Sunyaev-Zel'dovich observations using large-format millimeter arrays

Galaxy clusters are the largest gravitationally bound objects in the observable universe, and they are formed from the largest perturbations of the primordial matter power spectrum. During initial cluster collapse, matter is accelerated to supersonic velocities, and the baryonic component is heated as it passes through accretion shocks. This process stabilizes when the pressure of the bound matter prevents further gravitational collapse. Galaxy clusters are useful cosmological probes, because their formation progressively freezes out at the epoch when dark energy begins to dominate the expansion and energy density of the universe. A diverse set of observables, from radio through X-ray wavelengths, are sourced from galaxy clusters, and this is useful for self-calibration. The distributions of these observables trace a cluster's dark matter halo, which represents more than 80% of the cluster's gravitational potential. One such observable is the Sunyaev-Zel'dovich effect (SZE), which results when the ionized intercluster medium blueshifts the cosmic microwave background via Compton scattering. Great technical advances in the last several decades have made regular observation of the SZE possible. Resolved SZE science, such as is explored in this analysis, has benefitted from the construction of large-format camera arrays consisting of highly sensitive millimeter-wave detectors, such as Bolocam. Bolocam is a submillimeter camera, sensitive to 140 GHz and 268 GHz radiation, located at one of the best observing sites in the world: the Caltech Submillimeter Observatory on Mauna Kea in Hawaii. Bolocam fielded 144 of the original spider web NTD bolometers used in an entire generation of ground-based, balloon-borne, and satellite-borne millimeter wave instrumention. Over approximately six years, our group at Caltech has developed a mature galaxy cluster observational program with Bolocam. This thesis describes the construction of the instrument's full cluster catalog: BOXSZ. Using this catalog, I have scaled the Bolocam SZE measurements with X-ray mass approximations in an effort to characterize the SZE signal as a viable mass probe for cosmology. This work has confirmed the SZE to be a low-scatter tracer of cluster mass. The analysis has also revealed how sensitive the SZE-mass scaling is to small biases in the adopted mass approximation. Future Bolocam analysis efforts are set on resolving these discrepancies by approximating cluster mass jointly with different observational probes.

Synthesis and matrix isolated photolysis of 2,3-dimethylbicyclo [2.2.0]hexa-2,5-diene-1,4-dicarboxylic acid anhydride: a potential percursor to 2,3-dimethyl-1,4-dehydrobenzene

The synthesis of the first member of a new class of Dewar benzenes has been achieved. The synthesis of 2,3- dimethylbicyclo[2.2.0]hexa-2,5-diene-1, 4-dicarboxylic acid and its anhydride are described. Dibromomaleic anhydride and dichloroethylene were found to add efficiently in a photochemical [2+2] cycloaddition to produce 1,2-dibromo- 3,4-dichlorocyclobutane-1,2-dicarboxylic acid. Removal of the bromines with tin/copper couple yielded dichloro- cyclobutenes which added to 2-butyne under photochemical conditions to yield 5,6-dichloro-2,3-dimethylbicyclo [2.2.0] hex-2-ene dicarboxylic acids. One of the three possible isomers yielded a stable anhydride which could be dechlorinated using triphenyltin radicals generated by the photolysis of hexaphenylditin.

Photolysis of argon matrix isolated 2,3-dimethylbicyclo [2.2.0]hexa-2, 5-diene-1,4-dicarboxylic acid anhydride produced traces whose strongest bands in the infrared were at 3350 and 600 cm^(-1). This suggested the formation of terminal acetylenes. The spectra of argon matrix isolated E- and Z- 3,4-dimethylhexa-1,5-diyne-3-ene and cis-and trans-octa- 2,6-diyne-4-ene were compared with the spectrum of the photolysis products. Possibly all four diethynylethylenes were present in the anhydride photolysis products. Gas chromatograph-mass spectral analysis of the volatiles from the anhydride photolysis again suggested, but did not confirm, the presence of the diethynylethylenes.

Geochemistry and resonance ionization of platinum-group elements

Experimental studies were conducted with the goals of 1) determining the origin of Pt- group element (PGE) alloys and associated mineral assemblages in refractory inclusions from meteorites and 2) developing a new ultrasensitive method for the in situ chemical and isotopic analysis of PGE. A general review of the geochemistry and cosmochemistry of the PGE is given, and specific research contributions are presented within the context of this broad framework.

An important step toward understanding the cosmochemistry of the PGE is the determination of the origin of POE-rich metallic phases (most commonly εRu-Fe) that are found in Ca, AJ-rich refractory inclusions (CAI) in C3V meteorites. These metals occur along with γNi-Fe metals, Ni-Fe sulfides and Fe oxides in multiphase opaque assemblages. Laboratory experiments were used to show that the mineral assemblages and textures observed in opaque assemblages could be produced by sulfidation and oxidation of once homogeneous Ni-Fe-PGE metals. Phase equilibria, partitioning and diffusion kinetics were studied in the Ni-Fe-Ru system in order to quantify the conditions of opaque assemblage formation. Phase boundaries and tie lines in the Ni-Fe-Ru system were determined at 1273, 1073 and 873K using an experimental technique that allowed the investigation of a large portion of the Ni-Fe-Ru system with a single experiment at each temperature by establishing a concentration gradient within which local equilibrium between coexisting phases was maintained. A wide miscibility gap was found to be present at each temperature, separating a hexagonal close-packed εRu-Fe phase from a face-centered cubic γNi-Fe phase. Phase equilibria determined here for the Ni-Fe-Ru system, and phase equilibria from the literature for the Ni-Fe-S and Ni-Fe-O systems, were compared with analyses of minerals from opaque assemblages to estimate the temperature and chemical conditions of opaque assemblage formation. It was determined that opaque assemblages equilibrated at a temperature of ~770K, a sulfur fugacity 10 times higher than an equilibrium solar gas, and an oxygen fugacity 10⁶ times higher than an equilibrium solar gas.

Diffusion rates between -γNi-Fe and εRu-Fe metal play a critical role in determining the time (with respect to CAI petrogenesis) and duration of the opaque assemblage equilibration process. The diffusion coefficient for Ru in Ni (D^Ru_Ni) was determined as an analog for the Ni-Fe-Ru system by the thin-film diffusion method in the temperature range of 1073 to 1673K and is given by the expression:

D^Ru_Ni (cm² sec^-1) = 5.0(±0.7) x 10^-3 exp(-2.3(±0.1) x 10¹² erg mole^-1/RT) where R is the gas constant and T is the temperature in K. Based on the rates of dissolution and exsolution of metallic phases in the Ni-Fe-Ru system it is suggested that opaque assemblages equilibrated after the melting and crystallization of host CAI during a metamorphic event of ≥ 10³ years duration. It is inferred that opaque assemblages originated as immiscible metallic liquid droplets in the CAI silicate liquid. The bulk compositions of PGE in these precursor alloys reflects an early stage of condensation from the solar nebula and the partitioning of V between the precursor alloys and CAI silicate liquid reflects the reducing nebular conditions under which CAI were melted. The individual mineral phases now observed in opaque assemblages do not preserve an independent history prior to CAI melting and crystallization, but instead provide important information on the post-accretionary history of C3V meteorites and allow the quantification of the temperature, sulfur fugacity and oxygen fugacity of cooling planetary environments. This contrasts with previous models that called upon the formation of opaque assemblages by aggregation of phases that formed independently under highly variable conditions in the solar nebula prior to the crystallization of CAI.

Analytical studies were carried out on PGE-rich phases from meteorites and the products of synthetic experiments using traditional electron microprobe x-ray analytical techniques. The concentrations of PGE in common minerals from meteorites and terrestrial rocks are far below the ~100 ppm detection limit of the electron microprobe. This has limited the scope of analytical studies to the very few cases where PGE are unusually enriched. To study the distribution of PGE in common minerals will require an in situ analytical technique with much lower detection limits than any methods currently in use. To overcome this limitation, resonance ionization of sputtered atoms was investigated for use as an ultrasensitive in situ analytical technique for the analysis of PGE. The mass spectrometric analysis of Os and Re was investigated using a pulsed primary Ar⁺ ion beam to provide sputtered atoms for resonance ionization mass spectrometry. An ionization scheme for Os that utilizes three resonant energy levels (including an autoionizing energy level) was investigated and found to have superior sensitivity and selectivity compared to nonresonant and one and two energy level resonant ionization schemes. An elemental selectivity for Os over Re of ≥ 10³ was demonstrated. It was found that detuning the ionizing laser from the autoionizing energy level to an arbitrary region in the ionization continuum resulted in a five-fold decrease in signal intensity and a ten-fold decrease in elemental selectivity. Osmium concentrations in synthetic metals and iron meteorites were measured to demonstrate the analytical capabilities of the technique. A linear correlation between Os⁺ signal intensity and the known Os concentration was observed over a range of nearly 10⁴ in Os concentration with an accuracy of ~ ±10%, a millimum detection limit of 7 parts per billion atomic, and a useful yield of 1%. Resonance ionization of sputtered atoms samples the dominant neutral-fraction of sputtered atoms and utilizes multiphoton resonance ionization to achieve high sensitivity and to eliminate atomic and molecular interferences. Matrix effects should be small compared to secondary ion mass spectrometry because ionization occurs in the gas phase and is largely independent of the physical properties of the matrix material. Resonance ionization of sputtered atoms can be applied to in situ chemical analysis of most high ionization potential elements (including all of the PGE) in a wide range of natural and synthetic materials. The high useful yield and elemental selectivity of this method should eventually allow the in situ measurement of Os isotope ratios in some natural samples and in sample extracts enriched in PGE by fire assay fusion.

Phase equilibria and diffusion experiments have provided the basis for a reinterpretation of the origin of opaque assemblages in CAI and have yielded quantitative information on conditions in the primitive solar nebula and cooling planetary environments. Development of the method of resonance ionization of sputtered atoms for the analysis of Os has shown that this technique has wide applications in geochemistry and will for the first time allow in situ studies of the distribution of PGE at the low concentration levels at which they occur in common minerals.

Proteomic analysis of the Cdc48/Ubx network identifies a role for Ubx2 in the regulation of lipid biosynthesis

Cdc48/p97 is an essential, highly abundant hexameric member of the AAA (ATPase associated with various cellular activities) family. It has been linked to a variety of processes throughout the cell but it is best known for its role in the ubiquitin proteasome pathway. In this system it is believed that Cdc48 behaves as a segregase, transducing the chemical energy of ATP hydrolysis into mechanical force to separate ubiquitin-conjugated proteins from their tightly-bound partners.

Current models posit that Cdc48 is linked to its substrates through a variety of adaptor proteins, including a family of seven proteins (13 in humans) that contain a Cdc48-binding UBX domain. As such, due to the complexity of the network of adaptor proteins for which it serves as the hub, Cdc48/p97 has the potential to exert a profound influence on the ubiquitin proteasome pathway. However, the number of known substrates of Cdc48/p97 remains relatively small, and smaller still is the number of substrates that have been linked to a specific UBX domain protein. As such, the goal of this dissertation research has been to discover new substrates and better understand the functions of the Cdc48 network. With this objective in mind, we established a proteomic screen to assemble a catalog of candidate substrate/targets of the Ubx adaptor system.

Here we describe the implementation and optimization of a cutting-edge quantitative mass spectrometry method to measure relative changes in the Saccharomyces cerevisiae proteome. Utilizing this technology, and in order to better understand the breadth of function of Cdc48 and its adaptors, we then performed a global screen to identify accumulating ubiquitin conjugates in cdc48-3 and ubxΔ mutants. In this screen different ubx mutants exhibited reproducible patterns of conjugate accumulation that differed greatly from each other, pointing to various unexpected functional specializations of the individual Ubx proteins.

As validation of our mass spectrometry findings, we then examined in detail the endoplasmic-reticulum bound transcription factor Spt23, which we identified as a putative Ubx2 substrate. In these studies ubx2Δ cells were deficient in processing of Spt23 to its active p90 form, and in localizing p90 to the nucleus. Additionally, consistent with reduced processing of Spt23, ubx2Δ cells demonstrated a defect in expression of their target gene OLE1, a fatty acid desaturase. Overall, this work demonstrates the power of proteomics as a tool to identify new targets of various pathways and reveals Ubx2 as a key regulator lipid membrane biosynthesis.

Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging

Bio-orthogonal non-canonical amino acid tagging (BONCAT) is an analytical method that allows the selective analysis of the subset of newly synthesized cellular proteins produced in response to a biological stimulus. In BONCAT, cells are treated with the non-canonical amino acid L-azidohomoalanine (Aha), which is utilized in protein synthesis in place of methionine by wild-type translational machinery. Nascent, Aha-labeled proteins are selectively ligated to affinity tags for enrichment and subsequently identified via mass spectrometry. The work presented in this thesis exhibits advancements in and applications of the BONCAT technology that establishes it as an effective tool for analyzing proteome dynamics with time-resolved precision.

Chapter 1 introduces the BONCAT method and serves as an outline for the thesis as a whole. I discuss motivations behind the methodological advancements in Chapter 2 and the biological applications in Chapters 2 and 3.

Chapter 2 presents methodological developments that make BONCAT a proteomic tool capable of, in addition to identifying newly synthesized proteins, accurately quantifying rates of protein synthesis. I demonstrate that this quantitative BONCAT approach can measure proteome-wide patterns of protein synthesis at time scales inaccessible to alternative techniques.

In Chapter 3, I use BONCAT to study the biological function of the small RNA regulator CyaR in Escherichia coli. I correctly identify previously known CyaR targets, and validate several new CyaR targets, expanding the functional roles of the sRNA regulator.

In Chapter 4, I use BONCAT to measure the proteomic profile of the quorum sensing bacterium Vibrio harveyi during the time-dependent transition from individual- to group-behaviors. My analysis reveals new quorum-sensing-regulated proteins with diverse functions, including transcription factors, chemotaxis proteins, transport proteins, and proteins involved in iron homeostasis.

Overall, this work describes how to use BONCAT to perform quantitative, time-resolved proteomic analysis and demonstrates that these measurements can be used to study a broad range of biological processes.

Analysis of a concrete arch highway bridge reinforced with structural steel

An article in the Engineering News-Record for March 30, 1923, describes a new concrete arch bridge across the Connecticut River between Springfield and West Springfield, Mass.

Depth-sensitive analysis of fluorine on lunar sample surfaces and in carbonaceous chondrites by a nuclear resonant reaction technique

The nuclear resonant reaction ¹⁹F(ρ,αγ)¹⁶O has been used to perform depth-sensitive analyses of fluorine in lunar samples and carbonaceous chondrites. The resonance at 0.83 MeV (center-of-mass) in this reaction is utilized to study fluorine surface films, with particular interest paid to the outer micron of Apollo 15 green glass, Apollo 17 orange glass, and lunar vesicular basalts. These results are distinguished from terrestrial contamination, and are discussed in terms of a volcanic origin for the samples of interest. Measurements of fluorine in carbonaceous chondrites are used to better define the solar system fluorine abundance. A technique for measurement of carbon on solid surfaces with applications to direct quantitative analysis of implanted solar wind carbon in lunar samples is described.

Applications of a nuclear technique for depth-sensitive hydrogen analysis : trapped H in lunar samples and the hydration of terrestrial obsidian

The resonant nuclear reaction ¹⁹F(p,αy)¹⁶O has been used to perform depth-sensitive analyses for both fluorine and hydrogen in solid samples. The resonance at 0.83 MeV (center-of-mass) in this reaction has been applied to the measurement of the distribution of trapped solar protons in lunar samples to depths of ~1/2µm. These results are interpreted in terms of a redistribution of the implanted H which has been influenced by heavy radiation damage in the surface region. Fluorine determinations have been performed in a 1-µm surface layer on lunar and meteoritic samples using the same ¹⁹F(p,αy)¹⁶O resonance. The measurement of H depth distributions has also been used to study the hydration of terrestrial obsidian, a phenomenon of considerable archaeological interest as a means of dating obsidian artifacts. Additional applications of this type of technique are also discussed.