La Fontaine

Duchêne, Roger

doi:10.3917/fayar.duche.1990.01

Cited by 4 publications

(4 citation statements)

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“…In S. coelicolor, the IR of the groE operon was used in a gel retardation experiment and found to bind a protein. However, the binding was the same under heat shock conditions as under normal growth temperatures, with respect to the size of the protein and the amount of binding [24]. It is possible that after heat shock this protein is modified (phosphorylated or some other modification), and in this way induces activation or lowers the repression.…”

Section: Thefunction Of the Inverted Repeatmentioning

confidence: 97%

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Regulation and organization of the groE and dnaK operons in Eubacteria

Segal

1996

FEMS Microbiology Letters

117

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groEL and dnaK are the most highly conserved protein-coding genes known. Most groEL operons and several dnaK and dnaJ operons contain a highly conserved inverted repeat (IR) sequence in their regulatory region. So far, this IR has been found only as part of the groE, dnaK and dnaJ operons and genes. In most cases, the IR is part of the operon transcript, and is involved in the regulation of expression at both the DNA and mRNA levels. A detailed analysis of groE and dnaK operons indicates that the organization of the groE operons is highly conserved. They contain only the groES and groEL genes and always in the same order. In contrast, the organization of the dnaK operons has changed during evolution: genes have been added and deleted from it, and the gene order within the operon is variable.

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Section: Thefunction Of the Inverted Repeatmentioning

confidence: 97%

“…The role of the IR in heat shock regulation was characterized in four operons: the dnaf gene of L. lactis [20], the dnaK and groE operons of Bacillus subtilis [21-231 and the groE operon of Streptomyces coelicolor [24].…”

Section: Thefunction Of the Inverted Repeatmentioning

confidence: 99%

Regulation and organization of the groE and dnaK operons in Eubacteria

Segal

1996

FEMS Microbiology Letters

117

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“…To overcome this problem, we estimated the clock rate with 168 the least-squared dating method implemented in LSD . The advantage of this method is 169 that it is fast, therefore it can be used on data sets with thousands of taxa, and with more 170 randomizations compared to the10-20 typically used in a Bayesian setting (Duchene et al 2018). One 171 limitation of least squares dating is that it typically assumes a single tree topology and vector of branch 172 lengths, however, a simulation study showed that maximum likelihood trees produced similar estimates 173 compared to the true topology ).…”

Section: Temporal Structure Of the Mtb Lineages 148mentioning

confidence: 99%

“…We inferred phylogenetic trees with raxml 8.2.11 using a GTR model (-m GTRCAT -V 507 options). Since the alignments contained only variable positions, we rescaled the branch lengths of the 508 trees rescaled_branch_length = ((branch_length * alignment_lengths) / (alignment_length + 509 invariant_sites)), Duchene and colleagues (Duchene et al 2018) showed that this method produced 510 similar results compared to ascertainment bias correction. We then used the R package ape (Paradis et 511 al.…”

Section: Evaluation Of the Temporal Structure And Lsd Analysis 505mentioning

confidence: 99%

The molecular clock of Mycobacterium tuberculosis

Menardo

Duchêne

Brites

et al. 2019

Preprint

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23The molecular clock and its phylogenetic applications to genomic data have changed how we study and 24 understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the causal agent of 25 tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to 26 infer when a particular outbreak begun, when a drug resistant clone appeared and expanded, or when a 27 strain was introduced into a specific region. Despite the growing importance of the molecular clock in 28 tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and 29 about its rate of evolution. Here we performed a systematic study of the MTB molecular clock on a 30 large genomic data set (6,285 strains), covering most of the global MTB diversity and representing 31 different epidemiological settings. We found wide variation in the degree of clocklike structure among 32 data sets, indicating that sampling times are sometimes insufficient to calibrate the clock of MTB. For 33 data sets with temporal structure, we found that MTB genomes accumulate between 1x10 -8 and 5x10 -7 34 nucleotide changes per-site-per-year, which corresponds to 0.04 -2.2 SNPs per-genome- per-year. 35 Contrary to what expected, these estimates were not dependent on the time of the calibration points as 36 they did not change significantly when we used epidemiological isolates (sampled in the last 40 years) 37 or ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and 38 the discrepancies in the results of different methods were often large, highlighting the importance of 39 using different methods, and of considering carefully their assumptions and limitations. 40 41 Keywords 42 Evolution, Phylogenetics, Pathogen, Bacteria 43 44 45 3 Significance Statement 46 47One of the major recent advancement in evolutionary biology is the development of statistical methods 48 to infer the past evolutionary history of species and populations with genomic data. In the last five 49 years, many researchers have used the molecular clock to study the evolution of Mycobacterium 50 tuberculosis, a bacterial pathogen that causes tuberculosis and is responsible for millions of human 51deaths every year. The application of the molecular clock to tuberculosis is extremely useful to 52 understand the evolution of drug resistance, the spread of different strains and the origin of the disease. 53Since some of these studies found contrasting results, we performed a systematic analysis of the 54 molecular clock of MTB. This study will provide an important guideline for future analyses of 55 tuberculosis and other organisms.

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Andersen et La Fontaine: deux ecrivains representatifs des cultures danoise et francaise?1

Auchet¹

2005

Orbis Litterarum

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Le présent article a pour objectif de montrer qu’à beaucoup d’égards Andersen et La Fontaine sont représentatifs des cultures danoise et française. Ce sont deux grands classiques de la littérature universelle, mais cela n'empêche pas leurs œuvres d’être mal connues. Ils doivent l'un et l'autre leur célébritéà un petit nombre de textes (un nombre très réduit de fables ou de contes), et ceux‐ci ont fait oublier les autres aspects de leur production littéraire: en particulier les nombreux contes du fabuliste français et les romans, récits de voyage, poèmes ou pièces de théâtre du conteur danois. Leur rapport à la nature est caractéristique de leurs cultures respectives. Le style soigné et rigoureux de l'un s'oppose à la pseudo‐oralité de l'autre, un peu comme le jardin à la française s'oppose au jardin à l'anglaise. On trouve par ailleurs chez l'un et l'autre une dimension de critique sociale. Ces deux auteurs originaux sont partis de genres littéraires déjà existants, l'apologue pour l'un, le conte populaire pour l'autre, mais ils ont su en faire un instrument parfaitement adaptéà leur génie propre. Ne reculant pas devant les expérimentations, ils ont introduit une révolution en matière de style.

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La Fontaine

Cited by 4 publications

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Regulation and organization of the groE and dnaK operons in Eubacteria

Regulation and organization of the groE and dnaK operons in Eubacteria

The molecular clock of Mycobacterium tuberculosis

Andersen et La Fontaine: deux ecrivains representatifs des cultures danoise et francaise?1

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