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

Distributed Stochastic Optimization over Time-Varying Noisy Network

This paper is concerned with distributed stochastic multi-agent optimization problem over a class of time-varying network with slowly decreasing communication noise effects. This paper considers the problem in composite optimization setting which is more general in noisy network optimization. It is noteworthy that existing methods for noisy network optimization are Euclidean projection based. We present two related different classes of non-Euclidean methods and investigate their convergence behavior. One is distributed stochastic composite mirror descent type method (DSCMD-N) which provides a more general algorithm framework than former works in this literature. As a counterpart, we also consider a composite dual averaging type method (DSCDA-N) for noisy network optimization. Some main error bounds for DSCMD-N and DSCDA-N are obtained. The trade-off among stepsizes, noise decreasing rates, convergence rates of algorithm is analyzed in detail. To the best of our knowledge, this is the first work to analyze and derive convergence rates of optimization algorithm in noisy network optimization. We show that an optimal rate of $O(1/\sqrt{T})$ in nonsmooth convex optimization can be obtained for proposed methods under appropriate communication noise condition. Moveover, convergence rates in different orders are comprehensively derived in both expectation convergence and high probability convergence sense.Comment: 27 page

Rapid, quantitative determination of bacteria in water

A bioluminescent assay for ATP in water borne bacteria is made by adding nitric acid to a water sample with concentrated bacteria to rupture the bacterial cells. The sample is diluted with sterile, deionized water, then mixed with a luciferase-luciferin mixture and the resulting light output of the bioluminescent reaction is measured and correlated with bacteria present. A standard and a blank also are presented so that the light output can be correlated to bacteria in the sample and system noise can be substracted from the readings. A chemiluminescent assay for iron porphyrins in water borne bacteria is made by adding luminol reagent to a water sample with concentrated bacteria and measuring the resulting light output of the chemiluminescent reaction

Detection of Close-In Extrasolar Giant Planets Using the Fourier-Kelvin Stellar Interferometer

We evaluate the direct detection of extrasolar giant planets with a two-aperture nulling infrared interferometer, working at angles ${\theta}<{\lambda}/2B$, and using a new `ratio-of-two-wavelengths' technique. Simple arguments suggest that interferometric detection and characterization should be quite possible for planets much closer than the conventional inner working angle, or angular resolution limit. We show that the peak signal from a nulling infrared interferometer of baseline ($\lesssim 40$ meters) will often occur `inside the null', and that the signal variations from path-difference fluctuations will cancel to first order in the ratio of two wavelengths. Using a new interferometer simulation code, we evaluate the detectability of all the known extrasolar planets as observed using this two-color method with the proposed {\it Fourier Kelvin Stellar Interferometer (FKSI)}. In its minimum configuration {\it FKSI} uses two 0.5-meter apertures on a 12.5-meter baseline, and a $\pm 20^{\circ}$ field-of-regard. We predict that $\sim 7$ known extrasolar planets are directly detectable using {\it FKSI}, with low-resolution spectroscopy ($R \sim 20$) being possible in the most favorable cases. Spaceborne direct detection of extrasolar giant planets is possible with $\sim 12$ meter baselines, and does not require the much longer baselines provided by formation flying.Comment: Accepted for publication in ApJ Letter

Determination of antimicrobial susceptibilities on infected urines without isolation

A method is described for the quick determination of the susceptibilities of various unidentified bacteria contained in an aqueous physiological fluid sample, particularly urine, to one or more antibiotics. A bacterial adenosine triphosphate (ATP) assay is carried out after the elimination of non-bacterial ATP to determine whether an infection exists. If an infection does exist, a portion of the sample is further processed, including subjecting parts of the portion to one or more antibiotics. Growth of the bacteria in the parts are determined, again by an ATP assay, to determine whether the unidentified bacteria in the sample are susceptible to the antibiotic or antibiotics under test

Total Quality Management: Implications for Educational Assessment

The approach to quality that trans formed industry in Japan may help to improve educational quality in Ameri can schools. In 1982, W Edwards Deming identified 14 principles for the transformation of American industry. Recently he developed his "System of Profound Knowledge," which is even more fundamental than the 14 princi ples. Here's a look at their implica tions for education.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66966/2/10.1177_019263659207654510.pd

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

The role of bacteria in the turnover of organic carbon in deep-sea sediments

The cycling of organic carbon in the deep sea was inferred from measurements of sediment trap and box core samples taken on the Biscay and Demerara abyssal plains of the North Atlantic. Of the input of organic carbon to the bottom, less than 10% was buried, i.e., not consumed biologically. Based on laboratory measurements of bacterial activity in the sediment samples, incubated under in situ temperature and pressure, it was possible to attribute at least 13 to 30% of the total inferred biological consumption of organic carbon to microbial utilization. The complementarity of results from these biochemical and microbiological measurements implies that the decompression of cold abyssal samples during retrieval efforts does not prevent meaningful experiments on the microbial inhabitants, once returned to in situ pressure

The Importance of Phase in Nulling Interferometry and a Three Telescope Closure-Phase Nulling Interferometer Concept

We discuss the theory of the Bracewell nulling interferometer and explicitly demonstrate that the phase of the "white light" null fringe is the same as the phase of the bright output from an ordinary stellar interferometer. As a consequence a "closure phase" exists for a nulling interferometer with three or more telescopes. We calculate the phase offset as a function of baseline length for an Earth-like planet around the Sun at 10 pc, with a contrast ratio of $10^{-6}$ at 10 $\mu$m. The magnitude of the phase due to the planet is $\sim 10^{-6}$ radians, assuming the star is at the phase center of the array. Although this is small, this phase may be observable in a three-telescope nulling interferometer that measures the closure phase. We propose a simple non-redundant three-telescope nulling interferometer that can perform this measurement. This configuration is expected to have improved characteristics compared to other nulling interferometer concepts, such as a relaxation of pathlength tolerances, through the use of the "ratio of wavelengths" technique, a closure phase, and better discrimination between exodiacal dust and planets

Application of firefly luciferase assay for adenosine triphosphate (ATP) to antimicrobial drug sensitivity testing

The development of a rapid method for determining microbial susceptibilities to antibiotics using the firefly luciferase assay for adenosine triphosphate (ATP) is documented. The reduction of bacterial ATP by an antimicrobial agent was determined to be a valid measure of drug effect in most cases. The effect of 12 antibiotics on 8 different bacterial species gave a 94 percent correlation with the standard Kirby-Buer-Agar disc diffusion method. A 93 percent correlation was obtained when the ATP assay method was applied directly to 50 urine specimens from patients with urinary tract infections. Urine samples were centrifuged first to that bacterial pellets could be suspended in broth. No primary isolation or subculturing was required. Mixed cultures in which one species was predominant gave accurate results for the most abundant organism. Since the method is based on an increase in bacterial ATP with time, the presence of leukocytes did not interfere with the interpretation of results. Both the incubation procedure and the ATP assays are compatible with automation