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
Improved Multiple Displacement Amplification (iMDA) and Ultraclean Reagents
June 2014
Authors:
S Timothy Motley, John M Picuri, Chris D Crowder, Jeremiah J Minich, Steven A Hofstadler and Mark W Eshoo
Info:
In this methods paper, researchers from Ibis Biosciences report a superior whole-genome amplification protocol that can be used with very small samples to yield enough DNA for sequencing. Their method showed better efficiency and accuracy than commercially available whole-genome amplification kits for low-input samples. Testing was done on the PGM, and Pippin Prep was used for size selection.
Citation:
BMC Genomics 2014, 15:443
Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma
June 2014
Authors:
Kristina Warton, Vita Lin, Tina Navin, Nicola J Armstrong, Warren Kaplan, Kevin Ying, Brian Gloss, Helena Mangs, Shalima S Nair, Neville F Hacker, Robert L Sutherland, Susan J Clark and Goli Samimi1
Info:
This study from the the Garvan Institute and the Kinghorn Cancer Center, and St. Vincent’s Clinical School (Univ of South Wales), in Sydney Australia, suggests a method for collecting and sequencing free circulating DNA from human plasma. The authors were able to capture small amounts of methylated DNA and create sequencing libraries using the Illumina ChIP protocol. The Pippin Prep was used to size select 180bp DNA followed by bisulfate sequencing. The study suggest that high quality genomic data can be obtained with fcDNA for potential clinical applications.
Citation:
BMC Genomics 2014, 15:476