12023 research outputs found
Sort by
Retroviral Lineage Analysis of the Vagal Neural Crest Reveals Multipotency Towards the Cardiac and Enteric Fates
Get PDFThe neural crest is a migratory stem cell population that gives rise to the craniofacial skeleton, heart septa, pigment cells, and peripheral nervous system. Defects in neural crest development can lead to a broad range of congenital diseases, e.g., persistent truncus arteriosus, characterized by a mixture of oxygenated and deoxygenated blood, is related to the absence of the neural crest-derived outflow tract septum. Thus, a thorough understanding about neural crest migration, differentiation, and cell fate can shine lights on diagnosis and treatment of many congenital defects. A long-standing question is whether neural crest cells are composed of multipotent cells capable of giving rise to a wide range of cell types, or a mixture of fate-determined cells migrating to their destinations. Avian embryos resemble humans during neural crest development, but are more accessible to experimental manipulations than mammalian models, making them an ideal model to study the neural crest. Despite the abundance of information obtained from elegant experiments through interspecies grafting, the avian model lacks a direct tool to determine whether these cells are multipotent in vivo.
Here, we present a new clonal analysis tool that takes advantage of Replication Incompetent Avian retroviruses (RIAs). We validate the method in vitro and present the potential application in the chick embryo to test the multipotency of the trunk neural crest. Next, we perform RIA-mediated lineage tracing at a population level and uncover cardiomyocytes as a previously unknown cardiac neural crest derivative in both chicken and mouse. Furthermore, we utilize RIA-mediated clonal analysis to identify individual premigratory vagal neural crest cells as a multipotent stem cell that forms cell types in both the heart and the gut. We then confirm the results by single-cell photoconversion assay that further confirms that migrating neural crest cells are also multipotent. Time-lapse imaging shows that stochastic post-mitotic migration is a cellular mechanism underlying multipotency. Finally, molecular perturbation experiments show that CXCR4 and RET are essential guidance cues for migratory neural crest cells to enter the heart and the gut, respectively. Together, these results demonstrate the utility of using RIA viruses to tackle questions regarding the lineage, developmental potential, and migratory pathways followed by neural crest cells in avian embryos.</p
Non-Thermal Optical Engineering of Strongly-Correlated Quantum Materials
Get PDFThis thesis develops multiple optical engineering mechanisms to modulate the electronic, magnetic, and optical properties of strongly-correlated quantum materials, including polar metals, transition metal trichalcogenides, and copper oxides. We established the mechanisms of Floquet engineering and magnon bath engineering, and used optical probes, especially optical nonlinearity, to study the dynamics of these quantum systems.
Strongly-correlated quantum materials host complex interactions between different degrees of freedom, offering a rich phase diagram to explore both in and out of equilibrium. While static tuning methods of the phases have witnessed great success, the emerging optical engineering methods have provided a more versatile platform. For optical engineering, the key to success lies in achieving the desired tuning while suppressing other unwanted effects, such as laser heating.
We used sub-gap optical driving in order to avoid electronic excitation. Therefore, we managed to directly couple to low-energy excitation, or to induce coherent light-matter interactions. In order to elucidate the exact microscopic mechanisms of the optical engineering effects, we performed photon energy-dependent measurements and thorough theoretical analysis. To experimentally access the engineered quantum states, we leveraged various probe techniques, including the symmetry-sensitive optical second harmonic generation (SHG), and performed pump-probe type experiments to study the dynamics of quantum materials.
I will first introduce the background and the motivation of this thesis, with an emphasis on the principles of optical engineering within the big picture of achieving quantum material properties on demand (Chapter I). I will then continue to introduce the main probe technique used in this thesis: SHG. I will also introduce the experimental setups which we developed and where we conducted the works contained in this thesis (Chapter II). In Chapter III, I will introduce an often overlooked aspect of SHG studies -- using SHG to study short-range structural correlations. Chapter IV will contain the theoretical analysis and experimental realizations of using sub-gap and resonant optical driving to tune electronic and optical properties of MnPS₃. The main tuning mechanism used in this chapter is Floquet engineering, where light modulates material properties without being absorbed. In Chapter V, I will turn to another useful material property: magnetism. First I will describe the extension of the Floquet mechanism to the renormalization of spin exchange interaction. Then I will switch gears and describe the demagnetization in Sr₂Cu₃O₄Cl₂ by resonant coupling between photons and magnons. I will end the thesis with a brief closing remark (Chapter VI).</p
Evaluation of Flow Rate and Leakage on Mask Effectiveness and Investigation of Double Masks
Get PDFMask-wearing emerged as the primary safety measure to prevent spreading COVID-19. During the COVID-19 pandemic, there was growing evidence that SARS-CoV-2 could spread by aerosol transmission. Thus, increased understanding of mask performance was important to help reduce viral transmission. In addition, the CDC recommended wearing double masks to provide better fit and additional protection when people could not access respirators. This thesis aims to investigate the performance of single mask and double mask combinations, and using a parallel resistance model to quantify leakage.
Multiple copies of different mask types were tested: N95 respirators, KN95 respirators, procedure masks, and cloth masks. For all of the single masks, the penetration increased with flow rate, while the most penetrating particle size (MPPS) generally decreased. The peak penetration is lowest for N95 respirators, and the peak penetration is highest for cloth masks at all flow rates. For double masking, we observe that wearing a combination of cloth and procedure masks has a higher amount of decreased penetration and a lower amount of increased pressure drop than a combination involving N95 and KN95 respirators. For quantifying leakage, a parallel resistance model was used to calculate the resistance for leaks. The procedure and cloth masks had lower resistance for leaks and leakage flow rates than N95 and KN95 respirators. The procedure and cloth masks are more susceptible to leaks than respirators and thus reducing the effectiveness of these masks.</p
Cosmology and Astrophysics with Intensity Mapping
Get PDFIntensity mapping (IM) has emerged as a promising technique to probe the largescale structures and galaxy formation and evolution across cosmic history. As IM measures the aggregate emission from all sources, it can overcome the limitation of conventional detection-based observations, where the emission from diffuse populations and high-redshift faint galaxies cannot be resolved individually. As several IM experiments will come online in the next decade, demand for IM modeling and data analysis strategies has increased. In this thesis, we present a range of analysis techniques, theoretical modeling, and data analysis results related to IM.
In Chapter 2, we aim to answer the question: When should we use IM? We present a formalism to describe both IM and galaxy detection (GD) approaches, and use it to quantify their individual performance when measuring the large-scale structure (LSS). With this formalism, we can identify the scenarios where each approach is advantageous. We also develop a simple metric for determining the optimal strategy to map the LSS with future experiments.
In Chapters 3 and 4, we interrogate methods for improving the line intensity mapping (LIM) analysis. LIM traces the three-dimensional structure of the universe by probing the emission field from a spectral line. One particular challenge for LIM is to separate the target line signals from interloper lines along the line of sight in order to extract the desired cosmological and astrophysical information. Previously proposed methods of line de-blending, such as masking and cross-correlation, rely on the external galaxy tracers, but sometimes a galaxy catalog with sufficient depth and sky coverage does not exist. Therefore, we develop two new methods for performing line de-confusion that do not require any external information. The first method (Chapter 3) uses the distinct shape of large-scale two-dimensional power spectra of signals and interlopers to distinguish the line emission from different redshifts. The second method (Chapter 4) reconstructs the intensity maps of individual lines from LIM data in the phase space, using multiple lines from the same source to identify the source redshift. We show that both of our methods are able to effectively extract desired line signals from the upcoming LIM experiments.
In Chapter 5, we discuss the application of IM for studying the extragalactic background light (EBL), the integrated light from all sources of emission in the universe. Previous studies on the fluctuations of the EBL indicate that the intra-halo light (IHL) has a significant contribution to the near-infrared EBL. Chapter 5 presents the results on probing the IHL using a stacking analysis of images from the Cosmic Infrared Background Experiment (CIBER). CIBER is a rocket-borne experiment designed to image and perform photometry of the near-infrared EBL. Our results suggest that at z ∼ 0.3 the IHL comprises a large fraction of light associated with ∼ L∗ galaxies, implying that the IHL accounts for a non-negligible fraction of the near-infrared cosmic radiation budget.
In Chapter 6, we present a forecast on the EBL constraints with the upcoming SPHEREx mission. We consider cross correlating SPHEREx intensity maps with galaxy catalogs from several current and future surveys. Our model predicts that the EBL spectrum as a function of redshift can be detected from the local universe to the epoch of reionization.
The analysis techniques developed in this thesis can help better extract the information from the IM data; the future IM experiments will extend our current works on investigating the EBL. Therefore, the research in this thesis provides important toolkits and foundations for upcoming IM experiments.</p
Physical Biology of Cellular Information Processing
Get PDFThe state of matter that we define as life is different from anything else we have encountered so far in the universe. Living systems not only perpetuate their existence out of equilibrium against the will of the second law of thermodynamics, but they do so while keeping up with an ever-changing environment. A key part of this capacity to adapt to environmental changes is the ability of organisms to gather information from their surroundings to put together an adequate response to the challenges presented to them. This thesis presents an effort to understand, from first principles, this fundamental feature of information gathering that all life on earth shares. We dig into the physics behind one of the most pervasive mechanisms through which living systems sense and respond to the environment–the ability to turn on and off genes. In doing so, we hope to uncover general principles of how organisms deal with the problem of collecting information about the world that surrounds them.
In Chapter 1, we develop the theoretical and conceptual tools to navigate the rest of the thesis. I introduce the idea of gene regulation, as well as different theoretical models of this pervasive biological phenomenon. We also delve into the realm of information theory and learn how the plastic concept of information can be mathematically defined and quantified.
The second stop in our exploration (Chapter 2) asks the following question: can we understand, from first principles, how it is that proteins allow cells to regulate their genes on-demand upon sensing environmental cues? For this, we explore the physics behind transcriptional control due to allosteric transcription factors. Using simple quasi-equilibrium models of the two processes involved in this type of regulation—the regulation of the gene by the binding and unbinding of the transcription factor, and the regulation of the activity of the transcription factor itself by the binding and unbinding of an effector molecule—we are able to predict the input-output function of a simple genetic circuit, and compare such predictions with experimental determinations of the mean response of a population of bacterial cells.
We then expand on these insights to ask questions about the inescapable cell-to-cell variability that isogenic cells encounter. For this, we have to leave behind the pure thermodynamic framework and work in the language of chemical kinetics. This allows us to make predictions beyond the mean input-output gene expression response of cells by reconstructing full gene expression distributions. With these probabilistic input-output functions, in Chapter 3 we formalize the question of the amount of information that cells can gather from the environment. For this, we turn to information-theoretic concepts of maximal mutual information (otherwise known as channel capacity) between the state of the environment and the gene expression response from bacterial cells. Finally, we compare our predictions of the maximum amount of information—measured in bits—that cells can gather with single-cell inferences of this quantity.</p
Precision Measurement of the Neutron Lifetime
Get PDFThe neutron lifetime plays a critical role in Big Bang nucleosynthesis (BBN) calculations, and measurements of the neutron lifetime can also be used to probe the unitarity of the Cabibbo-Kobayashi-Maskawa quark weak mixing matrix. Most experiments that measure the neutron lifetime fall into two classes: "bottle" and "beam" experiments. A bottle experiment stores neutrons in a bottle and counts the number of neutrons that do not decay. A beam experiment counts the decay products of a beam of neutrons that passes through an electrostatic trap. An unresolved ≈ 4σ difference remains between the current global averages of measurements of the neutron lifetime using the bottle method and measurements using the beam method. This difference is the dominant uncertainty in BBN calculations of the helium mass fraction in the early universe. The UCNτ experiment is a bottle experiment which uses a magneto-gravitational trap to store ultra-cold neutrons (UCN) without any physical interactions between the UCN and the walls of the trap. The UCN that do not decay are counted with an in situ detector that is lowered into the trap. These two features stand in contrast to most past bottle experiments, which had to make significant corrections to the extracted lifetime to account for losses of neutrons due to material interactions with walls and losses while removing the neutrons from the bottle in order to be counted. This thesis will present an analysis of the 2017-2018 UCNτ data set that extracted a value for the neutron lifetime of 877.79 ± 0.27 (stat.) +0.19-0.12 (sys.) s. This measurement has an uncertainty of roughly half of the current global average for the neutron lifetime.</p
Discrete Deligne Cohomology and Discretized Abelian Chern-Simons Theory
Get PDFThe differential cohomology groups of a smooth manifold are discretized with respect to a triangulation. The realization of differential cohomology used is Deligne cohomology. A discretized version of the smooth Deligne double complex is constructed from cochain groups defined on simplices of the triangulation. The total cohomology of this double complex is studied and shown to satisfy exact sequences analogous to the standard structural sequences satisfied by differential cohomology. In the degree corresponding to line bundles with connection, our cohomology classes are shown to correspond to isomorphism classes of an existing notion of discrete line bundles with connection. Explicit examples of these discrete line bundles with connection are constructed. A ring structure is defined on the discrete Deligne cohomology groups; it is graded-commutative and non-associative (however, associativity is recovered in the continuum limit). The ring structure allows one to define a more general discrete Chern-Simons action than has previously appeared in the literature.</p
Engineering Logical Inflammation Sensing and Secreting Circuit for Gut Modulation
Get PDFThe mammalian gut contains trillions of microbes that interact with host cells and monitor changes in the environment. Opportunistic pathogens exploit environmental conditions to stimulate their growth and virulence, leading to a resurgence of chronic disorders such as inflammatory bowel disease (IBD). Current therapies are effective in less than 30% of patients due to the lack of adherence to prescription schedules and overall, off-target effects. Microbial therapeutics can be engineered to colonize the gut, providing in situ surveillance and conditional disease modulation. However, many current engineered microbes can only respond to single gut environmental factors, limiting their effectiveness. In this work, we implement a previously characterized split activator AND logic gate in the probiotic E. coli strain Nissle 1917. Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, IPTG or aTC. We report 4-6 fold induction with minimal leak when both signals are present. We model the dynamics of the AND gate using chemical reaction networks, and by tuning parameters in silico, we identified perturbations that affect our circuit’s selectivity. We then engineer our optimized AND gate to secrete an anti-inflammatory therapeutic cytokine, IL-22, using the hemolysin secretion pathway. We anticipate that our results will prove useful for designing living therapeutics for spatial targeting and signal processing in complex environments.</p
Biocatalytic Lactone Carbene C–H, B–H, and N–H Insertion Reactions Enabled by Directed Evolution
Get PDFEnzymes are biological catalysts, and they accelerate reactions by lowering the activation barrier. In nature, enzymes have been optimized by natural selection and possess precise three-dimensional active sites. With these active sites, they can typically catalyze reactions with high efficiency and specificity. Compared to traditional catalysts, enzymes are generally more environmentally friendly, and they can catalyze reactions in water and at ambient temperature and pressure. However, native enzymes are usually only well suited for a restricted range of substrates and are limited in the types of reactions they perform. The Arnold lab has recently focused on endowing enzymes with the ability to catalyze new-to-nature reactions through directed evolution. Here, we present a set of enzymes engineered for the ability to insert a lactone carbene into B–H, C–H, and N–H bonds with high yield and enantioselectivity. B–H insertion is achieved by engineered cytochrome c enzymes, while N–H and C–H insertions are achieved by engineered cytochrome P450 enzymes. With this work, we expand nature’s toolbox for lactone insertion chemistry. Since lactones are highly bioactive, these engineered enzymes could be powerful tools in the synthesis of a range of pharmaceuticals and natural product targets
Precision at Scale: System Design from Tiny Biosensors to Giant Arrays
Get PDFIn order to change the world, technological advancements must be made affordable and available for the general public to use. In other words, we must be able to scale our inventions effectively. Silicon integrated circuits are crucial components in scaling electronic systems because they are mass producible and offer a phenomenal cost-to-complexity ratio. This thesis summarizes the author’s work on highly scalable sensor and array systems. It presents three high precision systems, that demonstrate how the use of highly functional radio-frequency integrated circuits enables the realization of previously unfeasible architectures