Spectral signatures of photosynthesis II: coevolution with other stars and the atmosphere on extrasolar worlds

As photosynthesis on Earth produces the primary signatures of life that can be detected astronomically at the global scale, a strong focus of the search for extrasolar life will be photosynthesis, particularly photosynthesis that has evolved with a different parent star. We take planetary atmospheric compositions simulated by Segura, et al. (2003, 2005) for Earth-like planets around observed F2V and K2V stars, modeled M1V and M5V stars, and around the active M4.5V star AD Leo; our scenarios use Earth's atmospheric composition as well as very low O2 content in case anoxygenic photosynthesis dominates. We calculate the incident spectral photon flux densities at the surface of the planet and under water. We identify bands of available photosynthetically relevant radiation and find that photosynthetic pigments on planets around F2V stars may peak in absorbance in the blue, K2V in the red-orange, and M stars in the NIR, in bands at 0.93-1.1 microns, 1.1-1.4 microns, 1.5-1.8 microns, and 1.8-2.5 microns. In addition, we calculate wavelength restrictions for underwater organisms and depths of water at which they would be protected from UV flares in the early life of M stars. We estimate the potential productivity for both surface and underwater photosynthesis, for both oxygenic and anoxygenic photosynthesis, and for hypothetical photosynthesis in which longer wavelength, multi-photosystem series are used.Comment: 59 pages, 4 figures, 4 tables, forthcoming in Astrobiology ~March 200

Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

Depinning of three-dimensional drops from wettability defects

Substrate defects crucially influence the onset of sliding drop motion under lateral driving. A finite force is necessary to overcome the pinning influence even of microscale heterogeneities. The depinning dynamics of three-dimensional drops is studied for hydrophilic and hydrophobic wettability defects using a long-wave evolution equation for the film thickness profile. It is found that the nature of the depinning transition explains the experimentally observed stick-slip motion.Comment: 6 pages, 9 figures, submitted to ep

L^2 stability estimates for shock solutions of scalar conservation laws using the relative entropy method

We consider scalar nonviscous conservation laws with strictly convex flux in one spatial dimension, and we investigate the behavior of bounded L^2 perturbations of shock wave solutions to the Riemann problem using the relative entropy method. We show that up to a time-dependent translation of the shock, the L^2 norm of a perturbed solution relative to the shock wave is bounded above by the L^2 norm of the initial perturbation.Comment: 17 page

Molecular and Ionic shocks in the Supernova Remnant 3C391

New observations of the supernova remnant 3C391 are in the H2 2.12 micron and [Fe II] 1.64 micron narrow-band filters at the Palomar 200-inch telescope, and in the 5-15 micron CVF on ISOCAM. Shocked H2 emission was detected from the region 3C391:BML, where broad millimeter CO and CS lines had previously been detected. A new H2 clump was confirmed to have broad CO emission, demonstrating that the near-infrared H2 images can trace previously undetected molecular shocks. The [Fe II] emission has a significantly different distribution, being brightest in the bright radio bar, at the interface between the supernova remnant and the giant molecular cloud, and following filaments in the radio shell. The near-infrared [Fe II] and the mid-infrared 12-18 micron filter images are the first images to reveal the radiative shell of 3C391. The mid-infrared spectrum is dominated by bright ionic lines and H2 S(2) through S(7). There are no aromatic hydrocarbons associated with the shocks, nor is their any mid-infrared continuum, suggesting that macromolecules and very small grains are destroyed. Comparing 3C391 to the better-studied IC443, both remnants have molecular- and ionic-dominated regions; for 3C391, the ionic-dominated region is the interface into the giant molecular cloud, showing that the main bodies of giant molecular clouds contain significant regions with densities 100 to 1000/cm^3 and a small filling factor with higher-density. The molecular shocked region resolves into 16 clumps of H2 emission, with some fainter diffuse emission but with no associated near-infrared continuum sources. One of the clumps is coincident with a previously-detected OH 1720 MHz maser. These clumps are interpreted as a cluster of pre-stellar, dense molecular cores that are presently being shocked by the supernova blast wave

Mid-Infrared Images of Stars and Dust in Irregular Galaxies

We present mid-infrared to optical properties of 22 representative irregular galaxies: 18 Im, 3 BCDs, and one Sm. The mid-IR is based on images from the Spitzer Space Telescope archives. The 3.6 and 4.5 micron bands and the UBVJHK images are used to examine disk morphology and the integrated and azimuthally averaged magnitudes and colors of stars. The non-stellar contribution to the 4.5 micron images is used to trace hot dust. The 5.8 and 8.0 micron images reveal emission from hot dust and PAHs, and both may contribute to these passbands, although we refer to the non-stellar emission as PAH emission. We compare the 8.0 micron images to Halpha. Im galaxies have no hidden bars, and those with double-exponential optical light profiles have the same at mid-IR. Most galaxies have similar optical mid-IR scale lengths. Four galaxies have super star clusters that are not visible at optical bands. Galaxies with higher area-normalized star formation rates have more dust and PAH emission relative to starlight. Hot dust and PAH emission is found mostly in high surface brightness HII regions, implying that massive stars are the primary source of heating. Galaxies with intense, wide-spread star formation have more extended PAH emssion. The ratio of PAH to Halpha emission is not constant on small scales. PAHs are associated with shell and giant filaments, so they are not destroyed during shell formation.Comment: To be published in AJ Available from ftp.lowell.edu/pub/dah/papers/ira

The MrCYP52 Cytochrome P450 Monoxygenase Gene of Metarhizium robertsii Is Important for Utilizing Insect Epicuticular Hydrocarbons

Fungal pathogens of plants and insects infect their hosts by direct penetration of the cuticle. Plant and insect cuticles are covered by a hydrocarbon-rich waxy outer layer that represents the first barrier against infection. However, the fungal genes that underlie insect waxy layer degradation have received little attention. Here we characterize the single cytochrome P450 monoxygenase family 52 (MrCYP52) gene of the insect pathogen Metarhizium robertsii, and demonstrate that it encodes an enzyme required for efficient utilization of host hydrocarbons. Expressing a green florescent protein gene under control of the MrCYP52 promoter confirmed that MrCYP52 is up regulated on insect cuticle as well as by artificial media containing decane (C10), extracted cuticle hydrocarbons, and to a lesser extent long chain alkanes. Disrupting MrCYP52 resulted in reduced growth on epicuticular hydrocarbons and delayed developmental processes on insect cuticle, including germination and production of appressoria (infection structures). Extraction of alkanes from cuticle prevented induction of MrCYP52 and reduced growth. Insect bioassays against caterpillars (Galleria mellonella) confirmed that disruption of MrCYP52 significantly reduces virulence. However, MrCYP52 was dispensable for normal germination and appressorial formation in vitro when the fungus was supplied with nitrogenous nutrients. We conclude therefore that MrCYP52 mediates degradation of epicuticular hydrocarbons and these are an important nutrient source, but not a source of chemical signals that trigger infection processes

Mid-Infrared Emission Features in the ISM: Feature-to-Feature Flux Ratios

Using a limited, but representative sample of sources in the ISM of our Galaxy with published spectra from the Infrared Space Observatory, we analyze flux ratios between the major mid-IR emission features (EFs) centered around 6.2, 7.7, 8.6 and 11.3 microns, respectively. In a flux ratio-to-flux ratio plot of EF(6.2)/EF(7.7) as a function of EF(11.3)/EF(7.7), the sample sources form roughly a $\Lambda$-shaped locus which appear to trace, on an overall basis, the hardness of a local heating radiation field. But some driving parameters other than the radiation field may also be required for a full interpretation of this trend. On the other hand, the flux ratio of EF(8.6)/EF(7.7) shows little variation over the sample sources, except for two HII regions which have much higher values for this ratio due to an ``EF(8.6\um) anomaly,'' a phenomenon clearly associated with environments of an intense far-UV radiation field. If further confirmed on a larger database, these trends should provide crucial information on how the EF carriers collectively respond to a changing environment.Comment: 16 pages, 1 figure, 1 table; accepted for publication in ApJ Letter

Transparent dense sodium

Under pressure, metals exhibit increasingly shorter interatomic distances. Intuitively, this response is expected to be accompanied by an increase in the widths of the valence and conduction bands and hence a more pronounced free-electron-like behaviour. But at the densities that can now be achieved experimentally, compression can be so substantial that core electrons overlap. This effect dramatically alters electronic properties from those typically associated with simple free-electron metals such as lithium and sodium, leading in turn to structurally complex phases and superconductivity with a high critical temperature. But the most intriguing prediction - that the seemingly simple metals Li and Na will transform under pressure into insulating states, owing to pairing of alkali atoms - has yet to be experimentally confirmed. Here we report experimental observations of a pressure-induced transformation of Na into an optically transparent phase at 200 GPa (corresponding to 5.0-fold compression). Experimental and computational data identify the new phase as a wide bandgap dielectric with a six-coordinated, highly distorted double-hexagonal close-packed structure. We attribute the emergence of this dense insulating state not to atom pairing, but to p-d hybridizations of valence electrons and their repulsion by core electrons into the lattice interstices. We expect that such insulating states may also form in other elements and compounds when compression is sufficiently strong that atomic cores start to overlap strongly.Comment: Published in Nature 458, 182-185 (2009

Optical probing of spin fluctuations of a single magnetic atom

We analyzed the photoluminescence intermittency generated by a single paramagnetic spin localized in an individual semiconductor quantum dot. The statistics of the photons emitted by the quantum dot reflect the quantum fluctuations of the localized spin interacting with the injected carriers. Photon correlation measurements which are reported here reveal unique signatures of these fluctuations. A phenomenological model is proposed to quantitatively describe these observations, allowing a measurement of the spin dynamics of an individual magnetic atom at zero magnetic field. These results demonstrate the existence of an efficient spin relaxation channel arising from a spin-exchange with individual carriers surrounding the quantum dot. A theoretical description of a spin-flip mechanism involving spin exchange with surrounding carriers gives relaxation times in good agreement with the measured dynamics