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
DNA methylation is required for the control of stem cell differentiation in the small intestine
March 2014
Authors:
Karyn L. Sheaffer, Rinho Kim, Reina Aoki, Ellen N. Elliott, Jonathan Schug, Lukas Burger, Dirk Schubeler, and Klaus H. Kaestner
Info:
Scientists in Switzerland and Pennsylvania sought to understand the role of methylation in stem cell-directed regeneration of the intestinal epithelium in mice. They size selected for 300-600 bp DNA fragments and sequenced them with Illumina. Results indicate that losing DNA methylation at particular enhancer sites delayed stem cell differentiation and led to unusual gene expression, both of which could contribute to development of cancer.
Citation:
Genes Dev. 2014 28: 652-664
Redefining the Human Oral Mycobiome with Improved Practices in Amplicon-based Taxonomy: Discovery of Malassezia as a Prominent Commensal
March 2014
Authors:
Amanda K. Dupuy, Marika S. David, Lu Li, Thomas N. Heider, Jason D. Peterson, Elizabeth A. Montano, Anna Dongari-Bagtzoglou, Patricia I. Diaz, Linda D. Strausbaugh
Info:
In this PLoS One paper, scientists from the University of Connecticut describe the evaluation and analysis of the fungal ecosystem, or mycobiome, in a healthy human mouth. They used Pippin Prep to remove low molecular weight content and improve sequencing efficiency, followed by sequencing on the 454 GS FLX+ system. In addition to developing improved protocols for sequence-based taxonomy assignments, the team found an abundance of the genus Malassezia, which was not known to populate the oral cavity.
Citation:
PLoS ONE 9(3): e90899
Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia
March 2014
Authors:
Steven D Brown, Shilpa Nagaraju, Sagar Utturkar, Sashini De Tissera, Simón Segovia, Wayne Mitchell, Miriam L Land, Asela Dassanayake, and Michael Köpke
Info:
Scientists generated a closed, high-quality genome sequence for a Clostridium autoethanogenum strain capable of fermenting CO, CO2, and H2 into biofuels or industrial chemicals. They used BluePippin to collect fragments 4 Kb and greater for sequencing on the PacBio® platform. Among novel findings was the discovery that the organism has a CRISPR system, which may make it more amenable to use in biotechnology than closely related strains without that system.
Citation:
Biotechnology for Biofuels 2014, 7:40
Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing
March 2014
Authors:
Adam Ameur, Tracy L. Meiring, Ignas Bunikis, Susana Ha¨ggqvist, Cecilia Lindau, Julia Hedlund Lindberg, Inger Gustavsson, Zizipho Z. A. Mbulawa, Anna-Lise Williamson and Ulf Gyllensten
Info:
Researchers at Uppsala University, Sweden, along with the University of Cape Town and the National Health Laboratory in South Africa, examined co-infections in 20 HIV positive women with a rapid detection sequencing method using rolling circle amplification and the Ion Proton platform. The authors indicate a more comprehensive detection when compared to existing genotyping methods, with the added benefit genomic information being collected. The BluePippin was used to size select samples for Proton template generation.
Citation:
Scientific Reports 4:4398