Big datasets, accumulated from biomedical and agronomic studies, provide the potential to identify genes that control complex human diseases agriculturally important traits through genome-wide association studies (GWAS). However, big datasets also lead extreme computational challenges, especially when sophisticated statistical models are employed simultaneously reduce false positives negatives. The newly developed fixed random model circulating probability unification (FarmCPU) method uses a...

(1974). Anaerobic digestion of organic matter. C R Critical Reviews in Environmental Control: Vol. 4, No. 1-4, pp. 131-191.

Surmmary Modifications to an anaerobic continuous culture apparatus allow pH control, and Eh measurements, are described. Two rumen bacteria were grown under different conditions, but as carbohydrate-limited cultures. The effects of growth rate, value on yields bacteria, enzyme activities fermentation products Optimum bacterial per mole substrate fermented ATP presumably formed in the variable with particular bacterium substrate, high for hexose fermentations. Yields varied being lowest at...

The molecular basis for the ability of bacteria to live on caffeine as a sole carbon and nitrogen source is unknown. Pseudomonas putida CBB5, which grows several purine alkaloids, metabolizes related methylxanthines via sequential N-demethylation xanthine. Metabolism by CBB5 was previously attributed one broad-specificity methylxanthine N-demethylase composed two subunits, NdmA NdmB. Here, we report that NdmB are actually independent Rieske nonheme iron monooxygenases with N(1)-...

Pseudomonas putida CBB5 was isolated from soil by enrichment on caffeine. This strain used not only caffeine, theobromine, paraxanthine, and 7-methylxanthine as sole carbon nitrogen sources but also theophylline 3-methylxanthine. Analyses of metabolites in spent media resting cell suspensions confirmed that initially N demethylated via a hitherto unreported pathway to 1- 3-methylxanthines. NAD(P)H-dependent conversion 3-methylxanthines detected the crude extracts theophylline-grown CBB5....

N-Demethylation of many xenobiotics and naturally occurring purine alkaloids such as caffeine theobromine is primarily catalysed in higher organisms, ranging from fungi to mammals, by the well-studied membrane-associated cytochrome P450s. In contrast, there no well-characterized enzyme for N-demethylation bacteria, despite several reports on their utilization sole source carbon nitrogen. Here, we provide what believe be first detailed characterization a purified N-demethylase Pseudomonas...

SUMMARY The ATP pool in Selenomonas ruminantium growing continuous culture under carbohydrate-limited conditions was low (averaging 2·3 nmoles/mg dry wt bacteria) and appeared independent of growth rate over the range optimum growth. high maximum yield (Y gluc62) previously found for another strain sele-nomonad confirmed on glucose plus pyruvate gave a calculated value Y pyr about 21. A tentative scheme is suggested production from electron-transfer reactions which would make growth-yield...

Significance All cells age and do so in relation to how many times a cell divides (replicative aging) long nondividing can live (chronological aging). Bakers’ yeast has been used study both, but because when nutrient levels permit, the genetics of its chronological lifespan only studied under calorie restriction, mimicked by starvation. Because terminally differentiated animal are long-lived rarely starve, we developed model calorie-unrestricted conditions. When encapsulated fed ad libitum,...

Methylxanthines, including caffeine and theophylline, are a class of natural synthetic compounds with important roles in food, cosmetics, medicine. These metabolized by bacteria using five enzymes from the Rieske non-heme iron oxygenase family, NdmABCDE. The NdmCDE complex is responsible for N7-demethylation 7-methylxanthine to xanthine was originally described as being highly specific 7-methylxanthine. Here, we report that also active toward theobromine, producing 3-methylxanthine due...

Understanding the genes and enzymes involved in caffeine metabolism can lead to applications such as production of methylxanthines environmental waste remediation. Pseudomonas sp. CES may provide insights into these applications, since this bacterium degrades thrives concentrations that are three times higher (9.0 g L–1) than maximum tolerable levels other reported bacteria. We took a novel approach toward identifying enzymatic pathways metabolize caffeine, which largely circumvented need...

The coffee berry borer, the most economically important insect pest of worldwide, is only capable feeding and reproducing solely on seed, a food source containing purine alkaloid caffeine. Twenty-one bacterial species associated with borers from Hawai’i, Mexico, or laboratory colony in Maryland ( Acinetobacter sp. S40, S54, S55, Bacillus aryabhattai , Delftia lacustris Erwinia S38, S43, S63, Klebsiella oxytoca Ochrobactrum S45, S46, Pantoea S61, Pseudomonas aeruginosa P. parafulva S30, S31,...

7-Methylxanthine, a derivative of caffeine noted for its lack toxicity and ability to treat even prevent myopia progression, is high-value biochemical with limited natural availability. Attempts produce 7-methylxanthine through purely chemical methods synthesis are faced complicated processes and/or the requirement variety hazardous chemicals, resulting in low yields racemic mixtures products. In recent years, we have developed engineered microbial cells several methylxanthines, including...

Caffeine and other N-methylated xanthines are natural products found in many foods, beverages, pharmaceuticals. Therefore, it is not surprising that bacteria have evolved to live on caffeine as a sole carbon nitrogen source. The degradation pathway of Pseudomonas putida CBB5 utilizes an unprecedented glutathione-S-transferase-dependent Rieske oxygenase for demethylation 7-methylxanthine xanthine, the final step N-demethylation. gene coding this function unusual, iron-sulfur non-heme iron...

Methylxanthines are natural and synthetic compounds found in many foods, drinks, pharmaceuticals, cosmetics. Aside from caffeine, production of methylxanthines is currently performed by chemical synthesis. This process utilizes chemicals, multiple reactions, different reaction conditions, making it complicated, environmentally dissatisfactory, expensive, especially for monomethylxanthines paraxanthine. A microbial platform could provide an economical, friendly approach to produce these...

Abstract Caffeine is a natural plant product found in many drinks, including coffee, tea, soft and energy drinks. Due to caffeine’s presence the environment, microorganisms have evolved two different mechanisms live on caffeine. The genetic maps of caffeine N-demethylation pathway C-8 oxidation been discovered Pseudomonas putida CBB5 sp. CBB1, respectively. These genes are only characterized bacterial caffeine-degrading genes, may be great value producing fine chemicals, biofuels, animal...

The β-galactosidase enzyme is a common reporter that has been used extensively in microbiological and synthetic biology research. Here, we demonstrate caffeine theophylline, natural methylxanthine products found many foods pharmaceuticals, negatively impact both the expression activity of Escherichia coli. E. coli grown with increasing concentrations theophylline was reduced over sixfold dose-dependent manner. We also observed decreasing lacZ mRNA transcript levels growth media. Similarly,...