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Background
Despite several recent advances in the automated generation of draft metabolic reconstructions, the manual curation of these networks to produce high quality genome-scale metabolic models remains a labour-intensive and challenging task.Results
We present PathwayBooster, an open-source software tool to support the manual comparison and curation of metabolic models. It combines gene annotations from GenBank files and other sources with information retrieved from the metabolic databases BRENDA and KEGG to produce a set of pathway diagrams and reports summarising the evidence for the presence of a reaction in a given organism’s metabolic network. By comparing multiple sources of evidence within a common framework, PathwayBooster assists the curator in the identification of likely false positive (misannotated enzyme) and false negative (pathway hole) reactions. Reaction evidence may be taken from alternative annotations of the same genome and/or a set of closely related organisms.Conclusions
By integrating and visualising evidence from multiple sources, PathwayBooster reduces the manual effort required in the curation of a metabolic model. The software is available online at http://www.theosysbio.bio.ic.ac.uk/resources/pathwaybooster/.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0447-2) contains supplementary material, which is available to authorized users. 相似文献84.
Suruchi Mishra Tamara B. Harris Wen-Chi Hsueh Trisha Hue Tennille S. Leak Rongling Li Mira Mehta Christian Vaisse Nadine R. Sahyoun 《PloS one》2015,10(10)
Objective
Elevated levels of serum leptin are associated with increased adiposity and production of pro-inflammatory cytokines. Both cytokines and body adiposity have been shown to predict cardiovascular events and mortality. The primary objective of the present study is to explore the associations between serum leptin and all-cause mortality and mortality from cardiovascular disease (CVD) over a span of 10 years, controlling for body adiposity and proinflammatory cytokines.Methods
The Health, Aging and Body Composition (Health ABC) study is a prospective cohort of 3,075 older adults aged 70 to 79 years. This analysis includes 2,919 men and women with complete serum leptin and vital status data. Data on all-cause mortality and incident cardiovascular events (including Coronary Heart Disease and Congestive Heart Failure) were collected over 10 years of follow-up (mean 8.4 years).Results
Women with leptin in quartile 2 and 3 were at lower risk of all-cause mortality, and those with leptin in quartile 2 were at lower risk of mortality from CVD as compared to women with lowest leptin values when adjusted for age, race, site, years of education, alcohol use, smoking, and physical activity. When these associations were additionally adjusted for body fat, C-reactive protein and pro-inflammatory cytokines, women with leptin values in quartile 3 were at lower risk of all-cause mortality and women with leptin in quartile 2 and 3 were at lower risk of mortality from CVD than women with lowest leptin values. These associations were not significant among men after adjusting for body fat and cytokines.Conclusions
The present study suggests that moderately elevated concentrations of serum leptin are independently associated with lower risk of all-cause mortality and CVD-related mortality among older women. Among men, serum leptin is not associated with reduced risk of all-cause and CVD mortality after controlling for body fat and cytokines. 相似文献85.
Xi-Wen Jiang Hong Liu Ying Xu Shu-Jun Wang David J. Leak Ning-Yi Zhou 《Archives of microbiology》2009,191(6):485-492
Pandoraea sp. strain MCB032 was isolated as an emerging chlorobenzene degrader from a functionally stable bioreactor where species
succession had occurred. In this study, two gene clusters encoding chlorobenzene metabolic functions have been cloned. Within
the cbs gene cluster, CbsA and CbsB are similar to the chlorobenzene dioxygenase and the cis-chlorobenzene dihydrodiol dehydrogenase in Ralstonia sp. JS705 and shown to transform chlorobenzene to 3-chlorocatechol. The clc gene cluster shows strong similarity to the clc genes of Ralstonia sp. JS705 and encodes chlorocatechol 1,2-dioxygenase (ClcA) and other enzymes, which catalyze the conversion of chlorocatechol
to 3-oxoadipate. The Michaelis constants (K
m) values of ClcA for catechol, 3-methylcatechol and 3-chlorocatechol were determined as 10.0, 8.9 and 3.4 μM, respectively.
CbsX, a putative transport protein present in the cbs cluster of strain MCB032 but not in those of other chlorobenzene degraders, shows 76 and 53% identities to two previously
identified transport proteins involved in toluene degradation, TbuX from Ralstonia pickettii PKO1 and TodX from Pseudomonas putida F1. The presence of the transport protein in strain MCB032 likely provides a mechanistic explanation for its higher chlorobenzene
affinity and may well be the basis for the competitive advantage of this strain in the bioreactor. 相似文献
86.
AE Clarke S Bernatsky KH Costenbader MB Urowitz DD Gladman PR Fortin M Petri S Manzi DA Isenberg A Rahman D Wallace C Gordon C Peschken MA Dooley EM Ginzler C Aranow SM Edworthy O Nived S Jacobsen G Ruiz-Irastorza E Yelin SG Barr L Criswell G Sturfelt L Dreyer I Blanco L Gottesman CH Feldman R Ramsey-Goldman 《Arthritis research & therapy》2012,14(Z3):A16
87.
Propene monooxygenase has been cloned from Mycobacterium sp. strain M156, based on hybridization with the amoABCD genes of Rhodococcus corallinus B276. Sequencing indicated that the mycobacterial enzyme is a member of the binuclear nonheme iron monooxygenase family and, in gene order and sequence, is most similar to that from R. corallinus B-276. Attempts were made to express the pmoABCD operon in Escherichia coli and Mycobacterium smegmatis mc(2)155. In the former, there appeared to be a problem resolving overlapping reading frames between pmoA and -B and between pmoC and -D, while in the latter, problems were encountered with plasmid instability when the pmoABCD genes were placed under the control of the hsp60 heat shock promoter in the pNBV1 vector. Fortuitously, constructs with the opposite orientation were constitutively expressed at a level sufficient to allow preliminary mutational analysis. Two PMO active-site residues (A94 and V188) were targeted by site-directed mutagenesis to alter their stereoselectivity. The results suggest that changing the volume occupied by the side chain at V188 leads to a systematic alteration in the stereoselectivity of styrene oxidation, presumably by producing different orientations for substrate binding during catalysis. Changing the volume occupied by the side chain at A94 produced a nonsystematic change in stereoselectivity, which may be attributable to the role of this residue in expansion of the binding site during substrate binding. Neither set of mutations changed the enzyme's specificity for epoxidation. 相似文献
88.
Effect of age and housing location on antibiotic resistance of fecal coliforms from pigs in a non-antibiotic-exposed herd. 总被引:5,自引:2,他引:3
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The relationship of age and housing location to single antibiotic resistance, multiple antibiotic resistance, and resistance patterns of fecal coliforms obtained during a 20-month period from pigs in a herd that was not exposed to antibiotics for 126 months was determined. Bacteria resistant to single and multiple antibiotics were isolated more frequently (P less than 0.01) from pigs under 7 months of age. A greater proportion of isolates from pigs over 6 months of age was sensitive to the 13 antimicrobial agents tested (P less than 0.01), while a smaller proportion showed resistance to single (P less than 0.05) and multiple (P less than 0.01) antibiotics. More than 80% of the resistant isolates were resistant to tetracycline, streptomycin, or sulfisoxazole. Resistance was greater (P less than 0.01) for pigs in the finishing unit than for those on pasture. Resistance to ampicillin, carbenicillin, and tetracycline was greater (P less than 0.05) for pigs in the finishing unit than for those in the farrowing house. More isolates from pigs on pasture were sensitive to all antimicrobial agents tested (P less than 0.01). A greater proportion of isolates from pigs in the finishing unit showed resistance to a single antibiotic (P less than 0.01). The data from this study suggest that exposure to antibiotics is not the only factor that influences the prevalence of bacteria that are resistant to single and multiple antibiotics in the feces of domestic animals and that considerable research is needed to define the factors influencing antibiotic resistance in fecal bacteria. 相似文献
89.
Evolutionary rates for tuf genes in endosymbionts of aphids 总被引:5,自引:1,他引:4
The gene encoding elongation factor Tu (tuf) in aphid endosymbionts (genus
Buchnera) evolves at rates of 1.3 x 10(-10) to 2.5 x 10(-10) nonsynonymous
substitutions and 3.9 x 10(-9) to 8.0 x 10(-9) synonymous substitutions per
position per year. These rates, which are at present among the most
reliable substitution rates for protein-coding genes of bacteria, have been
obtained by calibrating the nodes in the phylogenetic tree produced from
the Buchnera EF-Tu sequences using divergence times for the corresponding
ancestral aphid hosts. We also present data suggesting that the rates of
nonsynonymous substitutions are significantly higher in the endosymbiont
lineages than in the closely related free-living bacteria Escherichia coli
and Salmonella typhimurium. Synonymous substitution rates for Buchnera
approximate estimated mutation rates for E. coli and S. typhimurium, as
expected if synonymous changes act as neutral mutations in Buchnera. We
relate the observed differences in substitution frequencies to the absence
of selective codon preferences in Buchnera and to the influence of Muller's
ratchet on small asexual populations.
相似文献
90.
Doig SD Boam AT Leak DI Livingston AG Stuckey DC 《Biotechnology and bioengineering》1998,58(6):587-594
The Membrane Bioreactor for Biotransformations (MBB) is based on the aqueous/organic two-phase system, and uses a tubular silicone rubber membrane to separate the two liquid phases. This avoids the key problem associated with direct contact two-phase processes, specifically, product emulsification. The baker's yeast mediated reduction of geraniol to citronellol was used as a model biotransformation to demonstrate MBB operation. Values for the overall mass transfer coefficient were determined for geraniol, (2.0 x 10(-5) ms-1), and for citronellol, (2.1 x 10(-5) ms-1) diffusion across the silicone rubber membrane. Using these values, and the specific activity of the biocatalyst (5 nmols-1g biomass-1), a suitable membrane surface area: biomass ratio was determined as 2.4 x 10(-3) m2g biomass-1. The bioreactor was operated at this surface area: biomass ratio and achieved a product accumulation rate 90-95% that of a conventional direct contact two-phase system. The slight reduction in product accumulation rate was shown not to be due to mass transfer limitations with respect to reactant delivery or product extraction. Copyright 1998 John Wiley & Sons, Inc. 相似文献