On the Insignificance of Photochemical Hydrocarbon Aerosols in the Atmospheres of Close-in Extrasolar Giant Planets

The close-in extrasolar giant planets (CEGPs) reside in irradiated environments much more intense than that of the giant planets in our solar system. The high UV irradiance strongly influences their photochemistry and the general current view believed that this high UV flux will greatly enhance photochemical production of hydrocarbon aerosols. In this letter, we investigate hydrocarbon aerosol formation in the atmospheres of CEGPs. We find that the abundances of hydrocarbons in the atmospheres of CEGPs are significantly less than that of Jupiter except for models in which the CH$_4$ abundance is unreasonably high (as high as CO) for the hot (effective temperatures $\gtrsim 1000$ K) atmospheres. Moreover, the hydrocarbons will be condensed out to form aerosols only when the temperature-pressure profiles of the species intersect with the saturation profiles--a case almost certainly not realized in the hot CEGPs atmospheres. Hence our models show that photochemical hydrocarbon aerosols are insignificant in the atmospheres of CEGPs. In contrast, Jupiter and Saturn have a much higher abundance of hydrocarbon aerosols in their atmospheres which are responsible for strong absorption shortward of 600 nm. Thus the insignificance of photochemical hydrocarbon aerosols in the atmospheres of CEGPs rules out one class of models with low albedos and featureless spectra shortward of 600 nm.Comment: ApJL accepte

Multigene analyses identify the three earliest lineages of extant flowering plants

AbstractFlowering plants (angiosperms) are by far the largest, most diverse, and most important group of land plants, with over 250,000 species and a dominating presence in most terrestrial ecosystems. Understanding the origin and early diversification of angiosperms has posed a long-standing botanical challenge [1]. Numerous morphological and molecular systematic studies have attempted to reconstruct the early history of this group, including identifying the root of the angiosperm tree. There is considerable disagreement among these studies, with various groups of putatively basal angiosperms from the subclass Magnoliidae having been placed at the root of the angiosperm tree (reviewed in [2–4]). We investigated the early evolution of angiosperms by conducting combined phylogenetic analyses of five genes that represent all three plant genomes from a broad sampling of angiosperms. Amborella, a monotypic, vesselless dioecious shrub from New Caledonia, was clearly identified as the first branch of angiosperm evolution, followed by the Nymphaeales (water lilies), and then a clade of woody vines comprising Schisandraceae and Austrobaileyaceae. These findings are remarkably congruent with those from several concurrent molecular studies [5–7] and have important implications for whether or not the first angiosperms were woody and contained vessels, for interpreting the evolution of other key characteristics of basal angiosperms, and for understanding the timing and pattern of angiosperm origin and diversification

The WiggleZ Dark Energy Survey: Final data release and cosmological results

This paper presents cosmological results from the final data release of the WiggleZ Dark Energy Survey. We perform full analyses of different cosmological models using the WiggleZ power spectra measured at z=0.22, 0.41, 0.60, and 0.78, combined with other cosmological data sets. The limiting factor in this analysis is the theoretical modeling of the galaxy power spectrum, including nonlinearities, galaxy bias, and redshift-space distortions. In this paper we assess several different methods for modeling the theoretical power spectrum, testing them against the Gigaparsec WiggleZ simulations (GiggleZ). We fit for a base set of six cosmological parameters, {Ω_(b)h^2,Ω_(CDM)h^2,H_0,τ,A_s,n_s}, and five supplementary parameters {n_(run),r,w,Ω_k,∑m_ν}. In combination with the cosmic microwave background, our results are consistent with the ΛCDM concordance cosmology, with a measurement of the matter density of Ωm=0.29±0.016 and amplitude of fluctuations σ_8=0.825±0.017. Using WiggleZ data with cosmic microwave background and other distance and matter power spectra data, we find no evidence for any of the extension parameters being inconsistent with their ΛCDM model values. The power spectra data and theoretical modeling tools are available for use as a module for CosmoMC, which we here make publicly available at http://smp.uq.edu.au/wigglez-data. We also release the data and random catalogs used to construct the baryon acoustic oscillation correlation function

Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region

<p>Abstract</p> <p>Background</p> <p>The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other unusual features, including short tRNAs and other genes, and a duplicated control region that has been stably maintained since it originated more than 70 million years ago. Here, we provide a detailed analysis of evolutionary dynamics in snake mitochondrial genomes to better understand the basis of these extreme characteristics, and to explore the relationship between mitochondrial genome molecular evolution, genome architecture, and molecular function. We sequenced complete mitochondrial genomes from Slowinski's corn snake (<it>Pantherophis slowinskii</it>) and two cottonmouths (<it>Agkistrodon piscivorus</it>) to complement previously existing mitochondrial genomes, and to provide an improved comparative view of how genome architecture affects molecular evolution at contrasting levels of divergence.</p> <p>Results</p> <p>We present a Bayesian genetic approach that suggests that the duplicated control region can function as an additional origin of heavy strand replication. The two control regions also appear to have different intra-specific versus inter-specific evolutionary dynamics that may be associated with complex modes of concerted evolution. We find that different genomic regions have experienced substantial accelerated evolution along early branches in snakes, with different genes having experienced dramatic accelerations along specific branches. Some of these accelerations appear to coincide with, or subsequent to, the shortening of various mitochondrial genes and the duplication of the control region and flanking tRNAs.</p> <p>Conclusion</p> <p>Fluctuations in the strength and pattern of selection during snake evolution have had widely varying gene-specific effects on substitution rates, and these rate accelerations may have been functionally related to unusual changes in genomic architecture. The among-lineage and among-gene variation in rate dynamics observed in snakes is the most extreme thus far observed in animal genomes, and provides an important study system for further evaluating the biochemical and physiological basis of evolutionary pressures in vertebrate mitochondria.</p

Methanol on Enceladus

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95284/1/grl26203.pd

Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae

Background: Rates of synonymous nucleotide substitutions are, in general, exceptionally low in plant mitochondrial genomes, several times lower than in chloroplast genomes, 10-20 times lower than in plant nuclear genomes, and 50-100 times lower than in many animal mitochondrial genomes. Several cases of moderate variation in mitochondrial substitution rates have been reported in plants, but these mostly involve correlated changes in chloroplast and/or nuclear substitution rates and are therefore thought to reflect whole-organism forces rather than ones impinging directly on the mitochondrial mutation rate. Only a single case of extensive, mitochondrial-specific rate changes has been described, in the angiosperm genus Plantago. Results: We explored a second potential case of highly accelerated mitochondrial sequence evolution in plants. This case was first suggested by relatively poor hybridization of mitochondrial gene probes to DNA of Pelargonium hortorum (the common geranium). We found that all eight mitochondrial genes sequenced from P. hortorum are exceptionally divergent, whereas chloroplast and nuclear divergence is unexceptional in P. hortorum. Two mitochondrial genes were sequenced from a broad range of taxa of variable relatedness to P. hortorum, and absolute rates of mitochondrial synonymous substitutions were calculated on each branch of a phylogenetic tree of these taxa. We infer one major, similar to 10-fold increase in the mitochondrial synonymous substitution rate at the base of the Pelargonium family Geraniaceae, and a subsequent similar to 10-fold rate increase early in the evolution of Pelargonium. We also infer several moderate to major rate decreases following these initial rate increases, such that the mitochondrial substitution rate has returned to normally low levels in many members of the Geraniaceae. Finally, we find unusually little RNA editing of Geraniaceae mitochondrial genes, suggesting high levels of retroprocessing in their history. Conclusion: The existence of major, mitochondrial-specific changes in rates of synonymous substitutions in the Geraniaceae implies major and reversible underlying changes in the mitochondrial mutation rate in this family. Together with the recent report of a similar pattern of rate heterogeneity in Plantago, these findings indicate that the mitochondrial mutation rate is a more plastic character in plants than previously realized. Many molecular factors could be responsible for these dramatic changes in the mitochondrial mutation rate, including nuclear gene mutations affecting the fidelity and efficacy of mitochondrial DNA replication and/or repair and consistent with the lack of RNA editing - exceptionally high levels of mutagenic retroprocessing. That the mitochondrial mutation rate has returned to normally low levels in many Geraniaceae raises the possibility that, akin to the ephemerality of mutator strains in bacteria, selection favors a low mutation rate in plant mitochondria

An ancient adaptive episode of convergent molecular evolution confounds phylogenetic inference

Convergence can mislead phylogenetic inference by mimicking shared ancestry, but has been detected only rarely in molecular evolution. Here, we show that significant convergence occurred in snake and agamid lizard mitochondrial genomes. Most evidence, and most of the mitochondrial genome, supports one phylogenetic tree, but a subset of mostly amino acid-altering mitochondrial sites strongly support a radically different phylogeny. These sites are convergent, probably selected, and overwhelm the signal from other sites. This suggests that convergent molecular evolution can seriously mislead phylogenetics, even with large data sets. Radical phylogenies inconsistent with previous evidence should be treated cautiously

Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast

Ubiquitin-protein ligases (E3s) are responsible for target recognition and regulate stability, localization or function of their substrates. However, the substrates of most E3 enzymes remain unknown. Here, we describe the development of a novel proteomic in vitro ubiquitination screen using a protein microarray platform that can be utilized for the discovery of substrates for E3 ligases on a global scale. Using the yeast E3 Rsp5 as a test system to identify its substrates on a yeast protein microarray that covers most of the yeast (Saccharomyces cerevisiae) proteome, we identified numerous known and novel ubiquitinated substrates of this E3 ligase. Our enzymatic approach was complemented by a parallel protein microarray protein interaction study. Examination of the substrates identified in the analysis combined with phage display screening allowed exploration of binding mechanisms and substrate specificity of Rsp5. The development of a platform for global discovery of E3 substrates is invaluable for understanding the cellular pathways in which they participate, and could be utilized for the identification of drug targets

Methanol on Enceladus

Near infrared spectra of the surface of Enceladus returned by Cassini show the presence of an absorption feature at 3.53 μm, ascribed by Brown et al. (2006) to “short chain organics,” and by Newman et al. (2007) to hydrogen peroxide. We assign this feature tentatively to methanol. Variations in the peak position of the feature suggest that methanol in the “tiger stripes” region may be segregated from the water ice, and not homogeneously distributed in the ice matrix. The photolytic destruction of methanol implies that methane or methanol itself must be continually deposited on the surface. On Enceladus, methanol may be generated photochemically from a mixed methane/water ice, or deposited from the plume itself. The variation in the concentration of methanol over the surface could be used to distinguish between these two processes

The Study of TeV Variability and Duty Cycle of Mrk 421 from 3 Years of Observations with the Milagro Observatory

TeV flaring activity with time scales as short as tens of minutes and an orphan TeV flare have been observed from the blazar Markarian 421 (Mrk 421). The TeV emission from Mrk 421 is believed to be produced by leptonic synchrotron self-Compton (SSC) emission. In this scenario, correlations between the X-ray and the TeV fluxes are expected, TeV orphan flares are hardly explained and the activity (measured as duty cycle) of the source at TeV energies is expected to be equal or less than that observed in X-rays if only SSC is considered. To estimate the TeV duty cycle of Mrk 421 and to establish limits on its variability at different time scales, we continuously observed Mrk 421 with the Milagro observatory. Mrk 421 was detected by Milagro with a statistical significance of 7.1 standard deviations between 2005 September 21 and 2008 March 15. The observed spectrum is consistent with previous observations by VERITAS. We estimate the duty cycle of Mrk 421 for energies above 1 TeV for different hypothesis of the baseline flux and for different flare selections and we compare our results with the X-ray duty cycle estimated by Resconi et al. 2009. The robustness of the results is discussed.Comment: 27 pages, 6 figures, ApJ accepte