12023 research outputs found
Sort by
The Neural Basis of Sodium Appetite
Get PDFFluid homeostasis, which maintains a stable internal environment, is critical for survival. Body fluid is tightly monitored and regulated through its main components, water and salt. Here, I focus on the aspect of sodium regulation when sodium is the main cation in the extracellular fluid and is also required for primary metabolism. The depletion of sodium induces the retention of sodium but also a central mechanism to obtain sodium from the external sources. This need for sodium specifically drives animals towards sodium consumption, called sodium appetite. Even though sodium appetite is specific for only sodium ion, sodium appetite observed as an innate behavior across the animal kingdom.
Sodium appetite is strictly regulated by both peripheral sensory signals and central appetite signals. Due to the development of genetic tools, I was able to investigate the neural basis of sodium appetite from searching sodium appetite dedicated neurons. Here, I identify two genetically defined neural circuits in mice that control sodium intake. The activation of these neurons drives robust sodium intake in sated animals. Particularly, prodynorphin expressing neurons in the pre-locus coeruleus shown specific consumption to sodium compounds, including rock salt. In terms of loss-of-function, inhibition of these neurons selectively reduced sodium consumption. It was further shown that these neurons receive sodium depleted signals by aldosterone-sensitive neurons.
Previously, it was suggested that taste signals have a central role in sodium satiation. I demonstrate that the oral detection of sodium rapidly suppresses sodium appetite neurons. The blockage of the sodium taste or gastric infusion of sodium abolished the sodium suppression in the sodium appetite neurons. Consistently, gastric infusion of sodium did not cause sodium satiation. Moreover, retrograde-viral methods showed that specific inhibitory neurons partially mediate sensory modulation in the bed nucleus of the stria terminalis.
Together, I identified a specific neural population as a functional unit for sodium appetite. By knowing the dedicated circuits for sodium appetite, I demonstrated chemosensory and physiological signals regulate the neural circuits. The genetically defined neural population can be handle as an entry point of further investigation of the neural basis of sodium appetite.</p
Modeling the Impact of Biomass Combustion on Atmospheric Aerosol
Get PDFBiomass burning is a significant source of atmospheric particulate matter less than 2.5 micrometers in diameter (PM2.5) and encompasses a variety of activities, fuels, and emissions profiles. A significant portion of the world population relies on solid biofuels for cooking and other household activities. Residential use of solid biofuels can have negative impacts on human health, particularly in southeast Asia, and contribute to ambient air quality. In addition, wildfires are of increasing concern as climate changes and human activity expands further into the wildland-urban interface. Understanding the contributions of biomass combustion to air quality is critical for creating mitigation strategies.
In this work, the impact of biomass burning on air quality is examined using numerical and observational methods. The Community Multiscale Air Quality modeling system (CMAQ) and the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) are used to study two biomass burning scenarios: the combustion of solid biofuels for cooking in rural India and the November 2018 Camp Fire in northern California. Model simulations are combined with surface and satellite observational data to evaluate their performance as well as their applicability to health and economic impact assessment studies. Additionally, discrepancies in methods used in laboratory experiments and field studies of cookstove emissions are investigated. Contributions of cookstove and wildfire emissions to PM2.5 are estimated, and climate and health co-benefits of residential solid biofuel use is assessed. This thesis strives to expand the current understanding of sources of PM2.5 and provide a base for future computational studies of biomass burning impacts on air quality, climate, and human health.</p
Modifying Ultrasound Waveform Parameters to Control, Influence, or Disrupt Cells
Get PDFUltrasound can be focused into deep tissues with millimeter precision to perform non-invasive ablative therapy for diseases such as cancer. In most cases, this ablation uses high intensity ultrasound to deposit non-selective thermal or mechanical energy at the ultrasound focus, damaging both healthy bystander tissue and cancer cells. Here we describe an alternative low intensity pulsed ultrasound approach known as “oncotripsy” that leverages the distinct mechanical properties of neoplastic cells to achieve inherent cancer selectivity. We show that when applied at a specific frequency and pulse duration, focused ultrasound selectively disrupts a panel of breast, colon, and leukemia cancer cell models in suspension without significantly damaging healthy immune or red blood cells. Mechanistic experiments reveal that the formation of acoustic standing waves and the emergence of cell-seeded cavitation lead to cytoskeletal disruption, expression of apoptotic markers, and cell death. The inherent selectivity of this low intensity pulsed ultrasound approach offers a potentially safer and thus more broadly applicable alternative to non-selective high intensity ultrasound ablation.
In this dissertation, I describe the oncotripsy theory in its initial formulation, the experimental validation and investigation of testable predictions from that theory, and the refinement of said theory with new experimental evidence. Throughout, I describe how careful modifications to the ultrasound waveform directly can significantly impact how the ultrasound bio-effects control, influence, or disrupt cells in a selective and controlled manner.</p
Towards Single Molecule Imaging Using Nanoelectromechanical Systems
Get PDFWe incorporate nanoelectromechanical systems (NEMS) into a state-of-the-art commercial mass spectrometer (Q Exactive Plus with Orbitrap detection). This unique hybrid instrument is capable of ionizing molecules up to 4.5 MDa in their intact native state, isolating molecules of interest according to their mass-to-charge ratio, performing high resolution mass spectrometry (MS), and delivering those molecules to the NEMS. We use NEMS optimized for detecting the inertial mass of adsorbed species directly, which contrasts with indirect measurements of the mass-to-charge ratio performed with typical instruments. This unique form of mass spectrometry, NEMS-MS, with its single-molecule sensitivity, has promising applications to the fields of proteomics and native mass spectrometry, including deep proteomic profiling, single-cell proteomics, mass spectrometry-based imaging, or identifying viruses in their in vivo state.
We analyze intact E. coli GroEL chaperonin, a noncovalent 801 kDa complex consisting of 14 identical subunits. GroEL was sent to NEMS operated with the first two vibrational modes monitored in real time. Molecules physisorbing to the NEMS cause an abrupt shift in its resonance frequencies. The change in resonance frequencies is used to calculate the mass of each molecule. A mass spectrum is compiled with a main peak of 846 kDa, close to the expected value, and a secondary peak resolved near twice the mass of GroEL.
Measurements are then performed operating the first three modes simultaneously. Using a technique called inertial imaging, frequency shifts are used to calculate the first three mass moments: mass, position, and variance (size). This is used to distinguish between adsorbates arriving in a single, point-like distribution or a more extended distribution, thus demonstrating a rudimentary form of molecular imaging.
Two new theories are presented for analyzing frequency-shift data. The first approach offers a more streamlined approach for calculating the mass moments. This approach is used to improve the mass spectrum of the GroEL calculated using three-mode data, producing a main peak almost fully resolved at 805 kDa. An entirely different approach is presented that allows for obtaining the mass density distribution of an adsorbed molecule (i.e., imaging) with a higher number of modes.</p
Leveraging the Rest-Ultraviolet and Rest-Optical Spectra of Galaxies at 2 < z < 3
Get PDFGalaxies at the peak of cosmic star formation (2 < z < 3) are fundamentally different from local galaxies, in terms of the properties of their massive stellar populations and physical conditions in the interstellar medium (ISM). This thesis presents a detailed analysis of the stellar and nebular properties of high-redshift galaxies, using the rest-frame UV and rest-frame optical spectra of galaxies from the Keck Baryonic Structure Survey (KBSS), a large, targeted spectroscopic survey of galaxies at 2 < z < 3.
Chapter 2 compares inferences of dust attenuation, star formation, and metallicity from strong nebular emission lines, the far-UV continuum, and spectral energy distribution (SED) fits. These results indicate that the majority of high-redshift galaxies display different dust properties than those at low redshift, and that the assumption of a dust attenuation curve can dramatically change inferred properties such as star formation rates (SFRs). I find that SFRs estimated using different methods only agree under specific combinations of assumptions, and caution that SFR calibrations established in the local Universe do not apply at higher redshifts.
Chapter 3 utilizes rest-UV absorption lines to study the outflow kinematics of high-redshift galaxies. I compare several velocity metrics used in the literature, and search for correlations between outflow velocity and galaxy properties. These results are consistent with the picture of winds driven by momentum injected into the ISM by stellar feedback. I confirm that large-scale outflows are ubiquitous at high redshift due to these galaxies' high SFRs and compact sizes.
Finally, Chapter 4 analyzes the systematic uncertainties involved in fitting stellar population synthesis (SPS) models to rest-UV spectra as well as the full SEDs of galaxies. I quantify differences in galaxy parameters estimated using different combinations of models and assumptions, and explore the dependence of the rest-UV portion of model spectra on stellar metallicity and population age.</p
High-Resolution Photoacoustic Spectroscopy of the Oxygen A-Band
Get PDFThere have been many advances in recent years in remote sensing and ground-based measurement technologies utilizing optical detection to identify and quantify species in the atmosphere. Many of these instruments record high signal-to-noise spectra requiring sophisticated spectral modeling beyond the Voigt profile. In order to properly quantify the higher order spectral effects, high-resolution laboratory data measuring samples of known composition under carefully controlled conditions are required.
The oxygen A-band is used in a number of atmospheric composition measurements due to the uniform, well-known concentration of oxygen throughout the atmosphere. Previous laboratory A-band measurements using cavity ring-down spectroscopy and Fourier transform spectroscopy have greatly improved the understanding of spectral parameters. However, current spectral models are insufficient to fit some high quality remote sensing data, such as the OCO missions. The largest spectroscopic uncertainties in modeling result from characterization of line mixing and collision-induced absorption. These collisional effects, resulting in small absorption changes in the baseline and wings, which become more prominent at elevated pressures can be accurately measured with photoacoustic spectroscopy, a background free measurement with a large dynamic range producing high signal-to-noise spectra.
A novel high-resolution photoacoustic spectrometer was designed and constructed to improve the understanding of A-band spectral parameters to meet the OCO mission goals. The spectrometer is capable of measuring both the P and R-branches of the A-band up to J'=28 with a signal-to-noise ratio of 30,000 for pressures of 50-4,000 Torr. A temperature control system was also implemented to allow for measurements over the range of atmospherically relevant temperatures.
Results from spectral fitting of data from the newly developed spectrometer provide the most accurate A-band pressure shift coefficients for both oxygen and air measured to date. The data also indicates the importance of lineshape profile choice for resonant absorption in order to accurately characterize line mixing and collision-induced absorption; the speed-dependent Nelkin-Ghatak profile is required for the current data set. Finally, preliminary fitting of line mixing and collision-induced absorption suggests the photoacoustic data achieves the required sensitivity to provide improved understanding of line mixing and collision-induced absorption based on fundamental physical principles.</p
Attributes of the [4Fe4S] Cofactor Coordinated by UvrC, a DNA Repair Enzyme
Get PDFProtein-bound iron sulfur clusters are critical in cells and allow proteins to carry out many essential functions as electron carriers, catalysts for challenging organic reactions, and sensors of cellular environments. A wide range of protein families are known to coordinate iron sulfur clusters, and a growing category includes proteins involved in maintenance of the genome. Within the last three decades, iron sulfur clusters have been demonstrated to be important for enzymes that function in DNA repair, DNA replication, and transcription pathways. To date, iron sulfur clusters in the cubane [4Fe4S] geometry with all cysteine ligands have been exclusively reported for DNA repair and replication enzymes. In contrast to enzymes where the cofactor is necessary for active site chemistry or directly-linked to protein function, the [4Fe4S] cluster in the overwhelming majority of repair and replication enzymes is not involved in the catalytic modification of DNA substrates. Rather, the role of the cofactor appears to vary in function from protein to protein, and has been demonstrated to be important for protein stability, in the assembly of multisubunit proteins, and for substrate recognition, among other roles. Through investigations of the redox chemistry of the cofactor, our group has found that these enzymes participate in DNA-mediated charge transport chemistry, the process through which electrons rapidly migrate through well-stacked, duplex DNA. Long-range, DNA-mediated redox signaling provides a means of rapid communication among DNA-processing proteins for organizing repair and replication activities across the nucleus.
Notably, the first observations of the [4Fe4S] cofactor associated with repair and replications enzymes has consistently occurred well after the first biochemical studies of these enzymes. In some cases, the demonstration of a [4Fe4S] center has taken place decades later after initial work. Some proteins have required use of anaerobic methods in order to detect the cofactor, perhaps explaining why in some cases the metal center had eluded observation. Analysis of protein sequences might be expected to help accelerate identification of new iron sulfur centers in repair and replication enzymes. However, even with the abundance of sequencing data available in the post-genomic era, prediction of a metal center based on sequences alone has been challenging. This is in large part because the spacing of the coordinating cysteine residues can be quite irregular, leading to a weak bioinformatic signature.
Identifying proteins with overlooked [4Fe4S] cofactors poses an exciting challenge, and there are some elegant examples in the literature where data from genetics assays has been used in combination with careful sequence analysis to predict and discover iron sulfur centers in repair and replication enzymes. Described here is the evolution of our studies on one well-known repair enzyme from Escherichia coli, UvrC. UvrC is part of the nucleotide excision repair pathway in the Bacteria domain which is responsible for addressing the wide class of bulky, helix-distorting lesions that can form after exposure to sources such as ultraviolet light, cigarette smoke, chemotherapeutics, and protein-DNA crosslinks. UvrC, an excision nuclease with two distinct active sites that incise the phosphodiester backbone on either side of the site of damage, has been historically challenging to study. Given how essential UvrC is in repairing damaged substrates, new insight has been greatly needed.
Through integration of several key reports from the literature regarding the sequence of UvrC and evidence that pointed to a cofactor from genetics assays, our group predicted that UvrC is a [4Fe4S] protein. Development of a new overexpression system and an anaerobic purification method allowed for isolation of UvrC in holo form. We used spectroscopic techniques to confirm that the cluster type was [4Fe4S], and a combination of spectroscopy and chromatography to demonstrate that the UvrC-bound cofactor is susceptible to oxidative degradation. We also found that loss of the cofactor, either through aerobic degradation or mutation of coordinating cysteines, is associated with aggregation of apoprotein. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 ± 20 nM and 80 ± 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with DNA-bound midpoint potential of 90 mV vs. NHE.
The work detailed in this dissertation has highlighted how critical the [4Fe4S] center is for UvrC, where the cofactor has been implicated in protein stabilization, substrate binding, and redox signaling on DNA. Handling an apo form of UvrC may have led to the previous challenges catalogued by researchers. Through the development of entirely new methods to study UvrC under anaerobic conditions, many opportunities are now available to study UvrC and the NER pathway anew in vitro and in vivo. Such work will contribute additional insight on how iron sulfur clusters are essential for enzymes that maintain genomic integrity.</p
Electromagnetism is Time Reversible and the Magnetic Field is a Dynamical Condition
No full textElectromagnetism is Time Reversible and the Magnetic Field is a Dynamical Condition Examining the symmetries under which physical theories are invariant has been a particularly important part of physics in the 20th century. All of the fundamental forces of nature ( gravitation, electromagnetism, the weak force, and the strong force ) are normally considered to be time reversible, symmetric with respect to the forward and backward directions in time. These theories are time reversible in the sense that there exists a transformation under which the laws are invariant which includes a reversal of time. This is controversial, and proposals by people like Albert suggest that a time reversible theory should allow a straightforward reversal of time without additional transformations. They argue that theories beyond Newtonian mechanics, such as classical electromagnetism, are not time reversible in this sense, and provide reasons why. In this essay, I will present a counterargument, showing that even within the scheme outlined by Albert, classical electromagnetism is time reversal
invariant
Statistical Methods for Gene Differential Expression Analysis of RNA-Sequencing
Get PDFRNA-Sequencing ("RNA-Seq") is performed to measure gene expression, often to ask the question of what genes are differentially expressed across various biological conditions. Statistical methods have been used to model RNA-Seq quantifications in order to determine differential expression, and have traditionally be divided into gene-level methods and transcript-level methods. There has been little attempt to connect the statistical divide, although transcript expression and gene expression are biologically inextricably linked. In this thesis, we provide a case study of a comparative differential expression analysis, demonstrating that many differential expression events happen on the isoform-level, and that performing an analysis using only summarized gene quantifications would fail to capture these events. Furthermore, we develop statistical methods that unify the transcript-level and gene-level analysis. In bulk RNA-Seq, by using p-value aggregation methods, we are able to translate transcript-level results into gene-level results under a unified framework. For single cell RNA-Seq, we propose using multiple logistic regression, leveraging the high dimensionality of the data in order to determine if the transcript quantifications pertaining to a gene are able to constitute a linear discriminant for cell type. This method combines differential transcript expression analysis and differential gene expression analysis into a unified framework which we call “gene differential expression.” Lastly, we demonstrate that our methods could be used on transcript compatibility counts instead of transcript quantifications in order to bypass ambiguous read assignment and improve accuracy. We show that transcript compatibility counts obtained via transcriptome pseudoalignment are comparable in quantification accuracy to quantifications from genome alignment methods.</p
Nanophotonic Structures: Fundamentals and Applications in Narrowband Transmission Color Filtering
Get PDFThe optical properties of materials can be manipulated by structures roughly the size of the wavelength of light of interest. For visible wavelengths, many different types of structures sized on the order of 10s-100s of nanometers have been used to engineer materials to produce a targeted optical response. Multilayer stacks of nanoscale metal and dielectric films are a widely explored geometry that has been used to make composite materials with effective optical properties that vary significantly from their constituent films. In this thesis, carefully designed multilayer stacks were used to induce artificial magnetism in non-magnetic materials, opening new directions for tailoring wave propagation in optical media. By perforating these multilayer structures with an array of sub-wavelength slits, these nanophotonic structures were shown to be able to function as narrowband transmission color filters. Using numerical optimization methods, these narrowband filterswere further refined and simplified to only require a single thin film sandwiched between two mirrors to achieve this high resolution spectral filtering. Novel methods were used to fabricate these ultracompact narrowband transmission color filters, which were shown to possess extremely narrow transmission resonances that can be controllably pushed across the visible and near IR parts of the spectrum. These mirrored color filters have footprints as small as 400 nm, well below the size of state-of-the-art CMOS pixels, inviting the possibility for integrating multi- and hyperspectral imaging capabilities into small portable electronic devices.</p