Inégalité raciale au Brésil et aux États-Unis, 1990-2010

Andrews, George Reid; Mônica, Raisa Schpun; Pablo, Elisabeth de; Gousset, Eugène; Thi, Thuong Le; Cong, Khanh Nguyen; Seto, Momoko; Mareglia, Laura; Ah-Hee-Ayan, Kévin

doi:10.4000/bresils.940

Cited by 26 publications

(26 citation statements)

References 31 publications

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“…Sequence quality was initially evaluated with FastQC 0.11.9 ( Andrews, 2010 ) and trimmed for quality and contaminants with Trimmomatic ( Bolger, Lohse & Usadel, 2014 ), using the SLIDINGWINDOW mode with a 5-base wide window and quality cut off of 20, dropping reads shorter than 36 bp. Due to the availability of a published chloroplast genome from a closely related taxon, Helianthus.…”

Section: Methodsmentioning

confidence: 99%

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Loeuille

Thode

Siniscalchi

et al. 2021

PeerJ

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Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.

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Section: Methodsmentioning

confidence: 99%

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Loeuille

Thode

Siniscalchi

et al. 2021

PeerJ

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“…Machine generated data was transferred to the Ion Torrent server where data was processed through signal processing, base calling algorithms and adapter trimming to produce mate pair reads in FASTQ format. The FASTQ reads quality was assessed by the FastQC tool ( Andrews, 2010 ) followed by trimming of low quality reads and reads less than 200 bp using the Trimmomatic tool ( Bolger, Lohse & Usadel, 2014 ), where quality cut off value was Phred-20. De novo assembly of the reads was performed using SPAdes, (version 3.5.0) genome assembler ( Bankevich et al, 2012 ).…”

Section: Methodsmentioning

confidence: 99%

Adaptation of metal and antibiotic resistant traits in novel β-ProteobacteriumAchromobacter xylosoxidansBHW-15

Istiaq

Shuvo

Rahman

et al. 2019

PeerJ

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Chromosomal co-existence of metal and antibiotic resistance genes in bacteria offers a new perspective to the bacterial resistance proliferation in contaminated environment. In this study, an arsenotrophic bacteriumAchromobacter xylosoxidansBHW-15, isolated from Arsenic (As) contaminated tubewell water in the Bogra district of Bangladesh, was analyzed using high throughput Ion Torrent Personal Genome Machine (PGM) complete genome sequencing scheme to reveal its adaptive potentiality. The assembled draft genome ofA. xylosoxidansBHW-15 was 6.3 Mbp containing 5,782 functional genes, 1,845 pseudo genes, and three incomplete phage signature regions. Comparative genome study suggested the bacterium to be a novel strain ofA. xylosoxidansshowing significant dissimilarity with other relevant strains in metal resistance gene islands. A total of 35 metal resistance genes along with arsenite-oxidizingaioSXBA, arsenate reducingarsRCDAB, and mercury resistancemerRTPADEoperonic gene cluster and 20 broad range antibiotic resistance genes including β-lactams, aminoglycosides, and multiple multidrug resistance (MDR) efflux gene complex with a tripartite system OM-IM-MFP were found co-existed within the genome. Genomic synteny analysis with reported arsenotrophic bacteria revealed the characteristic genetic organization ofarsandmeroperonic genes, rarely described in β-Proteobacteria. A transposonTn21and mobile element protein genes were also detected to the end ofmer(mercury) operonic genes, possibly a carrier for the gene transposition. In vitro antibiotic susceptibility assay showed a broad range of resistance against antibiotics belonging to β-lactams, aminoglycosides, cephalosporins (1st, 2nd, and 3rd generations), monobactams and even macrolides, some of the resistome determinants were predicted during in silico analysis. KEGG functional orthology analysis revealed the potential of the bacterium to utilize multiple carbon sources including one carbon pool by folate, innate defense mechanism against multiple stress conditions, motility, a proper developed cell signaling and processing unit and secondary metabolism-combination of all exhibiting a robust feature of the cell in multiple stressed conditions. The complete genome of the strain BHW-15 stands as a genetic basis for the evolutionary adaptation of metal and the antibiotic coexistence phenomenon in an aquatic environment.

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“…Quality of sequencing samples was assessed with FastQC (v0.11.2) ( Andrews, 2010 ). Samples were mapped to the mm10 genome using STAR (v2.4) with default parameters for paired-end reads ( Dobin et al, 2013 ).…”

Section: Purification Of Primary Mouse Cellsmentioning

confidence: 99%

Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth

Dave

Sur

Yan

et al. 2017

eLife

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The gene desert upstream of the MYC oncogene on chromosome 8q24 contains susceptibility loci for several major forms of human cancer. The region shows high conservation between human and mouse and contains multiple MYC enhancers that are activated in tumor cells. However, the role of this region in normal development has not been addressed. Here we show that a 538 kb deletion of the entire MYC upstream super-enhancer region in mice results in 50% to 80% decrease in Myc expression in multiple tissues. The mice are viable and show no overt phenotype. However, they are resistant to tumorigenesis, and most normal cells isolated from them grow slowly in culture. These results reveal that only cells whose MYC activity is increased by serum or oncogenic driver mutations depend on the 8q24 super-enhancer region, and indicate that targeting the activity of this element is a promising strategy of cancer chemoprevention and therapy.DOI: http://dx.doi.org/10.7554/eLife.23382.001

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Inégalité raciale au Brésil et aux États-Unis, 1990-2010

Cited by 26 publications

References 31 publications

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Adaptation of metal and antibiotic resistant traits in novel β-ProteobacteriumAchromobacter xylosoxidansBHW-15

Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth

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