Negative regulators of a growth factor-mediated signaling pathway in the nematode Caenorhabditis elegans

Vulval differentiation in C. elegans is mediated by an Epidermal growth factor (EGF)- EGF receptor (EGFR) signaling pathway. I have cloned unc-101, a negative regulator of vulval differentiation of the nematode C. elegans. unc-101 encodes a homolog of AP47, the medium chain of the trans-Golgi clathrin-associated protein complex. This identity was confirmed by cloning and comparing sequence of a C. elegans homolog of AP50, the medium chain of the plasma membrane clathrin-associated protein complex. I provided the first genetic evidence that the trans-Golgi clathrin-coated vesicles are involved in regulation of an EGF signaling pathway. Most of the unc-101 alleles are deletions or nonsense mutations, suggesting that these alleles severely reduce the unc-101 activity. A hybrid gene that contains parts of unc-101 and mouse AP4 7 rescued at least two phenotypes of unc-101 mutations, the Unc and the suppression of vulvaless phenotype of let-23(sy1) mutation. Therefore, the functions of AP47 are conserved between nematodes and mammals.

unc-101 mutations can cause a greater than wild-type vulval differentiation in combination with certain mutations in sli-1, another negative regulator of the vulval induction pathway. A mutation in a new gene, rok-1, causes no defect by itself, but causes a greater than wild-type vulval differentiation in the presence of a sli-1 mutation. The unc-101; rok-1; sli-1 triple mutants display a greater extent of vulval differentiation than any double mutant combinations of unc-101, rok-1 and sli-1. Therefore, rok-1 locus defines another negative regulator of the vulval induction pathway.

I analyzed a second gene encoding an AP47 homolog in C. elegans. This gene, CEAP47, encodes a protein 72% identical to both unc-101 and mammalian AP47. A hybrid gene containing parts of unc-101 and CEAP47 sequences can rescue phenotypes of unc-101 mutants, indicating that UNC- 101 and CEAP47 proteins can be redundant if expressed in the same set of cells.

On the determination of the properties of a medium from its reflection coefficient

This thesis demonstrates how the parameters of a slightly non-homogeneous medium can be derived approximately from the reflection coefficient.

Two types of media are investigated. The first is described by the one-dimensional wave equation, the second by the more complex Timoshenko beam equation. In both cases, the media are assumed to be infinite in extent, with the media parameters becoming homogeneous as the space variable approaches positive or negative infinity.

Much effort is placed in deriving properties of the reflection coefficient for both cases. The wave equation is considered primarily to introduce the techniques used to investigate the more complex Timoshenko equation. In both cases, an approximation is derived for one of the medium parameters involving the reflection coefficient.

Wave propagation in an inhomogeneous medium

This paper is in two parts. In the first part we give a qualitative study of wave propagation in an inhomogeneous medium principally by geometrical optics and ray theory. The inhomogeneity is represented by a sound-speed profile which is dependent upon one coordinate, namely the depth; and we discuss the general characteristics of wave propagation which result from a source placed on the sound channel axis. We show that our mathematical model of the sound- speed in the ocean actually predicts some of the behavior of the observed physical phenomena in the underwater sound channel. Using ray theoretic techniques we investigate the implications of our profile on the following characteristics of SOFAR propagation: (i) the sound energy traveling further away from the axis takes less time to travel from source to receiver than sound energy traveling closer to the axis, (ii) the focusing of sound energy in the sound channel at certain ranges, (iii) the overall ray picture in the sound channel.

In the second part a more penetrating quantitative study is done by means of analytical techniques on the governing equations. We study the transient problem for the Epstein profile by employing a double transform to formally derive an integral representation for the acoustic pressure amplitude, and from this representation we obtain several alternative representations. We study the case where both source and receiver are on the channel axis and greatly separated. In particular we verify some of the earlier results derived by ray theory and obtain asymptotic results for the acoustic pressure in the far-field.

The intergalactic and circumgalactic medium surrounding star-forming galaxies at redshifts 2 < z < 3

We present measurements of the spatial distribution, kinematics, and physical properties of gas in the circumgalactic medium (CGM) of 2.0<z<2.8 UV color-selected galaxies as well as within the 2<z<3 intergalactic medium (IGM). These measurements are derived from Voigt profile decomposition of the full Lyα and Lyβ forest in 15 high-resolution, high signal-to-noise ratio QSO spectra resulting in a catalog of ∼6000 HI absorbers.

Chapter 2 of this thesis focuses on HI surrounding high-z star-forming galaxies drawn from the Keck Baryonic Structure Survey (KBSS). The KBSS is a unique spectroscopic survey of the distant universe designed to explore the details of the connection between galaxies and intergalactic baryons within the same survey volumes. The KBSS combines high-quality background QSO spectroscopy with large densely-sampled galaxy redshift surveys to probe the CGM at scales of ∼50 kpc to a few Mpc. Based on these data, Chapter 2 presents the first quantitative measurements of the distribution, column density, kinematics, and absorber line widths of neutral hydrogen surrounding high-z star-forming galaxies.

Chapter 3 focuses on the thermal properties of the diffuse IGM. This analysis relies on measurements of the ∼6000 absorber line widths to constrain the thermal and turbulent velocities of absorbing "clouds." A positive correlation between the column density of HI and the minimum line width is recovered and implies a temperature-density relation within the low-density IGM for which higher-density regions are hotter, as is predicted by simple theoretical arguments.

Chapter 4 presents new measurements of the opacity of the IGM and CGM to hydrogen-ionizing photons. The chapter begins with a revised measurement of the HI column density distribution based on this new absorption line catalog that, due to the inclusion of high-order Lyman lines, provides the first statistically robust measurement of the frequency of absorbers with HI column densities 14 ≲ log(N_HI/cm^-2) ≲ 17.2. Also presented are the first measurements of the column density distribution of HI within the CGM (50 <d < 300 pkpc) of high-z galaxies. These distributions are used to calculate the total opacity of the IGM and IGM+CGM and to revise previous measurements of the mean free path of hydrogen-ionizing photons within the IGM. This chapter also considers the effect of the surrounding CGM on the transmission of ionizing photons out of the sites of active star-formation and into the IGM.

This thesis concludes with a brief discussion of work in progress focused on understanding the distribution of metals within the CGM of KBSS galaxies. Appendix B discusses my contributions to the MOSFIRE instrumentation project.

Signal transduction with hybridization chain reactions

Some of the most exciting developments in the field of nucleic acid engineering include the utilization of synthetic nucleic acid molecular devices as gene regulators, as disease marker detectors, and most recently, as therapeutic agents. The common thread between these technologies is their reliance on the detection of specific nucleic acid input markers to generate some desirable output, such as a change in the copy number of an mRNA (for gene regulation), a change in the emitted light intensity (for some diagnostics), and a change in cell state within an organism (for therapeutics). The research presented in this thesis likewise focuses on engineering molecular tools that detect specific nucleic acid inputs, and respond with useful outputs.

Four contributions to the field of nucleic acid engineering are presented: (1) the construction of a single nucleotide polymorphism (SNP) detector based on the mechanism of hybridization chain reaction (HCR); (2) the utilization of a single-stranded oligonucleotide molecular Scavenger as a means of enhancing HCR selectivity; (3) the implementation of Quenched HCR, a technique that facilitates transduction of a nucleic acid chemical input into an optical (light) output, and (4) the engineering of conditional probes that function as sequence transducers, receiving target signal as input and providing a sequence of choice as output. These programmable molecular systems are conceptually well-suited for performing wash-free, highly selective rapid genotyping and expression profiling in vitro, in situ, and potentially in living cells.

Chain-forming zintl antimonides as novel thermoelectric materials

Zintl phases, a subset of intermetallic compounds characterized by covalently-bonded "sub-structures," surrounded by highly electropositive cations, exhibit precisely the characteristics desired for thermoelectric applications. The requirement that Zintl compounds satisfy the valence of anions through the formation of covalent substructures leads to many unique, complex crystal structures. Such complexity often leads to exceptionally low lattice thermal conductivity due to the containment of heat in low velocity optical modes in the phonon dispersion. To date, excellent thermoelectric properties have been demonstrated in several Zintl compounds. However, compared with the large number of known Zintl phases, very few have been investigated as thermoelectric materials.

From this pool of uninvestigated compounds, we selected a class of Zintl antimonides that share a common structural motif: anionic moieties resembling infinite chains of linked MSb₄ tetrahedra, where $M$ is a triel element. The compounds discussed in this thesis (A₅M₂Sb₆ and A₃MSb₃, where A = Ca or Sr and M = Al, Ga and In) crystallize as four distinct, but closely related "chain-forming" structure types. This thesis describes the thermoelectric characterization and optimization of these phases, and explores the influence of their chemistry and structure on the thermal and electronic transport properties. Due to their large unit cells, each compound exhibits exceptionally low lattice thermal conductivity (0.4 - 0.6 W/mK at 1000 K), approaching the predicted glassy minimum at high temperatures. A combination of Density Functional calculations and classical transport models were used to explain the experimentally observed electronic transport properties of each compound. Consistent with the Zintl electron counting formalism, A₅M₂Sb₆ and A₃MSb₃ phases were found to have filled valence bands and exhibit intrinsic electronic properties. Doping with divalent transition metals (Zn²⁺ and Mn²⁺) on the M³⁺ site, or Na¹⁺ on the A³⁺ site allowed for rational control of the carrier concentration and a transition towards degenerate semiconducting behavior. In optimally-doped samples, promising peak zT values between 0.4 and 0.9 were obtained, highlighting the value of continued investigations of complex Zintl phases.

Phase conjugation via four-wave mixing in a resonant medium

This thesis describes the theoretical solution and experimental verification of phase conjugation via nondegenerate four-wave mixing in resonant media. The theoretical work models the resonant medium as a two-level atomic system with the lower state of the system being the ground state of the atom. Working initially with an ensemble of stationary atoms, the density matrix equations are solved by third-order perturbation theory in the presence of the four applied electro-magnetic fields which are assumed to be nearly resonant with the atomic transition. Two of the applied fields are assumed to be non-depleted counterpropagating pump waves while the third wave is an incident signal wave. The fourth wave is the phase conjugate wave which is generated by the interaction of the three previous waves with the nonlinear medium. The solution of the density matrix equations gives the local polarization of the atom. The polarization is used in Maxwell's equations as a source term to solve for the propagation and generation of the signal wave and phase conjugate wave through the nonlinear medium. Studying the dependence of the phase conjugate signal on the various parameters such as frequency, we show how an ultrahigh-Q isotropically sensitive optical filter can be constructed using the phase conjugation process.

In many cases the pump waves may saturate the resonant medium so we also present another solution to the density matrix equations which is correct to all orders in the amplitude of the pump waves since the third-order solution is correct only to first-order in each of the field amplitudes. In the saturated regime, we predict several new phenomena associated with degenerate four-wave mixing and also describe the ac Stark effect and how it modifies the frequency response of the filtering process. We also show how a narrow bandwidth optical filter with an efficiency greater than unity can be constructed.

In many atomic systems the atoms are moving at significant velocities such that the Doppler linewidth of the system is larger than the homogeneous linewidth. The latter linewidth dominates the response of the ensemble of stationary atoms. To better understand this case the density matrix equations are solved to third-order by perturbation theory for an atom of velocity v. The solution for the polarization is then integrated over the velocity distribution of the macroscopic system which is assumed to be a gaussian distribution of velocities since that is an excellent model of many real systems. Using the Doppler broadened system, we explain how a tunable optical filter can be constructed whose bandwidth is limited by the homogeneous linewidth of the atom while the tuning range of the filter extends over the entire Doppler profile.

Since it is a resonant system, sodium vapor is used as the nonlinear medium in our experiments. The relevant properties of sodium are discussed in great detail. In particular, the wavefunctions of the 3S and 3P states are analyzed and a discussion of how the 3S-3P transition models a two-level system is given.

Using sodium as the nonlinear medium we demonstrate an ultrahigh-Q optical filter using phase conjugation via nondegenerate four-wave mixing as the filtering process. The filter has a FWHM bandwidth of 41 MHz and a maximum efficiency of 4 x 10^-3. However, our theoretical work and other experimental work with sodium suggest that an efficient filter with both gain and a narrower bandwidth should be quite feasible.

Applications of nuclear magnetic resonance spectroscopy to the study of medium-sized rings. I. Conformational properties of cycloheptane. II. Conformational properties of cycloöctane

Conformational equilibrium in medium-sized rings has been investigated by the temperature variation of the fluorine-19 n.m.r. spectra of 1, 1-difluorocycloalkanes and various substituted derivatives of them. Inversion has been found to be fast on the n.m.r. time scale at -180˚ for 1, 1-difluorocycloheptane, but slow for 1, 1-difluoro-4, 4-dimethylcycloheptane at -150˚. At low temperature, the latter compound affords a single AB pattern with a chemical-shift difference of 841 cps. which has been interpreted in terms of the twist-chair conformation with the methyl groups on the axis position and the fluorine atoms in the 4-position. At room temperature, the n.m.r. spectrum of 1, 1-difluoro-4-t-butylcycloheptane affords an AB pattern with a chemical-shift difference of 185 cps. The presence of distinct trans and gauche couplings from the adjacent hydrogens has been interpreted to suggest the existence of a single predominant form, the twist chair with the fluorine atoms on the axis position.

Investigation of 1, 1-difluorocycloöctane and 1, 1, 4, 4-tetrafluorocycloöctane has led to the detection of two kinetic processes both having activation energies of 8-10 kcal./mole but quite different A values. In light of these results eleven different conformations of cycloöctane along with a detailed description of the ways in which they may be interconverted are discussed. An interpretation involving the twist-boat conformation rapidly equilibrating through the saddle and the parallel-boat forms at room temperature is compatible with the results.

A Multiwavelength Study of the Intracluster Medium and the Characterization of the Multiwavelength Sub/millimeter Inductance Camera

The first part of this thesis combines Bolocam observations of the thermal Sunyaev-Zel’dovich (SZ) effect at 140 GHz with X-ray observations from Chandra, strong lensing data from the Hubble Space Telescope (HST), and weak lensing data from HST and Subaru to constrain parametric models for the distribution of dark and baryonic matter in a sample of six massive, dynamically relaxed galaxy clusters. For five of the six clusters, the full multiwavelength dataset is well described by a relatively simple model that assumes spherical symmetry, hydrostatic equilibrium, and entirely thermal pressure support. The multiwavelength analysis yields considerably better constraints on the total mass and concentration compared to analysis of any one dataset individually. The subsample of five galaxy clusters is used to place an upper limit on the fraction of pressure support in the intracluster medium (ICM) due to nonthermal processes, such as turbulent and bulk flow of the gas. We constrain the nonthermal pressure fraction at r500c to be less than 0.11 at 95% confidence, where r500c refers to radius at which the average enclosed density is 500 times the critical density of the Universe. This is in tension with state-of-the-art hydrodynamical simulations, which predict a nonthermal pressure fraction of approximately 0.25 at r500c for the clusters in this sample.

The second part of this thesis focuses on the characterization of the Multiwavelength Sub/millimeter Inductance Camera (MUSIC), a photometric imaging camera that was commissioned at the Caltech Submillimeter Observatory (CSO) in 2012. MUSIC is designed to have a 14 arcminute, diffraction-limited field of view populated with 576 spatial pixels that are simultaneously sensitive to four bands at 150, 220, 290, and 350 GHz. It is well-suited for studies of dusty star forming galaxies, galaxy clusters via the SZ Effect, and galactic star formation. MUSIC employs a number of novel detector technologies: broadband phased-arrays of slot dipole antennas for beam formation, on-chip lumped element filters for band definition, and Microwave Kinetic Inductance Detectors (MKIDs) for transduction of incoming light to electric signal. MKIDs are superconducting micro-resonators coupled to a feedline. Incoming light breaks apart Cooper pairs in the superconductor, causing a change in the quality factor and frequency of the resonator. This is read out as amplitude and phase modulation of a microwave probe signal centered on the resonant frequency. By tuning each resonator to a slightly different frequency and sending out a superposition of probe signals, hundreds of detectors can be read out on a single feedline. This natural capability for large scale, frequency domain multiplexing combined with relatively simple fabrication makes MKIDs a promising low temperature detector for future kilopixel sub/millimeter instruments. There is also considerable interest in using MKIDs for optical through near-infrared spectrophotometry due to their fast microsecond response time and modest energy resolution. In order to optimize the MKID design to obtain suitable performance for any particular application, it is critical to have a well-understood physical model for the detectors and the sources of noise to which they are susceptible. MUSIC has collected many hours of on-sky data with over 1000 MKIDs. This work studies the performance of the detectors in the context of one such physical model. Chapter 2 describes the theoretical model for the responsivity and noise of MKIDs. Chapter 3 outlines the set of measurements used to calibrate this model for the MUSIC detectors. Chapter 4 presents the resulting estimates of the spectral response, optical efficiency, and on-sky loading. The measured detector response to Uranus is compared to the calibrated model prediction in order to determine how well the model describes the propagation of signal through the full instrument. Chapter 5 examines the noise present in the detector timestreams during recent science observations. Noise due to fluctuations in atmospheric emission dominate at long timescales (less than 0.5 Hz). Fluctuations in the amplitude and phase of the microwave probe signal due to the readout electronics contribute significant 1/f and drift-type noise at shorter timescales. The atmospheric noise is removed by creating a template for the fluctuations in atmospheric emission from weighted averages of the detector timestreams. The electronics noise is removed by using probe signals centered off-resonance to construct templates for the amplitude and phase fluctuations. The algorithms that perform the atmospheric and electronic noise removal are described. After removal, we find good agreement between the observed residual noise and our expectation for intrinsic detector noise over a significant fraction of the signal bandwidth.

I. The attenuation and dispersion of sound in a condensing medium. II. The flow of a gas-particle mixture downstream of a normal shock in a nozzle

I. The attenuation of sound due to particles suspended in a gas was first calculated by Sewell and later by Epstein in their classical works on the propagation of sound in a two-phase medium. In their work, and in more recent works which include calculations of sound dispersion, the calculations were made for systems in which there was no mass transfer between the two phases. In the present work, mass transfer between phases is included in the calculations.

The attenuation and dispersion of sound in a two-phase condensing medium are calculated as functions of frequency. The medium in which the sound propagates consists of a gaseous phase, a mixture of inert gas and condensable vapor, which contains condensable liquid droplets. The droplets, which interact with the gaseous phase through the interchange of momentum, energy, and mass (through evaporation and condensation), are treated from the continuum viewpoint. Limiting cases, for flow either frozen or in equilibrium with respect to the various exchange processes, help demonstrate the effects of mass transfer between phases. Included in the calculation is the effect of thermal relaxation within droplets. Pressure relaxation between the two phases is examined, but is not included as a contributing factor because it is of interest only at much higher frequencies than the other relaxation processes. The results for a system typical of sodium droplets in sodium vapor are compared to calculations in which there is no mass exchange between phases. It is found that the maximum attenuation is about 25 per cent greater and occurs at about one-half the frequency for the case which includes mass transfer, and that the dispersion at low frequencies is about 35 per cent greater. Results for different values of latent heat are compared.

II. In the flow of a gas-particle mixture through a nozzle, a normal shock may exist in the diverging section of the nozzle. In Marble’s calculation for a shock in a constant area duct, the shock was described as a usual gas-dynamic shock followed by a relaxation zone in which the gas and particles return to equilibrium. The thickness of this zone, which is the total shock thickness in the gas-particle mixture, is of the order of the relaxation distance for a particle in the gas. In a nozzle, the area may change significantly over this relaxation zone so that the solution for a constant area duct is no longer adequate to describe the flow. In the present work, an asymptotic solution, which accounts for the area change, is obtained for the flow of a gas-particle mixture downstream of the shock in a nozzle, under the assumption of small slip between the particles and gas. This amounts to the assumption that the shock thickness is small compared with the length of the nozzle. The shock solution, valid in the region near the shock, is matched to the well known small-slip solution, which is valid in the flow downstream of the shock, to obtain a composite solution valid for the entire flow region. The solution is applied to a conical nozzle. A discussion of methods of finding the location of a shock in a nozzle is included.

Nuclear magnetic resonance studies of protein conformation: I. Ribonuclease S. II. Hemoglobin

Fluorine nuclear magnetic resonance techniques have been used to study conformational processes in two proteins labeled specifically in strategic regions with covalently attached fluorinated molecules. In ribonuclease S, the ϵ-amino groups of lysines 1 and 7 were trifluoroacetylated without diminishing enzymatic activity. As inhibitors bound to the enzyme, changes in orientation of the peptide segment containing the trifluoroacetyl groups were detected in the nuclear magnetic resonance spectrum. pH Titration of one of the histidines in the active site produced a reversal of the conformational process.

Hemoglobin was trifluoroacetonylated at the reactive cysteine 93 of each β chain. The nuclear magnetic resonance spectrum of the fluorine moiety reflected changes in the equilibrium position of the β chain carboxy terminus upon binding of heme ligands and allosteric effectors. The chemical shift positions observed in deoxy- and methemoglobin were pH dependent, undergoing an abnormally steep apparent titration which was not observed in hemoglobin from which histidine β 146 had been removed enzymatically. The abnormal sharpness of these pH dependent processes is probably due to interactions between several ionizing groups.

The carbon monoxide binding process was studied by concurrent observation of the visible and nuclear magnetic resonance spectra of trifluoroacetonylated hemoglobin at fractional ligand saturations throughout the range 0-1.0. Comparison of the ligand binding process observed in these two ways yields evidence for a specific order of ligand binding. The sequence of events is sensitive to the pH and organic phosphate concentration of the medium, demonstrating the delicately balanced control system produced by interactions between the hemoglobin subunits and the effectors.