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.

Wireless parylene-based retinal implant

The degeneration of the outer retina usually causes blindness by affecting the photoreceptor cells. However, the ganglion cells, which consist of optic nerves, on the middle and inner retina layers are often intact. The retinal implant, which can partially restore vision by electrical stimulation, soon becomes a focus for research. Although many groups worldwide have spent a lot of effort on building devices for retinal implant, current state-of-the-art technologies still lack a reliable packaging scheme for devices with desirable high-density multi-channel features. Wireless flexible retinal implants have always been the ultimate goal for retinal prosthesis. In this dissertation, the reliable packaging scheme for a wireless flexible parylene-based retinal implants has been well developed. It can not only provide stable electrical and mechanical connections to the high-density multi-channel (1000+ channels on 5 mm × 5 mm chip area) IC chips, but also survive for more than 10 years in the human body with corrosive fluids.

The device is based on a parylene-metal-parylene sandwich structure. In which, the adhesion between the parylene layers and the metals embedded in the parylene layers have been studied. Integration technology for high-density multi-channel IC chips has also been addressed and tested with dummy and real 268-channel and 1024-channel retinal IC chips. In addition, different protection schemes have been tried in application to IC chips and discrete components to gain the longest lifetime. The effectiveness has been confirmed by the accelerated and active lifetime soaking test in saline solution. Surgical mockups have also been designed and successfully implanted inside dog's and pig's eyes. Additionally, the electrodes used to stimulate the ganglion cells have been modified to lower the interface impedance and shaped to better fit the retina. Finally, all the developed technologies have been applied on the final device with a dual-metal-layer structure.

Gene enrichment using antibodies to DNA/RNA hybrids : mapping the ribosomal DNA of slime mold and rat

A novel method for gene enrichment has been developed and applied to mapping the rRNA genes of two eucaryotic organisms. The method makes use of antibodies to DNA/RNA hybrids prepared by injecting rabbits with the synthetic hybrid poly(rA)•poly(dT). Antibodies which cross-react with non-hybrid nucleic acids were removed from the purified IgG fraction by adsorption on columns of DNA-Sepharose, oligo(dT)-cellulose, and poly(rA)-Sepharose. Subsequent purification of the specific DNA/RNA hybrid antibody was carried out on a column of oligo(dT)-cellulose to which poly(rA) was hybridized. Attachment of these antibodies to CNBr-activated Sepharose produced an affinity resin which specifically binds DNA/RNA hybrids.

In order to map the rDNA of the slime mold Dictyostelium discoideum, R-loops were formed using unsheared nuclear DNA and the 178 and 268 rRNAs of this organism. This mixture was passed through a column containing the affinity resin, and bound molecules containing R- loops were eluted by high salt. This purified rDN A was observed directly in the electron microscope. Evidence was obtained that there is a physical end to Dictyostelium rDN A molecules approximately 10 kilobase pairs (kbp) from the region which codes for the 268 rRNA. This finding is consistent with reports of other investigators that the rRNA genes exist as inverse repeats on extra-chromosomal molecules of DNA unattached to the remainder of the nuclear DNA in this organism.

The same general procedure was used to map the rRNA genes of the rat. Molecules of DNA which contained R-loops formed with the 188 and 288 rRNAs were enriched approximately 150- fold from total genomal rat DNA by two cycles of purification on the affinity column. Electron microscopic measurements of these molecules enabled the construction of an R-loop map of rat rDNA. Eleven of the observed molecules contained three or four R-loops or else two R-loops separated by a long spacer. These observations indicated that the rat rRNA genes are arranged as tandem repeats. The mean length of the repeating units was 37.2 kbp with a standard deviation of 1.3 kbp. These eleven molecules may represent repeating units of exactly the same length within the errors of the measurements, although a certain degree of length heterogeneity cannot be ruled out. If significantly shorter or longer repeating units exist, they are probably much less common than the 37.2 kbp unit.

The last section of the thesis describes the production of antibodies to non-histone chromosomal proteins which have been exposed to the ionic detergent sodium dodecyl sulfate (SDS). The presence of low concentrations of SDS did not seem to affect either production of antibodies or their general specificity. Also, a technique is described for the in situ immunofluorescent detection of protein antigens in polyacrylamide gels.