Local adaptation and ecological differentiation under selection, migration and drift in Arabidopsis lyrata

Posted on May 22, 2018 by Emilie Chabot

New application using the Bioruptor for DNA shearing before library preparation: In this study, researchers conducted a reciprocal transplant trial, a common garden trial, and a whole‐genome based demography analysis to understand how selection, migration and drift influence local adaptation in Arabidopsis lyrata. In a three‐year field experiment, they showed evidence of local adaptation at the level of hierarchical[…]

New publication! Application of next-generation sequencing to characterize novel mutations in clarithromycin-susceptible Helicobacter pylori strains with A2143G of 23S rRNA gene

Posted on April 4, 2018 by Emilie Chabot

Clarithromycin (CLR) resistance has become a predominant factor for treatment failure of H. pylori eradication. Although the molecular mechanism of CLR resistance has been clearly understood in H. pylori, it is lack of evidence of other genes involved in drug resistance. Furthermore, the molecular mechanism of phenotype susceptible to CLR while genotype of 23S rRNA is mutant with[…]

New article that highlights the power of the Bioruptor in DNA shearing for NGS – Phylogenomic evidence for a recent and rapid radiation of lizards in the Patagonian Liolaemus fitzingerii species group

Posted on March 24, 2018 by Emilie Chabot

Rapid evolutionary radiations are difficult to resolve because divergence events are synchronous and gene flow among nascent species can be high. Large datasets composed of sequence loci from across the genome can potentially help resolve some of these difficult phylogenetic problems. Researchers in this study chose a test case using the Liolaemus fitzingerii lizards, which includes twelve[…]

The repair of programmed DNA double-strand breaks (DSBs) physically tethers homologous chromosomes in meiosis to allow for accurate segregation through meiotic cell divisions. This process, known as recombination, also results in the exchange of alleles between parental chromosomes and contributes to genetic diversity. In mammals, meiotic DSBs occur predominantly in a small fraction of the genome, at sites known as hotspots. Studies of the formation and repair of meiotic DSBs in mammals are challenging, because few cells undergo meiotic DSB formation at a given time. To better understand the initiation and control of meiotic recombination in mammals, we have devised a highly sensitive method to map the sites of meiotic DSBs genome wide. Our method first isolates DNA bound to DSB repair proteins and then specifically sequences the associated single-stranded DNA. This protocol has generated the first meiotic DSB maps in several mammals and the only map of meiotic DSBs in humans.

Posted on March 17, 2018 by Emilie Chabot

New article in Methods in Enzymology: The repair of programmed DNA double-strand breaks (DSBs) physically tethers homologous chromosomes in meiosis to allow for accurate segregation through meiotic cell divisions. This process, known as recombination, also results in the exchange of alleles between parental chromosomes and contributes to genetic diversity. In mammals, meiotic DSBs occur predominantly in a small fraction of the genome, at sites[…]

Long read sequencing: Complete genome of the hospital-acquired strain Staphylococcus aureus Tager 104

Posted on February 20, 2017 by Emilie Chabot

Staphylococcus aureus infections range in severity due to mobile genetic elements (MGE) and single nucleotide polymorphisms. The understanding of the evolution of these dangerous pathogens requires the definition of reference strains. Richard W Davis and colleagues published a method to construct and validate the assembly of the 2.82Mb S. aureus genomes. Authors used a previously uncharacterized strain isolated from a[…]

NeuroD1 directly modifies chromatin to induce transcriptional reprogramming

Posted on December 5, 2016 by Emilie Chabot

NeuroD1 is known to support and induce the neuronal differenciation during embryogenesis. Abhijeet Pataskar and colleagues discovered new epigenetics mechanisms underlying this essential role for the devlopment. Their ChIP-, FAIRE- and RNA-sequencing and motif analysis experiments show that NeuroD1 directly binds regulatory elements of neuronal genes that are embedded in heterochromatic environment. The induction of NeuroD1 initiates the reprogramming of[…]

Best shearing of yeast genomic DNA for NGS

Posted on July 5, 2016November 29, 2016 by Emilie Chabot

DNA shearing is important step for next-generation sequencing library preparation, and reproducibility and efficiency of shearing are key factors. Nataliia Gralievska and Helle Ulrich at the Institute of Molecular Biology in Germany show that the Bioruptor®Pico is the best system to shear S. cerevisiae DNA. Since this yeast has smaller amounts of DNA per cell and a[…]