VictorJuiz/thesis huggingface dataset:
Applying riboswitches for novel sensing and chemistry

Riboswitches are cis-regulatory structured RNA elements capable of controlling expression of downstream genes by binding to small molecule ligands. These naturally evolved RNA elements possess remarkable affinity and selectivity for their small molecule ligands, high folding efficiencies, and thermostability for functioning in cellular environments. Due to these properties, a number of riboswitch-based technologies have emerged such as riboswitch reporters, aptazymes, and RNA-based fluorescent (RBF) biosensors which all have wide applications for detection, imaging, and regulatory circuits. While riboswitch reporters and aptazymes have been robustly studied to better understand how to improve their function, there are fewer studies that expand on RBF biosensor development. Here, novel approaches towards expanding the functional repertoire of RBF biosensors and systematically probing their properties are described./nFirst, we show that engineering circular permutations of the riboswitch aptamer domain yields functional biosensors for S-adenosyl-L-methionine (SAM), using the SAM-I riboswitch as our model. We reveal that this design can enhance fluorescence turn-on and ligand binding affinity compared to the non-permuted topology. Expanding upon these established design principles, novel biosensors for the ligand guanidine was developed. Two novel designs were added to our existing repertoire that generated functional RBF biosensors using the architecture of the guanidine-I riboswitch. A new base-pair mutation strategy was applied on these guanidine biosensors which, resulting in modest changes to biosensor activation speeds just from single base-pair mutations. Lastly, riboswitches were explored as potent scaffolds to generate a self-labeling ribozyme. Various natural or engineered riboswitches for the electrophilic ligand, SAM, were screened for reactivity with an analog, Hey-SAM, as a proxy to measure ribozyme activity. In collaboration with Agilent Labs, a high-throughput method was developed for probing and screening latent ribozyme activity using a microarray platform. The efforts and strategies put forth here use riboswitches outside their native context for applications in detection and catalysis further showcasing the broad utility of riboswitch-based tools.

Advisor: Hammond, Ming C
Francis, Matthew B
Untethered Microrobots of the Rolling, Jumping & Flying kinds

In this dissertation we study microrobot design for three modes of locomotion, namely rolling, jumping, and flying. This work covers power electronics, actuator and mechanical transmission design for these types of microrobots along with power source selection. Though interesting, we do not cover the sensors, controllers/computers, communications and useful payloads for these bots. This remains a topic for future work./nPiezoelectric and electrostatic actuators generally have been the actuators of choice for researchers working in microrobotics, since conventional electromagnetic motor designs don't scale down well. Here we design an electromagnetic actuator in a way that significantly reduces its scaling down disadvantages, while still retaining its original advantages. This has enabled us to achieve untethered operation for our bots, which is one of the coveted goals for researchers working in this domain. Though untethered rolling and jumping is demonstrated, the untethered flying bot reported in this dissertation remains underpowered and doesn't take flight yet./nFirst a micro-ratcheting mechanism is developed as a means to convert small periodic motions of actuators to continuous rotational motion. A supercapacitor, a fixed frequency H-bridge, and a low-voltage electromagnetic actuator is then used to drive this micro-ratchet to achieve untethered rolling motion for 8 seconds at 27mm/s. At 130mg mass, this is the lightest and fastest untethered rolling microrobot reported yet./nThe same continuous rotation mechanism developed for the rolling bot is then used to load a spring in an energy storage mechanism that can then release the stored energy rapidly and passively, via use of magnets, after the stored energy crosses a certain threshold. In this case, the continuous rotation mechanism is driven using laser-powered photovoltaic cells and untethered jumping up to heights of 8mm is demonstrated. At 75mg mass, it is the lightest untethered jumping microrobot with onboard power source./nNext, a highly efficient resonant low-voltage electromagnetic actuator is developed to generate insect-like flapping wing motion. It is demonstrated to produce 90% of its weight in lift. Further light-weight and power-efficient power electronics are developed to power this actuator using laser-powered photovoltaic cells. The designed power electronics are an order of magnitude lighter and two orders of magnitude more efficient than all other power electronics units reported yet for flying microrobots. While sufficient lift for flight is not achieved, due to the actuator being underpowered because of power source overheating, untethered flapping wing motion is demonstrated./nTo provide inspiration to future generations of microroboticists, a fruit fly scale flapping winged robot is developed. At 0.7mg mass, even though tethered, it is the lightest and smallest bot to demonstrate flapping wing kinematics.

Advisor: Tomlin, Claire J.
Smoothed Particle Hydrodynamics and Its Application Towards Extrusion Based Additive Manufacturing

The possibility of using the mesh-free method Smoothed Particle Hydrodynamics (SPH) towards analyzing modern additive manufacturing techniques, extrusion based ones in particular, is investigated in this report. The mathematical foundations and a number of corresponding topics regarding SPH is introduced, ranging from incompressible SPH and implicit timestepping methods to total Lagrangian formulations: displaying its robust capabilities for solving multiphyiscal mechanical problems. Finally, we demonstrate a swarm-intelligence based optimization scheme coupled with our SPH solver to optimize extrusion topologies for DIW (Direct Ink Writing) applications.

Advisor: Zohdi, Tarek I
The influence of inflammation on sleep, circadian functioning, and risk among adolescents with an evening circadian preference

Background. Adolescence is associated with a shift toward an evening circadian preference, which is linked to increased risk across health domains. This study examined the influence of inflammation on sleep, circadian functioning, and health at pretreatment and following participation in a psychosocial intervention targeting sleep and health./nMethod. Participants were 165 (96 female, average age = 14.7 years) adolescents randomized to receive 6-sessions of a psychosocial intervention targeting sleep and health. Sleep and circadian outcomes included weeknight total sleep time (TST), weeknight bedtime, and the Children's Morningness-Eveningness Preferences Scale. Health domains included emotional, cognitive, behavioral, social, and physical health. Sleep, circadian, and health outcomes were assessed at pretreatment, posttreatment, 6-month follow-up, and 12-month follow-up. Inflammatory markers were soluble tumor necrosis factor receptor 2 (sTNF-R2), interleukin (IL)-6, and C-reactive protein (CRP) measured at pretreatment./nResults. At pretreatment, shorter TST was associated with more emotional domain risk among adolescents with higher CRP. For adolescents with lower IL-6 at pretreatment, a greater evening circadian preference was associated with more behavioral risk. Inflammation also influenced treatment effects. Lower pretreatment sTNF-R2 was related to a decrease in self-reported evening circadian preference following treatment and through follow-up. Lower pretreatment IL-6 was associated with reduced behavioral and physical domain risk following treatment and through follow-up./nConclusions. These findings support a growing body of literature showing that biological factors such as inflammation may influence sensitivity to positive and negative experiences on outcomes across key domains of health during adolescence./nKeywords: Adolescent; Circadian Rhythm; Health; Inflammation; Sleep.

Advisor: Harvey, Allison G
De-Multiplexed Multiwavelength Interferometry for High Precision Metrology

In the era of global warming, harnessing green energy has become a top priority for nations around the world. Solar cells have been developed for over half a century, but the dull appearances of solar cells impede their widespread adaptation in size-constrained metropolitan cities like Singapore. Current colorful solar cell technologies are extremely inefficient, and their adaptation cannot be justified. In the first part of this thesis, we propose a new way to use High Contrast Gratings to materialize colorful solar cells with a very small penalty on efficiencies. We show optimized designs for Silicon, Indium-Phosphide, and Perovskite solar cells, and verify the viability of our idea through preliminary experimental demonstrations./nIn the second part of the thesis, we innovate in nanoscale metrology, a key component of nanomanufacturing. Many areas of science and technology rely on the precise determination of distance over a sufficiently long range. Advanced ranging technology has the potential to open up a wide application field including 3D sensing, robotics and inspection for automated manufacturing, where high-precision, long-range, efficiency, and noise-tolerance are key. The small wavelength of light makes it a suitable candidate for precision metrology. A single wavelength interferometer has a high accuracy, but a small range that is limited by the ambiguous interferometric fringe order. We present a new arithmetic algorithm for multiwavelength interferometry that has a theoretical maximum range of the lowest-common-multiple of the wavelengths used, the resolution of a single-wavelength interferometer, and the theoretical maximum noise tolerance of an algebraic approach. We first describe the analytical formulation, analyze the noise tolerance, and present a recursive solution to extend the range through multiple wavelengths. To justify the practicality, experimental results from a simultaneous phase shifting demultiplexed two-wavelength interferometry system, with a range-resolution ratio of > 3e5, are presented to demonstrate the reliability of our method in the absence of any error correction.

Advisor: Chang-Hasnain, Constance J.
Regulation of mTORC1-Dependent Growth Signaling by Lysosomal Cholesterol

Mechanistic target of rapamycin complex 1 (mTORC1) is an evolutionarily conserved serine/threonine protein kinase that acts as a master regulator of growth and proliferation in eukaryotic cells. mTORC1 integrates a variety of signals including cellular stress, nutrients and growth factors, and, in response, phosphorylates key substrates involved in coordinating cellular metabolism. When nutrients are abundant, mTORC1 fuels the biosynthesis of cellular building blocks including nucleotides and lipids, and enhances mRNA translation and ribosomal biogenesis. In addition, mTORC1 inhibits catabolic pathways such as autophagy, which consume cell mass./nA heterodimer of small guanosine triphosphatases, known as the Rag GTPases, communicates cellular nutrient status to mTORC1, such that the active nucleotide state (RagAGTP/RagCGDP) promotes translocation of mTORC1 from the cytosol to the surface of the lysosome. At the lysosome, another small GTPase, Rheb, binds to mTORC1 and unlocks the autoinhibited kinase domain in response to growth factor signals. Thus, growth regulation occurs via an elegant coincidence detection mechanism, whereby intracellular nutrients direct mTORC1 to a physical location, and growth factors provide long-range signals from distant tissues to activate mTORC1 kinase via Rheb./nDespite major advances in our understanding of mTORC1 regulation, it remains unclear how mTORC1 senses and integrates chemically diverse molecules. Here, I identify cholesterol, an essential lipid for cellular growth, as a nutrient input that drives mTORC1 recruitment and activation at the lysosomal surface. I found that the lysosomal transmembrane protein SLC38A9 is required for mTORC1 activation by cholesterol through conserved cholesterol-responsive motifs. Moreover, SLC38A9 enables cholesterol-mediated mTORC1 activation independently from its arginine-sensing function. Conversely, the Niemann-Pick C1 (NPC1) protein, which regulates cholesterol export from the lysosome, binds to SLC38A9 and inhibits mTORC1 signaling through its sterol transport function. Thus, lysosomal cholesterol drives mTORC1 activation and growth signaling through the SLC38A9-NPC1 complex. Importantly, this suggests that aberrant mTORC1 activity may contribute to the metabolic derangement observed in Niemann-Pick Type C (NPC) disease in humans./nThe mechanism of mTORC1 recruitment by the lysosomal scaffolding complex is not fully understood. To address this, I purified the full-length human Ragulator:RagA/C complex in the active nucleotide loading state and, in collaboration with the Hurley Lab, determined the cryo-EM structure. This is the first structure to reveal the nucleotide binding G domains of the Rag GTPases in the context of their lysosomal scaffold, Ragulator. Overall, this work elucidates a new nutrient input to the mTORC1 signaling network and provides structural insights into the regulation of mTORC1 docking at the lysosome, suggesting new strategies for therapeutically targeting metabolic diseases.

Advisor: Zoncu, Roberto
Statistical Inference under the Multispecies Coalescent: Methods and Theory

The rising availability of genome-scale data for a large number of species has allowed for more in-depth studies of the genetics between species using increasingly sophisticated methods. The accumulation of pairwise differences between individuals are indicative of how diverged they are in time. The multi-species coalescent (MSC) has been the most popular framework with which to model the dynamics of the coalescent process in the presence of species barriers, such as a tree structure. Modelling using the MSC in the presence of increasing amounts of data (loci and species) while maintaining feasible computational times is the main focus of many emerging methods./nIn this dissertation, I explore the use of the MSC in 3 different ways, using classical and novel statistical analysis to provide insight into species divergence parameters. I begin by constructing a novel statistical method for inferring species tree divergence times and population size parameters for any given tree topology from sequence data. The program COAL-PHYRE, presented here, makes use of the MSC marginally between individuals, as I demonstrate that pairwise information within the MSC is sufficient to learn times and population sizes on a tree. My focus then shifts to the derivation of the covariance between pairs of coalescence times and its application to studying average pairwise differences and the commonly used statistic, Fst. I confirm that estimates of Fst are biased, and quantify the effect of not accounting for this bias in different applications. I conclude by continuing to study the covariance between coalescence times and its use in inferring species tree topologies. I define a metric based on these statistics which, when paired with the minimum spanning tree algorithm, provides estimates of species tree topologies. I provide partial proofs of statistical consistency of the approach.

Advisor: Nielsen, Rasmus
Biosynthesis of isonitrile lipopeptides by conserved nonribosomal peptide synthetase gene clusters in Actinobacteria

Mycobacterium tuberculosis is the leading causative agent of tuberculosis, from/nwhich millions die annually. A putative lipopeptide biosynthetic gene cluster has been/nshown to be essential for the survival of this pathogen in hosts, and homologous gene/nclusters have also been found in all pathogenic mycobacteria and other species of/nActinobacteria. However, the specific functions of the encoded proteins have been/nelusive. Using both in vivo heterologous reconstitution and in vitro biochemical analyses,/nwe have revealed that the five encoded biosynthetic enzymes are capable of synthesizing/na family of isonitrile lipopeptides (INLPs) through a thio-template mechanism. The/nbiosynthesis features the generation of isonitrile from a single precursor Gly promoted by/na thioesterase and a nonheme iron(II)-dependent oxidase homolog and the acylation of/nboth amino groups of Lys by the same isonitrile acyl chain facilitated by a single/ncondensation domain of a nonribosomal peptide synthetase. Additionally, the/nbiosynthesis of this bioactive isonitrile moiety is extraordinary and is distinct from the/nIsnA family of isonitrile synthases. We herein provide the first structural and biochemical/nevidence of an alternative mechanism for isonitrile formation.

Advisor: Zhang, Wenjun
From Island to Museum: Narrating Puerto Rican Museum Object Itineraries

In a current political moment characterized by widespread diaspora movements and tense debates about the boundaries of national identities, the Caribbean case-study of the American commonwealth of Puerto Rico stands at an intersection as both American and a ‘cultural other.’/nThe historical and ever-developing contemporary narratives on Puerto Rico have long been dominated by macro-scale discussions of state-level events. An intervention in orientation towards thinking with archival and object sources introduces new forms of narratives that contribute on-the-ground material perspectives through a museum anthropological framework./nAs part of a larger research project on North American museum collecting in and representation of Puerto Rico between 1890-1990, the dissertation explores collection case-studies along varied object types and across different museums including national and university spaces. Tasked with the recovery, analysis, and interpretation of Puerto Rican collections in U.S. mainland museums, this comparative, multi-site object-based inquiry methodological approach works to redress a relative lack of Caribbean regional presence in existing museum anthropology and of museum as field-site historical analysis to cultural studies./nDiverse artifact groups – ranging in terms of material, time period, collector, and acquisition context – both evidence and trouble our ever-shifting understandings of the Commonwealth or unincorporated territory of Puerto Rico in the past and present as part of and set apart from the U.S. From miniature, rural-styled household objects commissioned by Spanish American officer wives to Pre-Columbian archaeological material entangled with growing U.S. economic dominance to contemporary carnival paraphernalia produced by craft-making island families and collected to document traditional practices by a local elite, Puerto Rican museum material indexes distinct microhistories within a complicated, evolving political narrative of U.S.-Puerto Rico relations. From local material experimentation in early tourist arts to unpublished archaeological notes written by a sugar plantation owner’s son to an island-wide photograph collection of Puerto Rico created by a suffragette for a public lecture, museum records grant differential access to the multiple, intersecting and sometimes conflicting gazes of the usually unnamed object makers and named museum collectors whose object definitions have shaped the course of Caribbean history - its tropes and silences.

Advisor: Joyce, Rosemary
Wilkie, Laurie
Waria Genres: Identity, Embodiment, and the Performance of Gendered Belonging in Contemporary Indonesia

Waria Genres: Identity, Embodiment, and the Performance of Gendered Belonging in Contemporary Indonesia describes the ways that the gendered body is experienced and produced for waria across performance genres within their geographic and historical contexts. It does so by describing, in dialogue with ethnographic and historical data, transformations in understandings and experiences of trans femininity within professional and amateur performance practices. The main focus of this thesis is the waria community, an Indonesian term which refers to diverse forms of gendered embodiment and social practices. Waria are persons who were assigned male at birth, yet practice a broad range of femininities. Given that embodiment and selfhood are understood by waria to be shaped by those with whom one interacts, a primary concern of this dissertation are understandings of waria generated between performers and audiences./n/nMy chief finding is that waria artists across generations actively construct gendered embodiments as a product of the intertwining forms of intimacy and self-making enabled through performance. Furthermore, I argue that the boundaries of waria intelligibility expand or constrict in relationship to genre. How then do embodied performance practices/nenable waria to narrate their own subjectivity and visibility—to help create the conditions for becoming waria? I answer this central question by analyzing how waria gendered embodiment is literally performed across genres with specific audiences and stages in mind and therefore consciously constructing the gendered performances in question. This suggests that while there is no stable embodiment to which all waria ascribe, their sense of gender and attendant performances are shaped by highly specific aesthetic and social scripts within their attendant historical and cultural contexts./n/nChapter one contextualizes “waria” by laying out histories of gender and “male-bodied femininity” within Indonesia as it relates to early generations of waria. Chapter two argues that waria actively negotiate the boundaries of their gender expression through involvement in formally gendered dance practices. Chapter three looks to how waria negotiate their most public stage—the street. Focusing on the pengamen street performance genre, I argue that waria renegotiate public perception in the face of difficult social and legislative pressures through street performance. Finally, chapter four looks to the genre of Lipsinc and the beauty practices that shape it. Here I argue that waria are able to cultivate space for embodied forms of gender that expand beyond accepted Indonesian regimes.

Advisor: Rodriguez, Juana M