Alkane hydroxylase genes in psychrophile genomes and the potential for cold active catalysis.

BackgroundPsychrophiles are presumed to play a large role in the catabolism of alkanes and other components of crude oil in natural low temperature environments. In this study we analyzed the functional diversity of genes for alkane hydroxylases, the enzymes responsible for converting alkanes to more labile alcohols, as found in the genomes of nineteen psychrophiles for which alkane degradation has not been reported. To identify possible mechanisms of low temperature optimization we compared putative alkane hydroxylases from these psychrophiles with homologues from nineteen taxonomically related mesophilic strains.ResultsSeven of the analyzed psychrophile genomes contained a total of 27 candidate alkane hydroxylase genes, only two of which are currently annotated as alkane hydroxylase. These candidates were mostly related to the AlkB and cytochrome p450 alkane hydroxylases, but several homologues of the LadA and AlmA enzymes, significant for their ability to degrade long-chain alkanes, were also detected. These putative alkane hydroxylases showed significant differences in primary structure from their mesophile homologues, with preferences for specific amino acids and increased flexibility on loops, bends, and α-helices.ConclusionA focused analysis on psychrophile genomes led to discovery of numerous candidate alkane hydroxylase genes not currently annotated as alkane hydroxylase. Gene products show signs of optimization to low temperature, including regions of increased flexibility and amino acid preferences typical of psychrophilic proteins. These findings are consistent with observations of microbial degradation of crude oil in cold environments and identify proteins that can be targeted in rate studies and in the design of molecular tools for low temperature bioremediation

Updated Spitzer Emission Spectroscopy of Bright Transiting Hot Jupiter HD189733b

We analyze all existing secondary eclipse time series spectroscopy of hot Jupiter HD189733b acquired with the now defunct Spitzer/IRS instrument. We describe the novel approaches we develop to remove the systematic effects and extract accurate secondary eclipse depths as a function of wavelength in order to construct the emission spectrum of the exoplanet. We compare our results to a previous study by Grillmair et al. that did not examine all data sets available to us. We are able to confirm the detection of a water feature near 6{\mu}m claimed by Grillmair et al. We compare the planetary emission spectrum to three model families -- based on isothermal atmosphere, gray atmosphere, and two realizations of the complex radiative transfer model by Burrows et al., adopted in Grillmair et al.'s study. While we are able to reject the simple isothermal and gray models based on the data at the 97% level just from the IRS data, these rejections hinge on eclipses measured within relatively narrow wavelength range, between 5.5 and 7{\mu}m. This underscores the need for observational studies with broad wavelength coverage and high spectral resolution, in order to obtain robust information on exoplanet atmospheres.Comment: 16 pages, 13 figures and 3 tables. Accepted for publication in Ap

On the Method to Infer an Atmosphere on a Tidally-Locked Super Earth Exoplanet and Upper limits to GJ 876d

We develop a method to infer or rule out the presence of an atmosphere on a tidally-locked hot super Earth. The question of atmosphere retention is a fundamental one, especially for planets orbiting M stars due to the star's long-duration active phase and corresponding potential for stellar-induced planetary atmospheric escape and erosion. Tidally-locked planets with no atmosphere are expected to show a Lambertian-like thermal phase curve, causing the combined light of the planet-star system to vary with planet orbital phase. We report Spitzer 8 micron IRAC observations of GJ 876 taken over 32 continuous hours and reaching a relative photometric precision of 3.9e-04 per point for 25.6 s time sampling. This translates to a 3 sigma limit of 5.13e-05 on a planet thermal phase curve amplitude. Despite the almost photon-noise limited data, we are unable to conclusively infer the presence of an atmosphere or rule one out on the non-transiting short-period super Earth GJ 876d. The limiting factor in our observations was the miniscule, monotonic photometric variation of the slightly active host M star, because the partial sine wave due to the planet has a component in common with the stellar linear trend. The proposed method is nevertheless very promising for transiting hot super Earths with the James Webb Space Telescope and is critical for establishing observational constraints for atmospheric escape.Comment: Published in Ap

Inversion of bottom-hole temperature data: the Pineview field, Utah-Wyoming thrust belt

Journal ArticleThe present day temperature field in a sedimentary basin is a constraint on the maturation of hydrocarbons; this temperature field may be estimated by inverting corrected bottom-hole temperature (BHT) data. Thirty-two BHTs from the Pineview oil field are corrected for drilling disturbances by a Horner plot and inverted for the geothermal gradient in nine formations

The phase-dependent Infrared brightness of the extrasolar planet upsilon Andromedae b

The star upsilon Andromeda is orbited by three known planets, the innermost of which has an orbital period of 4.617 days and a mass at least 0.69 that of Jupiter. This planet is close enough to its host star that the radiation it absorbs overwhelms its internal heat losses. Here we present the 24 micron light curve of this system, obtained with the Spitzer Space Telescope. It shows a clear variation in phase with the orbital motion of the innermost planet. This is the first demonstration that such planets possess distinct hot substellar (day) and cold antistellar (night) faces.Comment: "Director's cut" of paper to appear in Science, 27 October, 200

Volatile compounds of vegetarian soybean kapi, a fermented Thai food condiment

Kapi is a traditional shrimp paste used as a food condiment in Thailand. Several vegetarian soybean kapi, S1-S5, were fermented from various bacterial starter cultures isolated from commercial shrimp paste. The volatile compounds of S1-S5 were analyzed using SPME coupled with gaschromatography/mass spectrometry and compared to three samples of commercial vegetarian kapi (J1-J3) and commercial shrimp pastes (K1-K3). 124 volatile compounds consisting of aldehydes, alcohols,ketones, acids and esters, N-containing compounds, aromatic compounds, S-containing compounds, miscellaneous, indoles and hydrocarbons were identified. Principle component analysis and cluster analysis separated the volatile profile of the fermented samples into four groups. Vegetarian soybean kapi, S1, S4 and S5 produced from Bacillus subtilis IS4, TISTR10 and TISTR1, respectively, were classified into the following groups containing commercial kapi (J1, J2, K2 and K3), that had a predominance of indole, S-containing and N-containing compounds. Sensory evaluation of S1 showed a strong kapi odor with higher scores among the vegetarian soybean kapi and there were no significant differences in evaluation scores between S1 and commercial vegetarian kapi J1-J3. These data demonstrate that B. subtilis IS4 can be employed as a starter culture to produce an acceptable vegetarian soybean kapi substitute for shrimp paste kapi.Key words: Vegetarian kapi, volatile compounds, fermentation, principal component analysis, cluster analysis

KINEMATIC AND KINETIC STUDIES ON MEASUREMENT OF ROWING TECHNIQUE

China's rowing performance is good when compared with other Asian countries in Asia (e.g. Chinese athletes took away 7 of the 8 gold medals in the Xth Asian Games in 1986), but compared with world-class teams, there is still a long way to go. In the 1987 World Championships China won only bronze in the women's coxless four, and was only fourth of women's sculling in the World Youth Championships. In order to solve the problems in rowing technique, training and athletes-selection, a research group was set up and a series of studies were conducted on the rowing technique of elite Chinese rowers from national and some provincial teams. As a consequence, technical data, pictures and suggestions were provided, which have made contributions to the improvement of China's rowing performance

Volatile compounds of vegetarian soybean kapi, a fermented Thai food condiment

Kapi is a traditional shrimp paste used as a food condiment in Thailand. Several vegetarian soybean kapi, S1-S5, were fermented from various bacterial starter cultures isolated from commercial shrimp paste. The volatile compounds of S1-S5 were analyzed using SPME coupled with gaschromatography/mass spectrometry and compared to three samples of commercial vegetarian kapi (J1-J3) and commercial shrimp pastes  (K1-K3). 124 volatile compounds consisting of aldehydes, alcohols, ketones, acids and esters, N-containing compounds, aromatic compounds, S-containing compounds, miscellaneous, indoles and hydrocarbons were identified. Principle component analysis and cluster analysis separated the volatile profile of the fermented samples into four groups. Vegetarian soybean kapi, S1, S4 and S5 produced from Bacillus subtilis IS4, TISTR10 and TISTR1, respectively, were classified into the following groups containing commercial kapi (J1, J2, K2 and K3), that had a predominance of indole, S-containing and N-containing compounds. Sensory evaluation of S1 showed a strong kapi odor with higher scores among the vegetarian soybean kapi and there were no significant differences in evaluation scores between S1 and commercial vegetarian kapi J1-J3. These data demonstrate that B. subtilis IS4 can be employed as a starter culture to produce an acceptable vegetarian soybean kapi substitute for shrimp paste kapi.Key words: Vegetarian kapi, volatile compounds, fermentation, principal component analysis, cluster analysis