Analyses of planetary atmospheres across the spectrum : from Titan to exoplanets

Planetary atmospheres exist in a seemingly endless variety of physical and chemical environments. There are an equally diverse number of methods by which we can study and characterize atmospheric composition. In order to better understand the fundamental chemistry and physical processes underlying all planetary atmospheres, my research of the past four years has focused on two distinct topics. First, I focused on the data analysis and spectral retrieval of observations obtained by the Ultraviolet Imaging Spectrograph (UVIS) instrument onboard the Cassini spacecraft while in orbit around Saturn. These observations consisted of stellar occultation measurements of Titan's upper atmosphere, probing the chemical composition in the region 300 to 1500 km above Titan's surface. I examined the relative abundances of Titan's two most prevalent chemical species, nitrogen and methane. I also focused on the aerosols that are formed through chemistry involving these two major species, and determined the vertical profiles of aerosol particles as a function of time and latitude. Moving beyond our own solar system, my second topic of investigation involved analysis of infra-red light curves from the Spitzer space telescope, obtained as it measured the light from stars hosting planets of their own. I focused on both transit and eclipse modeling during Spitzer data reduction and analysis. In my initial work, I utilized the data to search for transits of planets a few Earth masses in size. In more recent research, I analyzed secondary eclipses of three exoplanets and constrained the range of possible temperatures and compositions of their atmospheres.

Studies on photoblastic germination in lettuce seed

It was shown, with the aid of osmotic inhibition of germination, that the action of the far-red-absorbing form of phytochrome (Pf) in promoting germination can be completed even if the seed is held under conditions where germination is not possible. An effect of the continuing action of Pf beyond the point of complete germination promotion was demonstrated by enhancement of germination rate after removal of the osmotically active solute.

Previous reports that the rate of growth in water of seeds freed from the expansion-restricting endosperm is independent of the state of phytochrome were confirmed. However, a marked, phytochrome-mediated enhancement of the growth potential of such seeds was demonstrated through restricting water uptake by incubation in an osmoticum.

An experimental system, utilizing the appearance of a geotropic curvature in the radicle of the excised axial portion of the seed, was developed for more detailed studies of the phytochrome-enhanced growth potential. It was possible to demonstrate the light effect in water as well as in osmotica; this apparently is not possible with de-endospermed entire seeds. As in intact seeds, the effect of the continuing action of Pf is to enhance the rate of the response. Secretion of a chemical inhibitor of growth by the endosperm as a possible mechanism of induction of light sensitivity has been ruled out.

The phytochrome-dependent rate of appearance of geotropic curvature in osmotica is paralleled in time by a similar dependence of the rate of early extension growth of the embryonic axis. Only the first small increment of growth is a differentially responsive to red (R) and far-red (F); the rate of later increase in length is independent of the light regime.

It was shown that the high concentrations of gibberellic acid required for germination promotion in the intact seed are due at least in part to a diffusion barrier in the endosperm, and that the occasional reports in the literature of the ineffectiveness of kinetin are probably due to the same phenomenon. It was shown that gibberellin, like red light, enhances the growth potential of the axis, but kinetin does not. The difference in rates of response obtained after R-irradiation or gibberellin treatment, together with other results reported in the literature, strongly suggests that gibberellic acid and red light promote germination by different means. The idea that kinetin promotes germination by yet another mechanism, probably operating in the cotyledons, was supported through two different experimental approaches.

The phenomenon of temperature-dependent dark germination was examined in detail, using a wide range of both temperatures and incubation times. With the aid of the half-seed system, it was demonstrated that the promotive effect of low temperature on germination could not be due to a low optimum temperature for early growth of the radicle, since the rate of that process increased with increasing temperature, up to the highest temperature used.

It was shown that phytochrome does not function at high temperatures. This fact is of considerable importance in interpreting the phenomenon of thermodormancy, since in the literature only a small part of the effect of high temperature has been ascribed to an effect on phytochrome, and at that, only to an acceleration of dark reversion of Pf to the red-absorbing form of phytochrome (Pr). Partial denaturation of phytochrome may also make some contribution.

It was shown that the germination-promoting effect of low temperature depends on the presence of Pf, and concluded that low temperatures act by delaying or preventing transformation of Pf. Support for the assumption that Pf, not Pr, is the active form of phytochrome in lettuce seeds was drawn from the same evidence.

Attempts to stimulate germination by repeated irradiation with F over relatively prolonged incubation times resulted in failure, as have similar attempts reported in the literature. However, an enhancement of growth potential in the half-seed system by the maintenance of a small amount of Pf over long periods at ordinary temperatures by repeated irradiation with F was demonstrated.

It was observed that cold storage of the dry seed prevents or delays loss of dark dormancy during post-harvest storage. No change in the response of the half-seed in osmoticum to R and F was observed in seeds that has lost dark dormancy; that is, no internal change took place to measurably increase the growth potential of the embryonic axis. This suggests that the endosperm is the seat of changes responsible for after-ripening of photoblastic lettuce seed.

Computationally Guided Monomerization of Red Fluorescent Proteins of the Class Anthozoa

Red fluorescent proteins (RFPs) have attracted significant engineering focus because of the promise of near infrared fluorescent proteins, whose light penetrates biological tissue, and which would allow imaging inside of vertebrate animals. The RFP landscape, which numbers ~200 members, is mostly populated by engineered variants of four native RFPs, leaving the vast majority of native RFP biodiversity untouched. This is largely due to the fact that native RFPs are obligate tetramers, limiting their usefulness as fusion proteins. Monomerization has imposed critical costs on these evolved tetramers, however, as it has invariably led to loss of brightness, and often to many other adverse effects on the fluorescent properties of the derived monomeric variants. Here we have attempted to understand why monomerization has taken such a large toll on Anthozoa class RFPs, and to outline a clear strategy for their monomerization. We begin with a structural study of the far-red fluorescence of AQ143, one of the furthest red emitting RFPs. We then try to separate the problem of stable and bright fluorescence from the design of a soluble monomeric β-barrel surface by engineering a hybrid protein (DsRmCh) with an oligomeric parent that had been previously monomerized, DsRed, and a pre-stabilized monomeric core from mCherry. This allows us to use computational design to successfully design a stable, soluble, fluorescent monomer. Next we took HcRed, which is a previously unmonomerized RFP that has far-red fluorescence (λemission = 633 nm) and attempted to monomerize it making use of lessons learned from DsRmCh. We engineered two monomeric proteins by pre-stabilizing HcRed’s core, then monomerizing in stages, making use of computational design and directed evolution techniques such as error-prone mutagenesis and DNA shuffling. We call these proteins mGinger0.1 (λem = 637 nm / Φ = 0.02) and mGinger0.2 (λem = 631 nm Φ = 0.04). They are the furthest red first generation monomeric RFPs ever developed, are significantly thermostabilized, and add diversity to a small field of far-red monomeric FPs. We anticipate that the techniques we describe will be facilitate future RFP monomerization, and that further core optimization of the mGingers may allow significant improvements in brightness.