Evolution of Protein Molecules

Jukes, Thomas H.

doi:10.1016/b978-1-4832-3211-9.50009-7

Cited by 9,266 publications

(6,813 citation statements)

References 165 publications

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“…Phylogenetic analyses were performed with MEGA5 (Tamura et al, 2011). The evolutionary history was inferred by using the maximum likelihood method based on the Jukes-Cantor model (Jukes and Cantor, 1969) and the percentage of trees in which the associated taxa clustered together is shown next to the branches. In total, 1000 bootstrap replications were performed to test for branch robustness.…”

Section: Physiological Characterizationmentioning

confidence: 99%

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

et al. 2016

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The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to 'Candidatus Nitrososphaera gargensis', and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. Incorporation of 13 C-derived bicarbonate into the respective characteristic membrane lipids during nitrification supported their activity as autotrophs. Specific activities up to 198 ± 10 and 894 ± 81 mg N g − 1 VSS per day for AOAs and NOBs were measured, where NOBs were 33% more sensitive to free ammonia. The NOBs were extremely sensitive to free nitrous acid, whereas the AOAs could only be inhibited by high nitrite concentrations, independent of the free nitrous acid concentration. The observed difference in product/substrate inhibition could facilitate the development of NOB inhibition strategies to achieve more cost-effective processes such as deammonification. This study describes the enrichment of autotrophic thermophilic nitrifiers from a nutrient-rich environment and the successful operation of a thermophilic nitrifying bioreactor for the first time, facilitating opportunities for thermophilic nitrogen removal biotechnology.

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Section: Physiological Characterizationmentioning

confidence: 99%

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

et al. 2016

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“…Sequences were aligned with ClustalW (http://www.ebi.ac.uk/clustalw/). Unrooted phylogenetic trees were constructed using a matrix of Jukes-Cantor distances [29] and the neighbor-joining method of Saito and Nei [54] with PHYLIP, version 3.5 [17]. A bootstrap analysis was conducted to test the reliability of the tree [16] using SEQBOOT (PHYLIP, version 3.5).…”

Section: S Rdna Sequencesmentioning

confidence: 99%

Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

et al. 2004

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Understanding how microbial genotypes are arrayed in space is crucial for identifying local factors that may influence the spatial distribution of genetic diversity. In this study we investigated variation in 16S rDNA sequences and rep-PCR fingerprints of Streptomyces stains isolated from prairie soil among three locations and four soil depths. Substantial variation in Streptomyces OTU (operational taxonomic unit) and BOX-PCR fingerprint diversity was found among locations within a limited spatial area (1 m 2 ). Further, phylogenetic lineages at each location were distinct. However, there was little variation in genetic diversity among isolates from different soil depths and similar phylogenetic lineages were found at each depth. Some clones were found at a localized scale while other clones had a relatively widespread distribution. There was poor correspondence between 16S rDNA groupings and rep-PCR fingerprint groupings. The finding of distinct phylogenetic lineages and the variation in spatial distribution of clones suggests that selection pressures may vary over the soil landscape.

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“…In place of the linear birthshift-death process model for transposons, appropriate genotype evolution models might be inserted for markers of interest. For DNA sequences, nucleotide substitution models might be used (Jukes and Cantor, 1969;Li, 1997, for example). The probability of an observed DNA sequence at time t given the initial DNA sequence and the sampling interval is then easily computed.…”

Section: Other Types Of Markersmentioning

confidence: 99%

Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis

Rosenberg

Tsolaki

Tanaka

2003

Theoretical Population Biology

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In infectious disease epidemiology, it is useful to know how quickly genetic markers of pathogenic agents evolve while inside hosts. We propose a modular framework with which these genotype change rates can be estimated. The estimation scheme requires a model of the underlying process of genetic change, a detection scheme that filters this process into observable quantities, and a monitoring scheme that describes the timing of observations. We study a linear ''birth-shift-death'' model for change in transposable element genotypes, obtaining maximum-likelihood estimators for various detection and monitoring schemes. The method is applied to serial genotypes of the transposon IS6110 in Mycobacterium tuberculosis. The estimated birth rate of 0.0161 (events per copy of the transposon per year) and death rate of 0.0108 are both significantly larger than the estimated shift rate of 0.0018. The sum of these estimates, which corresponds to a ''half-life'' of 2.4 years for a typical strain that has 10 copies of the element, substantially exceeds a previous estimate of 0.0135 total changes per copy per year. We consider experimental design issues that enable the precision of estimates to be improved. We also discuss extensions to other markers and implications for molecular epidemiology. r

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Evolution of Protein Molecules

Cited by 9,266 publications

References 165 publications

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis

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