Developmentally regulated transcription factors in Drosophila melanogaster

During early stages of Drosophila development the heat shock response cannot be induced. It is reasoned that the adverse effects on cell cycle and cell growth brought about by Hsp70 induction must outweigh the beneficial aspects of Hsp70 induction in the early embryo. Although the Drosophila heat shock transcription factor (dHSF) is abundant in the early embryo, it does not enter the nucleus in response to heat shock. In older embryos and in cultured cells the factor is localized within the nucleus in an apparent trimeric structure that binds DNA with high affinity. The domain responsible for nuclear localization upon stress resides between residues 390 and 420 of the dHSF. Using that domain as bait in a yeast two-hybrid system we now report the identification and cloning of a nuclear transport protein Drosophila karyopherin-α3(dKap- α3). Biochemical methods demonstrate that the dKap-α3 protein binds specifically to the dHSF's nuclear localization sequence (NLS). Furthermore, the dKap-α3 protein does not associate with NLSs that contain point mutations which are not transported in vivo. Nuclear docking studies also demonstrate specific nuclear targeting of the NLS substrate by dKap-α3.Consistant with previous studies demonstrating that early Drosophila embryos are refractory to heat shock as a result of dHSF nuclear exclusion, we demonstrate that the early embryo is deficient in dKap-α3 protein through cycle 12. From cycle 13 onward the transport factor is present and the dHSF is localized within the nucleus thus allowing the embryo to respond to heat shock.

The pair-rule gene fushi tarazu (ftz) is a well-studied zygotic segmentation gene that is necessary for the development of the even-numbered parasegments in Drosophila melanogastor. During early embryogenesis, ftz is expressed in a characteristic pattern of seven stripes, one in each of the even-numbered parasegments. With a view to understand how ftz is transcriptionally regulated, cDNAs that encode transcription factors that bind to the zebra element of the ftz promoter have been cloned. Chapter Ill reports the cloning and characterization of the eDNA encoding zeb-1 (zebra element binding protein), a novel steroid receptor-like molecule that specifically binds to a key regulatory element of the ftz promoter. In transient transfection assays employing Drosophila tissue culture cells, it has been shown that zeb-1 as well as a truncated zeb-1 polypeptide (zeb480) that lacks the putative ligand binding domain function as sequencespecific trans-activators of the ftz gene.

The Oct factors are members of the POU family of transcription factors that are shown to play important roles during development in mammals. Chapter IV reports the eDNA cloning and expression of a Drosophila Oct transcription factor. Whole mount in-situ hybridization experiments revealed that the spatial expression patterns of this gene during embryonic development have not yet been observed for any other gene. In early embryogenesis, its transcripts are transiently expressed as a wide uniform band from 20-40% of the egg length, very similar to that of gap genes. This pattern progressively resolves into a series of narrower stripes followed by expression in fourteen stripes. Subsequently, transcripts from this gene are expressed in the central nervous system and the brain. When expressed in the yeast Saccharomyces cerevisiae, this Drosophila factor functions as a strong, octamer-dependent activator of transcription. The data strongly suggest possible functions for the Oct factor in pattern formation in Drosophila that might transcend the boundaries of genetically defined segmentation genes.

Finding needles in the haystack : a search for AM CVn systems using the Palomar Transient Factory

The AM CVn systems are a rare class of ultra-compact astrophysical binaries. With orbital periods of under an hour and as short as five minutes, they are among the closest known binary star systems and their evolution has direct relevance to the type Ia supernova rate and the white dwarf binary population. However, their faint and rare nature has made population studies of these systems difficult and several studies have found conflicting results.

I undertook a survey for AM CVn systems using the Palomar Transient Factory (PTF) astrophysical synoptic survey by exploiting the "outbursts" these systems undergo. Such events result in an increase in luminosity by a factor of up to two-hundred and are detectable in time-domain photometric data of AM CVn systems. My search resulted in the discovery of eight new systems, over 20% of the current known population. More importantly, this search was done in a systematic fashion, which allows for a population study properly accounting for biases.

Apart from the discovery of new systems, I used the time-domain data from the PTF and other synoptic surveys to better understand the long-term behavior of these systems. This analysis of the photometric behavior of the majority of known AM CVn systems has shown changes in their behavior at longer time scales than have previously been observed. This has allowed me to find relationships between the outburst properties of an individual system and its orbital period.

Even more importantly, the systematically selected sample together with these properties have allowed me to conduct a population study of the AM CVn systems. I have shown that the latest published estimates of the AM CVn system population, a factor of fifty below theoretical estimates, are consistent with the sample of systems presented here. This is particularly noteworthy since my population study is most sensitive to a different orbital period regime than earlier surveys. This confirmation of the population density will allow the AM CVn systems population to be used in the study of other areas of astrophysics.

The needle in the hundred square degree haystack: The hunt for binary neutron star mergers with LIGO and Palomar Transient Factory

The Advanced LIGO and Virgo experiments are poised to detect gravitational waves (GWs) directly for the first time this decade. The ultimate prize will be joint observation of a compact binary merger in both gravitational and electromagnetic channels. However, GW sky locations that are uncertain by hundreds of square degrees will pose a challenge. I describe a real-time detection pipeline and a rapid Bayesian parameter estimation code that will make it possible to search promptly for optical counterparts in Advanced LIGO. Having analyzed a comprehensive population of simulated GW sources, we describe the sky localization accuracy that the GW detector network will achieve as each detector comes online and progresses toward design sensitivity. Next, in preparation for the optical search with the intermediate Palomar Transient Factory (iPTF), we have developed a unique capability to detect optical afterglows of gamma-ray bursts (GRBs) detected by the Fermi Gamma-ray Burst Monitor (GBM). Its comparable error regions offer a close parallel to the Advanced LIGO problem, but Fermi's unique access to MeV-GeV photons and its near all-sky coverage may allow us to look at optical afterglows in a relatively unexplored part of the GRB parameter space. We present the discovery and broadband follow-up observations (X-ray, UV, optical, millimeter, and radio) of eight GBM-IPTF afterglows. Two of the bursts (GRB 130702A / iPTF13bxl and GRB 140606B / iPTF14bfu) are at low redshift (z=0.145 and z = 0.384, respectively), are sub-luminous with respect to "standard" cosmological bursts, and have spectroscopically confirmed broad-line type Ic supernovae. These two bursts are possibly consistent with mildly relativistic shocks breaking out from the progenitor envelopes rather than the standard mechanism of internal shocks within an ultra-relativistic jet. On a technical level, the GBM--IPTF effort is a prototype for locating and observing optical counterparts of GW events in Advanced LIGO with the Zwicky Transient Facility.

Solar System Small-Body Demographics with the Palomar Transient Factory Survey

Observational studies of our solar system's small-body populations (asteroids and comets) offer insight into the history of our planetary system, as these minor planets represent the left-over building blocks from its formation. The Palomar Transient Factory (PTF) survey began in 2009 as the latest wide-field sky-survey program to be conducted on the 1.2-meter Samuel Oschin telescope at Palomar Observatory. Though its main science program has been the discovery of high-energy extragalactic sources (such as supernovae), during its first five years PTF has collected nearly five million observations of over half a million unique solar system small bodies. This thesis begins to analyze this vast data set to address key population-level science topics, including: the detection rates of rare main-belt comets and small near-Earth asteroids, the spin and shape properties of asteroids as inferred from their lightcurves, the applicability of this visible light data to the interpretation of ultraviolet asteroid observations, and a comparison of the physical properties of main-belt and Jovian Trojan asteroids. Future sky-surveys would benefit from application of the analytical techniques presented herein, which include novel modeling methods and unique applications of machine-learning classification. The PTF asteroid small-body data produced in the course of this thesis work should remain a fertile source of solar system science and discovery for years to come.