The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure
April 2014
Authors:
Sateesh Kagale, Chushin Koh, John Nixon, Venkatesh Bollina, Wayne E. Clarke, Reetu Tuteja, Charles Spillane, Stephen J. Robinson, Matthew G. Links, Carling Clarke, Erin E. Higgins, Terry Huebert, Andrew G. Sharpe & Isobel A.P. Parkin
Info:
Scientists in Canada and Ireland generated a genome sequence of Camelina sativa and annotated more than 89,000 protein-coding genes for the oilseed crop. They determined that C. sativa experienced a whole-genome triplication that may suggest hybridization between different ancestral species with lower numbers of chromosomes. Sequencing was performed with the Illumina HiSeq after Pippin Prep size selection and with the Roche 454 FLX Titanium sequencer.
Citation:
Nature Communications 5:3706
The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells
March 2014
Authors:
Makoto Kurachi, R Anthony Barnitz, Nir Yosef, Pamela M Odorizzi, Michael A DiIorio, Madeleine E Lemieux, Kathleen Yates, Jernej Godec, Martin G Klatt, Aviv Regev, E John Wherry and W Nicholas Haining
Info:
Collaborators led by scientists at Upenn’s Perelman School of Medicine and The Dana-Farber Cancer Institute show that BATF is a central regulator of early differentiation of CD8+ Tcells. Pippin Prep was used to size select Illumina libraries in a ChIP-Seq workflow.
Citation:
Nature Immunology15:4 (2014)
Genome-wide SNPs lead to strong signals of geographic structure and relatedness paterns in the major arbovirus vector, Aedes aegypti
April 2014
Authors:
Gordana Rašić, Igor Filipović, Andrew R Weeks and Ary A Hoffmann
Info:
From the Pest and Disease Vector Group, Department of Genetics, the University of Melbourne Australia. The researchers developed a new bioinformatics tool for the ddRAD technique. Used for characterizing SNPs in field-sampled mosquitos, the study advances understanding of population genetics for the purpose of devising better disease control measures. Pippin Prep was used for size selection for the ddRAD-seq.
Citation:
BMC Genomics 2014, 15:275
A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms
April 2014
Authors:
Lisa S Mathew, Manuel Spannagl, Ameena Al-Malki, Binu George, Maria F Torres, Eman K Al-Dous, Eman K Al-Azwani, Emad Hussein, Sweety Mathew, Klaus FX Mayer, Yasmin Ali Mohamoud, Karsten Suhre and Joel A Malek
Info:
The first genetic map and sex chromosome for the data palm is presented by scientists at Weill Cornell Medical College in Qatar. The Pippin Prep was used to size select Illumina HiSeq libraries using a genotyping-by-sequencing approach.
Citation:
BMC Genomics 2014, 15:285
Detection of 1,25-Dihydroxyvitamin D-Regulated miRNAs in Zebrafish by Whole Transcriptome Sequencing
March 2014 (epub ahead of print)
Authors:
Theodore A. Craig, Yuji Zhang, Andrew T. Magis, Cory C. Funk, Nathan D. Price, Stephen C. Ekker, and Rajiv Kumar
Info:
In this paper from the journal Zebrafish, scientists report a study of microRNAs regulating gene expression induced by the presence of vitamin D in zebrafish larvae. They found that the number of miRNAs increases significantly after a week of development and hypothesize that this is due to organ and other complexity. They used Pippin Prep together with the NEBNext Multiplex Small RNA Kit from New England Biolabs to enrich for miRNAs in the sample.
Citation:
Zebrafish 2014