that estimation using derivatives can be more efficient than function values if the derivatives are sparser than the function. Thirdly, we show that by exploiting the best k-term approximation} property of l-1-methods, we can quickly identify the most signfiicant uncertainties and reduce the dimensionality of the input space accordingly. We conclude by demonstrating the efficacy of these methods in a UQ analysis of a notional vertical axis wind turbine design.

Keywords: Aeronautics and Astronautics.
Advisor: Iaccarino Gianluca primary advisor. Thesis advisor
Alonso Juan José
Eldred Michael advisor. Thesis advisor
Pavone Marco
Methods for unraveling the phenotypic consequences of regulatory variation [electronic resource]

Most human variation lies outside of coding regions, where molecular functions are more difficult to determine than for variants in coding regions. As most disease-associated variants lie in non-coding regions, characterizing the role of regulatory variation is crucial to understanding the molecular mechanisms of these diseases and methods to do so are currently limited. Recently, a number of research efforts, including the ENCODE project, have produced a wealth of data on transcription factor binding sites and other regulatory information, in addition to increasingly available whole genome sequence and transcriptomics data. These data will crucial to understanding the molecular basis of many diseases, but their scale and disparate nature, as well as high levels of noise, require clever informatics methods to integrate and properly apply this information. In this thesis, I describe methods to address some of the major informatics challenges to characterize the role of regulatory variants in phenotypes and disease. In particular, I have shown that I can (1) detect cooperativity among transcription factors using human variation data, (2) associate transcription factors to functional modules and thus discover new TF interactions and disease associations, (3) provide molecular mechanisms for disease-associated non-coding variants, and (4) explore regulatory functional mechanisms using long-range interactions in the human genome.

Advisor: Montgomery Stephen
Snyder Michael
Altman Russ advisor. Thesis advisor
The MHC class II cofactor, HLA-DM, interacts with immunoglobulin in B cells [electronic resource]

B cells internalize antigen bound to membrane immunoglobulin and load antigen-derived peptides onto MHC class II proteins. How these pathways intersect is not well understood. We found that HLA-DM, a catalyst for peptide loading onto MHC class II, regulates immunoglobulin levels in human B cells and co-precipitates with immunoglobulin. In intact cells, HLA-DM and immunoglobulin are found in close proximity, and these complexes are in post-Golgi compartments. In vitro, in the endosomal pH range, the luminal domain of soluble HLA-DM (sDM) directly and specifically interacts with the immunoglobulin Fab domain, and sDM increases the amount of antigen released from immune complexes. These observations support a model in which HLA-DM facilitates the hand-off of antigen from immunoglobulin to MHC class II.

Advisor: Mellins Elizabeth primary advisor. Thesis advisor
Davis Mark M. advisor. Thesis advisor
Jardetzky Theodore advisor. Thesis advisor
Jones Patricia P. advisor. Thesis advisor
Miklos David (David B.) advisor. Thesis advisor
Microbial biogeochemistry of ammonia oxidation in coastal environments [electronic resource]

The processes responsible for the fixation and removal of nitrogen (N) from the ocean are ultimately linked by nitrification, the sequential oxidation of ammonia (NH3) to nitrite (NO2 ) and then nitrate (NO3-). It is estimated that almost all of the approximately 4x1011 kg of N that cycles through the ocean annually is nitrified at least one time. The degree to which nitrification occurs within a given environment alters the distribution of inorganic nitrogen available to support the growth of phytoplankton in surface waters of the ocean. In coastal environments, the process plays another critical part in N cycling, by linking the decomposition of organic matter to N loss via denitrification. It has been nearly a decade since the discovery of the ammonia oxidizing archaea expanded our perspective of N cycling in terrestrial and marine environments. Initial reports of their widespread abundance in all major biomes called for a reexamination of nitrification, and the role the archaea (and the ammonia oxidizing bacteria, AOB) play in the global N cycle. At present there is insurmountable support for nitrification being a largely archaeal-mediated process both on land and at sea. Estuaries remain a grey zone, where either the AOA or the AOB may be the primary organisms responsible for ammonia oxidation. This dissertation focuses on microbial N transformations through field studies of the distribution and activity of ammonia oxidizing microorganisms in sediments and water columns of the coastal environment, using an approach that includes molecular biology, microbial ecology and biogeochemistry.The broad objective of my thesis research was to investigate the roles of the AOA and AOB in the cycling of inorganic N, and how specific environmental conditions select for their activity in two important parts of the coastal environment: the upper ocean, where N plays a key role in supporting phytoplankton growth, and intertidal sediments, responsible for removing vast amounts of anthropogenic N pollution from coastal waters.

Keywords: Environmental Earth System Science.
Advisor: Francis Christopher primary advisor. Thesis advisor
Casciotti Karen Lynn
Welander Paula advisor. Thesis advisor
Microfabricated tools for functional assessment of developing cardiomyocytes [electronic resource]

Cardiomyocytes cultured from stem cells offer potential for use in regenerative tissue grafts, however the difficulty in manipulating and culturing these cells necessitates novel tools for both stimulating their development and assessing their mechanical and electrical function. Herein I introduce the tools for performing biomechanical investigations of cells and describe the challenges in working with cardiomyocytes and the development of two microfabricated sensors for quantifying the electricomechanical properties of immature cardiomyocytes throughout their development.

Keywords: Mechanical Engineering.
Advisor: Kuhl Ellen
Pruitt Beth primary advisor. Thesis advisor
Wu Joseph Ching-Ming
Microlocal analysis of lagrangian submanifolds of radial points [electronic resource]

Microlocal analysis relies on correspondences between quantum physics and classical physics to give information about certain PDEs -- for instance, linear variable-coefficient PDEs on manifolds. PDEs are interpreted as quantum systems. The corresponding classical systems tell us, for example, function spaces on which problems are solvable or almost solvable, existence and uniqueness results, and the structure of solution operators. Landmark papers of Hörmander and Duistermaat and Hörmander establish key results for the standard calculus of microlocal analysis, which gives a broad framework for dealing with variable-coefficient PDEs on manifolds. Their work is well-suited for dealing with PDEs which, in a generalized sense, are hyperbolic, with corresponding classical dynamics looking like wave propagation of geometric optics. In this thesis, we aim to extend many of their results to situations in which the corresponding classical dynamics are less well-behaved: those with a Lagrangian submanifold of radial points.

Keywords: Mathematics.
Advisor: Vasy András primary advisor. Thesis advisor
Brendle Simon
Mazzeo Rafe advisor. Thesis advisor
Venkatesh Akshay
Micromachined temperature compensated pressure sensor implemented using a multi-sensor integration platform [electronic resource]

Micromachined pressure sensors are widely used in our everyday lives; they are used in automobiles for tire pressure monitor, in medical devices for blood pressure track, and in indoor navigation for altitude measurement. While the requirements for a pressure sensor vary depending upon the specific application, a common requirement is accurate sensing over a wide operating temperature range. This dissertation begins by introducing our capacitive pressure sensor design and demonstrating how it outperforms a commercially available piezoresistive pressure sensor with respect to temperature insensitivity. The capacitive pressure sensors were designed to use a central subset of the entire circular diaphragm as the electrode to improve fractional capacitance change. The capacitive pressure sensors show an order of magnitude smaller temperature coefficient of sensitivity (TCS) compared to the piezoresistive reference pressure sensor. To further reduce temperature dependence, a resonant thermometer with resolution of 1 m°C was cofabricated with the capacitive pressure sensor, enabling the tracking of temperature fluctuations on the die to correct the associated pressure error. Experimental results indicate that the temperature-induced errors are successfully suppressed, and the sensors have remaining errors within ±0.15 kPa over the tested temperature range. In the second part of the dissertation, the design and performance of our resonant pressure sensors are discussed. The development of the resonant sensors was motivated by the emerging demand of altimeters which require high resolution in pressure sensing (a one-meter elevation change corresponds to a ten-Pascal pressure change, i.e., 10 Pa/meter). As the design is coupled to the die strain, the accuracy of the resonant pressure sensors is strongly influenced by errors induced by both temperature and package stress. We addressed this limitation with a multiple sensor solution whereby temperature and strain sensors were cofabricated to reduce the pressure sensor's temperature and package stress dependence, thus improving accuracy. The devices show sensitivity to pressure ranging between 50 and 150 ppm/kPa with a minimum detectable signal of approximately 7 Pa in a one-kHz bandwidth. After temperature is compensated for, the sensors have remaining offset errors within ±0.3 kPa. Throughout this work, a multiple sensor integration platform was used to fabricate the sensors. Key innovations include time insensitive vapor etching of silicon dioxide with hydrofluoric acid to release structures as well as the fabrication of structures that can be driven and sensed in both in-plane (x, y) and out-of-plane (z) directions on either bulk silicon or SOI wafer substrates. Such a multi-sensor integration platform is suitable for a variety of MEMS devices, such as accelerometers, gyroscopes, switches, and resonators.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas Williams
Howe Roger Thomas advisor. Thesis advisor
O'Brien Gary (Gary J.)
Microprobing mechanical and fracture behavior in complex structures [electronic resource]

As the feature size of device technologies scales to ever-smaller dimensions, they become more susceptible to mechanical damage. This is particularly true in microelectronics, where high temperatures are required for solder reflow during packaging of semiconductor dies. A mismatch in coefficient of thermal expansion between the silicon chip and the package causes mechanical stresses to be exerted on interconnect structures. Such chip-package interactions (CPI) cause damage and delamination of metals and dielectrics found in interconnects and other die structures. This damage occurs at the micron length scale and has been exacerbated by the integration of fragile ultra low-K (ULK) layers, stiffer lead-free solder and elevated reflow temperatures. To explore mechanics at the micron length scale, a microprobe system was designed and built. The system consists of custom-made micron-scale probe tips and a piezoelectric actuator mounted on a high-stiffness steel chassis for the accurate characterization of a range of mechanical properties under compressive, tensile or shear loading. These loading modes can also be performed cyclically, which allows for the study of fatigue phenomena. The system includes integrated heating and active cooling, allowing measurements at temperatures up to 300oC. The microprobe system is used to exert stresses on complex stacked structures consisting of Cu bumps or solder bumps and several layers of passivation and copper/low-K dielectrics. The interconnect architecture, dielectric porosity, loading mode mixity, temperature and the direction of shear loading were found to have a significant effect on damage processes. It was shown that the interconnect stack structures weaken dramatically with temperature and that fracture behavior is sensitive to the presence of high porosity dielectric films with sub-micron thickness. Failure analysis of the test structures was conducted using FIB milling and SEM imaging, revealing that rather than always occurring in the weakest layer, the location of ultimate failure depends on the damage initiation site as well as the overall stack mechanics dictated by both geometry and material properties. This study allows for a quantitative understanding of the mechanics of complex structures, particularly damage initiation and evolution processes. This information is useful for optimizing the manufacturing process of devices with micron-scale features.

Keywords: Materials Science and Engineering.
Advisor: Dauskardt R. H. (Reinhold H.) primary advisor. Thesis advisor
Nix William D. advisor. Thesis advisor
Salleo Alberto
MicroRNA control of T cell development and function [electronic resource]

Much has been learned about the molecular and cellular components critical for the control of immune responses and tolerance. It remains a challenge, however, to control the immune response and tolerance at the system level without causing significant toxicity to normal tissues. Recent studies suggest that microRNAs (miRNAs), an abundant class of ~22 nucleotides regulatory RNAs, play important roles in immune cells. In this thesis, I examined the function of miR-181 genes in regulating T cell selection, development, and immune tolerance. We show that genetic ablation of mir-181a-1/b-1 ---- a T cell sensitivity tuner ---- in double-positive (DP) thymocytes dampens TCR and Erk signaling and affects positive selection. Moreover, dampening TCR signaling as the result of mir-181a-1/b-1 deletion potentiates the reactivity of self-specific T cells without significantly affecting the pool sizes of naive T cells recognizing specific self-antigens. Finally, loss of mir-181a-1/b-1 in peripheral T cells reduces their basal TCR signaling and their ability to migrate from lymph nodes to the pathogenic sites during autoimmune perturbations. Interestingly, loss of mir-181a-1/b-1 results in quantitative defects in various T and B lymphocyte populations, but does not cause major structural damage to the immune system or spontaneous autoimmunity. Our findings illustrate that mir-181a-1/b-1 controls tolerance through opposing activities in selection and peripheral T cell function. Thus, despite the subtle effects of miRNAs on gene expression, miRNAs have the potential to influence the outcomes of normal and pathogenic immune responses by controlling the quantitative and dynamic aspects of immune responses.

Advisor: Chen Chang-Zheng primary advisor. Thesis advisor
Chien Yueh-Hsiu
Fathman C. Garrison
Mellins Elizabeth advisor. Thesis advisor