Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping
August 2014
Authors:
Frederico Henning, Hyuk Je Lee, Paolo Franchini and Axel Meyer
Info:
Scientists from the University of Konstanz in Germany use double-digest RADseq to determine the genetic basis for horizontal stripes seen on cichlid fishes. Sequencing was performed on an Illumina HiSeq2000, and Pippin Prep was used to select DNA fragments from 335 bp to 405 bp.
Citation:
Molecular Ecology.
Modified paired end rapid library preparation protocol for 454 GS Junior 8 kb library preparation using Covaris g-tubes and BluePippin electrophoresis
August 2014
Authors:
Janet Hill, Bonnie Chaban, Jennifer Town, Matthew Links & Tim Dumonceaux
Info:
The scientists report a guide for 454 sample prep for paired-end reads. In their method, they eliminate the need for several expensive pieces of lab equipment and use the BluePippin to perform DNA size selection. These adjustments make the process faster and less costly.
Citation:
Protocol Exchange
doi:10.1038/protex.2014.028
Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities
July 2014
Authors:
Y. Verastegui, J. Cheng, K. Engel, D. Kolczynski, S. Mortimer, J. Lavigne, J. Montalibet, T. Romantsov, M. Hall, B. J. McConkey, D. R. Rose, J. J. Tomashek, B. R. Scott, T. C. Charles, J. D. Neufeld
Info:
In this study, researchers from the University of Waterloo and Iogen Corporation used functional metagenomics and DNA stable-isotope probing to characterize bacterial communities in soil. They also focused on glycoside hydrolase genes for their value in industrial use. Sequencing was done with Illumina HiSeq and size selection was performed with Pippin Prep to choose fragments between 400 bp and 800 bp.
Citation:
mBio 5(4): doi:10.1128/mBio.01157-14
Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element
July 2014
Authors:
Meredith A. Benson, Elizabeth A. Ohneck, Chanelle Ryan, Francis Alonzo III, Hannah Smith, Apurva Narechania, Sergios-Orestis Kolokotronis, Sarah W. Satola, Anne-Catrin Uhlemann, Robert Sebra, Gintaras Deikus, Bo Shopsin, Paul J. Planet and Victor J. Torres
Info:
Scientists in Georgia and New York used MiSeq and PacBio sequencers to analyze a hypervirulent strain of methicillin-resistant Staphylococcus aureus, finding a novel evolutionary event. The project offers new findings about evolutionary strategies that have an impact on virulence. The team used BluePippin for to remove fragments smaller than 7 Kb from their libraries prior to sequencing on the PacBio instrument.
Citation:
Molecular Microbiology (2014) 93(4), 664–681
Single-Step Selection of Bivalent Aptamers Validated by Comparison with SELEX Using High-Throughput Sequencing
June 2014
Authors:
Robert Wilson, Christian Bourne, Roy R. Chaudhuri, Richard Gregory, John Kenny, Andrew Cossins
Info:
This study, conducted by researchers at the University of Liverpool, aimed at accelerating the identification of nucleic acid aptamers by finding ways to reduce the number of rounds of selection and amplification required. They determined that next-gen sequencing and motif-finding informatics both show promise for simplifying aptamer selection. Pippin Prep was used for DNA size selection at multiple points in this technical comparison.
Citation:
PLOS ONE 9(6): e100572. doi:10.1371/journal.pone.0100572