Single-Molecule Sequencing (PacBio) of the Staphylococcuscapitis NRCS-A Clone Reveals the Basis of Multidrug Resistance and Adaptation to the Neonatal Intensive Care Unit Environment
December 2016
Authors:
Patrícia MartinsSimões, HajarLemriss, YannDumont, SanâaLemriss, et al.
Info:
Scientists in France and Morocco fully sequenced the genome and accessory genome of a Staphylococcus capitis clone that has proven resistant to many drugs and is particularly detrimental to newborns. They identified many elements of antimicrobial resistance, including six genes carried on mobile genetic elements. BluePippin was used for size selection prior to sequencing on the PacBio RS II instrument.
Citation:
Frontiers in Microbiology
Generation of Full-Length Class I Human Leukocyte Antigen Gene Consensus Sequences for Novel Allele Characterization
December 2016
Authors:
Peter M. Clark, Jamie L. Duke, Deborah Ferriola, Valia Bravo-Egana, Tunde Vago, Aniqa Hassan, Anna Papazoglou, and Dimitri Monos
Info:
Scientists from The Children’s Hospital of Philadelphia evaluated an NGS-based HLA typing kit from Omixon. They analyzed 50 samples; 7.7% were found to have novel polymorphisms, suggesting that new sequencing approaches could usher in a new era of discovery for HLA alleles. The team used Pippin Prep to size-select libraries prior to sequencing on a MiSeq.
Citation:
Clinical Chemistry
DOI: 10.1373/clinchem.2016.260661
Plasmids from Shiga Toxin-Producing Escherichia coli Strains with Rare Enterohemolysin Gene (ehxA) Subtypes Reveal Pathogenicity Potential and Display a Novel Evolutionary Path
November 2016
Authors:
Sandra C. Lorenz, Steven R. Monday, Maria Hoffmann, Markus Fischer and Julie A. Kase
Info:
Scientists from the US FDA and the University of Hamburg used PacBio sequencing to characterize plasmids associated with heightened virulence in Shiga toxin-producing E. coli strains. They used BluePippin size selection to produce 20 kb libraries for sequencing.
Citation:
Appl. Environ. Microbiol.
November 2016 vol. 82 no. 216367-6377
Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma
November 2016
Authors:
Ruoyu Zhang, Kiichi Nakahira, Xiaoxian Guo, Augustine M.K. Choi & Zhenglong Gu
Info:
Scientists at Cornell University studied cell-free mitochondrial DNA found in plasma samples collected from sepsis patients. Along the way, they optimized sample prep protocols for short DNA fragments, producing nearly 12 times more fragments in the target size range than standard protocols. They used BluePippin to enrich libraries for fragments of 150 bp to 190 bp.
Citation:
Scientific Reports 6, Article number: 36097 (2016)
doi:10.1038/srep36097
Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples
November 2016
Authors:
Alan Van Goethem, Nurten Yigit, Celine Everaert, Myrthala Moreno-Smith, et al.
Info:
Scientists at Ghent University and Baylor College of Medicine evaluated protocols for depleting abundant RNAs from blood and serum samples to improve the ability to detect microRNAs of interest. They found a method that showed success in enriching miRNAs without bias. The team used Pippin Prep to perform size selection of small RNAs.
Citation:
Scientific Reports 6, Article number: 37876 (2016)
doi:10.1038/srep37876