VictorJuiz/thesis huggingface dataset:
Characterization of a Novel p53-Mettl3 Protein-Protein Interaction

The transcription factor p53, which can activate or repress gene expression, is known to be critical for suppressing tumorigenesis in humans and mice. Known as the guardian of the genome, p53 responds to DNA damage by inducing apoptosis, cell cycle arrest and senescence. p53 is a well characterized transcription factor involved in diverse cellular pathways, but its full protein interactome remains undefined. The Attardi lab has performed dual affinity purification and mass spectrometry to identify novel binding partners of mouse p53 and has developed a protein interactome for p53. One of the proteins identified in this interactome is Mettl3, which is a methyltransferase enzyme involved in the modification of RNA. It has been implicated in cellular differentiation, cell self-renewal and DNA-damage responses. We validated the interaction of p53 and Mettl3 by performing co-immunoprecipitation assays. Our data indicate that p53 does indeed co-immunoprecipitate with Mettl3 and corroborate the interaction between them as shown by affinity purification and mass spectrometry studies. We have shown that Mettl3 plays an important role in modulating p53 stability, and that Mettl3 deficiency results in decreased expression of several key p53 target genes in response to DNA damage. The findings in this study validate that Mettl3 interacts with p53 and that this interaction may have important implications in p53 biology.

Keywords:  Department of Biology
Biology
Cancer Biology
Thesis
Advisor: Attardi Laura
Dixon Scott
Characterization of arterial-venous cell fate plasticity during coronary vessel development

Understanding arterial-venous fate plasticity is important for innovating and improving vascular regenerative therapies. During coronary vessel development in the mouse, coronary arteries originate from a venous vessel. In this study, single-cell RNA-seq was used to investigate the characteristics of the arterial-venous fate switch during coronary vessel development. Results showed that instead of rapidly losing all arterial-venous identity as soon as they exit the vein, nascent coronary cells coexisted in a continuum of gradual venous fate loss and arterial fate gain. A rare subpopulation of surprisingly mature pre-artery cells within this continuum crossed a transcriptional threshold to resemble mature arterial cells. These pre-artery cells were specified at an unexpectedly early developmental stage, and they were necessary for coronary arteriogenesis. Modulations of the cell cycle was found to be an important regulator of arterial-venous plasticity: activation of the cell cycle correlated with the loss of venous identity, while inhibition of cell cycle was necessary for arterial redifferentiation. The transcription factor COUP-TF2 inhibited the development of the pre-artery cells by activating the cell cycle.

Keywords: Biology.
Advisor: Red-Horse Kristy
Krasnow Mark
Simon Michael (Biology professor)
Characterization of functional nucleic acid structure in translation, reverse transcription, and electronics applications

Ribonucleic acid (RNA) actively regulates all stages of genetic expression from transcription to translation. Actions performed by RNA molecules are made possible by the ability of RNA to fold into unique tertiary structures. Messenger RNA (mRNA) structure enables alternative translational pathways, such as frameshifting and bypassing, that recode the protein sequence. Transfer RNA (tRNA) structure is highly evolved for interfacing with the ribosome to maximize translational fidelity, but can be repurposed by retroviruses to act as a primer during reverse transcription. Ribosomal RNA (rRNA) is a majority component of the ribosome by mass and catalyzes amide bond formation between amino acids in a peptide chain. This work examines RNA structure in four systems: Escherichia coli rRNA, T4 bacteriophage mRNA, human tRNA, and synthetic conductive nanowires. Mutations in E. coli rRNA structure, as well as the effects of treatment with macrolide antibiotics, were probed by a novel quantitative fluorescent translation assay using the SNAPf reporter protein to evaluate changes in ribosomal processivity. The solution NMR structure of the T4 bacteriophage Gene 60 mRNA 5' stem-loop was solved, and the terminal loop sequence was determined to be important for the mechanism of translational bypassing. Human tRNALys3 in complex with HIV genomic RNA was also studied by solution NMR to reveal a unique structure adopted by the complex during HIV reverse transcription initiation. Finally, the thermal and chemical stability of Ag(I)-intercalated polycytosine nanowire structures was evaluated by enzymatic, spectrophotometric, and biophysical assays. These projects not only reflect the deep importance of RNA structure to all aspects of genetic expression but also highlight some of the applications of nucleic acid structure in bioengineering.

Keywords: Chemistry.
Advisor: Khosla Chaitan
Puglisi Joseph D. 
Solomon Edward I.
Characterization of Premixed Flames Using High Energy X-Ray Absorption

Experimental and numerical studies have shown that porous media burners (PMBs) can reduce many of the adverse effects of combustion. However, studying the porous microstructure of PMBs and the flames that stabilize within can be a difficult task. Recent advances in X-ray computed tomography (XCT) offer a non-invasive, high resolution technique that enables the investigation of three-dimensional (3D) fields such as temperature and density, which can be used to quantify the complex processes that occur within PMBs. The objective of this thesis work is to calibrate X-ray diagnostics and quantify uncertainties using well-characterized, stable flames, where temperature, gas concentrations, and flow velocities can be predictably controlled. A laboratory burner was designed and operated with a premixed methane/air/krypton flame. Flame characteristics for different setups and a range of equivalence ratios were studied using a tabletop X-ray system in the Stanford Medical School. The results obtained in this study demonstrate the usefulness of XCT in obtaining both quantitative and qualitative information about combustion experiments. Although this study focuses on simple systems that are optically accessible, the diagnostics developed can also be applied to other systems of interest that are optically inaccessible. This work furthers the recent development of XCT as a novel combustion diagnostic tool, capable of yielding non-intrusive 3D datasets in optically inaccessible environments.

Keywords:  Department of Mechanical Engineering
X-ray computed tomography
XCT
Pourous media burners
PMBs
combustion
Thesis
Advisor: Ihme Matthias
A characterization of the neural stem cell niche and lineage at single cell resolution during aging

The mammalian brain contains select neurogenic niches composed of neural stem cells (NSCs) and several other cell types, including microglia, and endothelial cells. Neurogenic niches become less functional with increasing age, and this decline could underlie cognitive and sensory deterioration. This functional deterioration could underlie cognitive and sensory restriction with age, although the exact age at which it occurs is still debated in humans. How the neurogenic niche changes with age, and whether new cell types arise in older individuals, is not known. Here we perform single cell RNA-sequencing of the young and old neurogenic niche in mice. We first show that cells in the youthful NSC lineage exist on a continuum through the processes of activation and differentiation. Interestingly, rare intermediate states with distinct molecular profiles can be identified and experimentally validated, and our analysis identifies putative surface markers and key intracellular regulators for these new subpopulations of NSCs. We also utilize the power of single cell profiling to conduct meta-analysis to compare in vivo NSCs and in vitro cultures, distinct fluorescent-activated cell sorting strategies, and different neurogenic niches. We go on to analyze the transcriptomes of 8993 single cells isolated in an unbiased fashion from the youthful and aged neurogenic niche. We identify clear age-dependent changes in the neurogenic niche, with a decrease in activated NSCs, changes in endothelial cells and microglia transcriptomes, and the striking appearance of T cells in old niches. T cells invading the old neurogenic niche exhibit characteristics of cytotoxic effector memory T cells. Surprisingly, T cells from old brains are clonally expanded, and express different T cell receptors than those from old blood, suggesting they experienced specific antigens. Furthermore, unlike their counterparts in old blood, old brain T cells express interferon γ (IFNγ) and immune checkpoint genes. Analysis of the response to IFNγ at the single cell level in the old neurogenic niche shows that several cell types, including NSCs, endothelial cells, and microglia, respond to IFNγ. The response of NSCs to IFNγ is heterogeneous, and the subset of NSCs experiencing a high IFN response shows decreased proliferation in vivo. Furthermore, IFNγ expressed by T cells was sufficient to inhibit NSC proliferation in co-cultures. Our study provides a system-level understanding of the old neurogenic niche and reveals the infiltration of T cells in old neurogenic niches. Our results also provide a possible cause for the decline of NSC during aging and could identify immune- or antigen-based strategies to ameliorate this decline.

Keywords: Stem Cell Biology and Regenerative Medicine.
Advisor: Brunet Anne
Palmer Theo 
Wyss-Coray Anton
Characterization of thermal systems using low level resistance measurements and the development and validation of a high-stability ALD platinum thermal accelerometer

The thermal properties of the materials used in microelectromechanical systems (MEMS) are of increasing concern as devices progressively miniaturize with improved fabrication technologies. Temperature sensitivity (or insensitivity) is often a major consideration for MEMS sensors, as many components of a sensor's output drift with and depend on temperature. Thus, thermal characterization should be a necessary step for any sensor material. This thesis begins with thermal conductivity measurements for size-limited highly-doped silicon and ALD platinum. Though these results were mainly internal to lab-group needs, the methods used are widely applicable to other studies. As MEMS manufacturing techniques and technologies advance and mature, previously encountered limitations should no longer be assumed. The thermal accelerometer is a device that has found limited use within the MEMS community, thanks to its high power consumption and notably low bandwidth. However, with new fabrication techniques the thermal accelerometer's performance can be pushed in new and exciting ways, potentially expanding its usability for a larger variety of applications. Here we present the results from the first thermal accelerometer fabricated using Plasma Enhanced Atomic Layer Deposition (PEALD). PEALD allows for ultra-thin, low defect, high-density platinum films that deliver excellent stability and accuracy. We offer a 100× cross-section reduction relative to previous thermal accelerometers, thereby increasing the heating efficiency and decreasing thermal time constants. The suspended resistance thermometers and heaters capitalize on the properties provided by PEALD and Pt: pronounced stability, high resistivity, and linear temperature coefficient of resistance (TcR), giving our device tractable and consistent results. For a heater temperature rise of 150 degrees C and acceleration between +/- 1g, this device has a raw sensitivity of 54e-3 C/g, excellent cross-axis isolation, high-linearity, and remarkably low drift.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William 
Goodson Kenneth E.
Prinz F. B.
Characterizing Temperature Variations in the Large Synoptic Survey Telescope Camera

We have measured how the temperature varies on a science raft for the Large Synoptic Survey Telescope (LSST) Camera, and have made preparations to repeat this test on the full Camera focal plane. Such tests are important in order to ensure that the LSST Camera behaves as expected in response to temperature changes, and in particular that spurious spatial patterns are not introduced into near-IR observations due to a spatially varying temperature profile. We describe first the construction of a Flat Field Projector that will be used to conduct a wide array of tests on the LSST Camera Focal Plane, including a test of temperature variation. Then we proceed to describe a pilot version of this test, in which a single LSST science raft was illuminated with flat fields at several temperatures and wavelengths. After developing several methods of removing fringe artifacts from these images we calculate the temperature variation, and find that the variation of the spatial pattern of temperature on a single raft is less than 0.25K when the bulk temperature is changed 10K, somewhat better than the specification of 0.5K variation.

Keywords:  Department of Physics
LSST
Large Synoptic Survey Telecope
Astronomy
Astronomical Instrumentation
CCD
Thesis
Advisor: Roodman Aaron J.
Burchat Patricia
Characterizing Toxin-Induced Neuronal Cell Death in Zebrafish

Zebrafish larvae are an ideal model organism for modeling spinal cord injury (SCI) and the subsequent biochemical response because of the unique ability to regenerate. Current methods to model injury suffer from a lack of cell specificity and reproducibility. By combining chemical and genetic tools, we can ablate cells in a spatiotemporal specific manner to model injury in the organism, as well as study regeneration. We developed a genetic method of neural ablation where SCI in zebra sh is initiated using encoded toxins, speci cally viral protein M2(H37A) and Nitroreductase (NTR), that are expressed within the CNS during development. Characterization of these toxins show that M2(H37A) kills more rapidly that NTR and leads to tissue loss throughout the CNS. Based on the speed and damaged caused by M2(H37A) we believe the viral toxin kills through necrosis, inducing apoptotic death in the surrounding cells due to activated Caspase-3 and TUNEL staining. A complete death and regeneration pro le following expression of M2(H37A) and NTR will develop a powerful model of SCI that can be applied widely. Transgenic zebra sh serve as a resource for studies investigating cell death and regeneration; and due to the severe and rapid ablation of M2(H37A) through a compound death mechanism, the toxic protein can be a tool of choice in injury modeling studies in a variety of model organisms.

Keywords: Stanford University
Chemical Engineering
ChEM-H
Chemical &amp; Systems Biology
Developmental Biology
Zebrafish
Model Organism
SCI
CNS
M2
NTR
Apoptosis
Necrosis
In situ hybridization
Honors Thesis
Thesis
Advisor: Mruk Karen
Chen James K.
Chemical approaches to the study of N-glycanase 1 : understanding NGLY1 deficiency and implications in cancer therapy

N-Glycanase 1 (NGLY1) is the human cytosolic protein N-glycosidase. The relationship between NGLY1 and the transcription factor Nrf1 is examined, particularly observing cellular response to proteasomal stress in healthy, NGLY1 deficient, and cancer model systems using genetic and chemical tools. Additionally, the role of NGLY1 in innate immunological signaling and other stress-response pathways that are regulated by the ERAD pathway is explored. Finally, the further development of the Quadricyclane (QC) ligation, a bioorthogonal reaction between QC and nickel bis(dithiolene) is described.

Keywords: Chemistry.
Advisor: Bertozzi Carolyn R.
Kool Eric T. 
Waymouth Robert M.
Chemical inhibition of apicoplast biogenesis

Malaria infections caused by Plasmodium spp. parasites are a serious public health problem that disproportionately affects the poorest and youngest people in the world. With 216 million infections occurring annually and growing resistance to all front-line drugs, we are in desperate need of new antimalarials with novel mechanisms-of-action. Plasmodium and other Apicomplexan parasites contain an essential, non-photosynthetic plastid organelle, called the apicoplast, which is a key antimalarial target. While the apicoplast was derived from a secondary endosymbiosis of a red alga, it is no longer photosynthetic and instead it participates in anabolic metabolism such as fatty acid, heme, iron-sulfur cluster, and isoprenoid biosynthesis. Apicoplast biogenesis depends on novel, but largely cryptic, mechanisms for the maintenance, replication, and inheritance of the organelle during parasite replication. These critical pathways present untapped opportunities to discover new parasite-specific drug targets. To discover novel factors involved in apicoplast biogenesis, we designed a chemical screen in Plasmodium falciparum to identify specific inhibitors of apicoplast biogenesis. This screen revealed the natural product antibiotic, actinonin, as a first-in-class antimalarial compound inhibiting apicoplast biogenesis. We further demonstrate that the unexpected target of actinonin in both P. falciparum and the related parasite Toxoplasma gondii is FtsH1, a AAA+ ATPase membrane metalloprotease. These findings provide an important proof-of-concept for inhibitors of apicoplast biogenesis, and lay a foundation for future studies on the role of FtsH1 in apicoplast biogenesis. Next, we provide a comparative characterization of the downstream cellular effects of the three major classes of apicoplast inhibitors in T. gondii. In contrast with P. falciparum, treatment of T. gondii with apicoplast inhibitors leads to loss of the apicoplast prior to growth defects. We find evidence that this surprising discrepancy is partially due to T. gondii's ability to scavenge host metabolites that are similar to apicoplast metabolites. Our results as whole demonstrate apicoplast biogenesis as an important and productive source of antimalarial drug targets that lead to complex downstream cellular effects that depend on the host cell environment.

Keywords: Microbiology and Immunology.
Advisor: Yeh Ellen
Bogyo Matthew
Kirkegaard Karla 
Straight Aaron
Chicha, Carporales y Charangos: Towards Building a "Soundscape of Migration" in Buenos Aires

This interdisciplinary exploration of aural cultures in Buenos Aires posits different genres of cumbia as comprising a “soundscape” of migration for Paraguayan, Bolivian and Peruvian immigrants residing in the porteño city. By close-reading two
films produced in the 2000s that have key scenes with cumbia soundtracks/performances (Bolivia and El niño pez) as well as formulating a proof-of-concept, temporal visualization of the movement of this aural culture across a city, I aimed to move towards theorizing on a soundscape of migration as itself a moving, migrating subject.

Keywords: Stanford University Center for Latin American Studies
Thesis
Children's information seeking during signed and spoken language processing

How do children comprehend and learn language despite noisy input and limits on their information processing capabilities? Social learning theories argue for the importance of acquiring language from more knowledgeable adults who can constrain the learning task. Statistical learning accounts emphasize the role of children's pattern detection abilities that can take advantage of the structure available in the input. Finally, active learning explanations focus on children's capacity to gather useful information to support their learning. This thesis presents an integrative explanation that brings together ideas from these theoretical accounts to investigate how children's information seeking adapts to learning within social contexts. I use the formalization of Optimal Experiment Design (OED) as a conceptual tool to bring together ideas from social and active learning. Then, I present a series of empirical studies motivated by the integrative account that ask how children's information seeking adapts during language processing across a diverse set of contexts: signed vs. spoken language (Chapters 2 and 3), (2) speech in clear vs. noisy environments (Chapter 3), and (3) novel words with or without an accompanied social cue to reference (Chapters 4 and 5). The upshot of the empirical work is that children are quite capable of flexibly seeking information from their communicative partners to support language processing.

Keywords: Psychology.
Advisor: Frank Michael C. (Professor of human biology) 
Gweon Hyowon
Marchman Virginia A. 
McClelland James L.
China's Security Cooperation: A Hidden Policy Dimension of the Belt and Road Initiative?

The modernization and increasing employment of the People’s Liberation Army (PLA) around the world lead many scholars to generate assumptions on the nature of the security policy of the People’s Republic of China (PRC). This thesis analyzes the historical development of PRC security concerns and their resultant security cooperation activities from. It explores the relationship between China’s security cooperation policies and the development of the Belt and Road Initiative (BRI) in Central Asia. In its early history, PRC security cooperation reflected the greater dynamics of the Cold War. The PRC conducted security cooperation and entered into conflict to support its ideological allies and balance against regional or global threats. Changing assessments of China’s security environment by Deng Xiaoping and subsequent leaders allowed the PRC to shift the focus of its security cooperation from preparation for imminent great-power conflict to supporting and enabling economic development and modernization. These new outlooks prompted evolution in PRC security cooperation activity. In some instances, PRC security considerations drove other policy priorities; security cooperation activity pioneered diplomatic or economic relationships. In other settings however, security cooperation quickly became an integral part, or even a consequence, of China’s greater development and engagement strategy. In the case of BRI development in Central and South Asian countries, PRC security cooperation addresses long-term, security-oriented relationship, fails to correlate with China’s investment activity, or is essentially non-existent. This thesis refutes monocausal characterizations of PRC security cooperation and finds a wide variance in its nature, motivation and conduct. This thesis also identifies a general trend of secular commercialization within PRC security cooperation that will aid in understanding China’s future security cooperation activity.

Keywords:  Stanford Global Studies
Stanford Global Studies
East Asian Studies
China
Central Asia
Security
Belt and Road Initiative
Security Cooperation
Thesis
Advisor: Fingar Thomas
Choice and Pro-Social Behavior: The Effect of Choosing Your Hands in a Virtual Reality Perspective-Taking Task

A 2017 study demonstrated taking the perspective of a homeless person in virtual reality (VR) is more effective at increasing empathy and pro-social behavior toward the homeless than other forms of perspective taking tasks. The present study aimed to replicate the results of the aforementioned study, as well as explore the difference in effects when participants chose the skin tone of their virtual hands, had hands assigned to them, or had no hands at all. Furthermore, this study looked at the variation in participants’ physical interaction with the virtual environment in the three conditions and whether tracking data could be used to predict if participants performed pro-social behavior toward the homeless. There was no significant difference in pro-social behavior between participants in the VR perspective taking conditions and participants in the control. Analysis of the tracking data showed no statistically significant differences in movement between the four conditions. Results also did not show a correlation between participant tracking data and whether or not participants performed pro-social behavior toward the homeless.

Keywords:  Department of Communication
virtual reality
empathy
Stanford University Department of Communication
Thesis
Advisor: Bailenson Jeremy