Production of the Bioactive Compounds Violacein and Indolmycin Is Conditional in a maeA Mutant of Pseudoalteromonas luteoviolaceaS4054 Lacking the Malic Enzyme
September 2016
Authors:
Mariane S. Thøgersen, Marina W. Delpin, Jette Melchiorsen, Mogens Kilstrup, Maria Månsson, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Kristian F. Nielsen, and Lone Gram
Info:
A team of scientists analyzed biological compounds produced by Pseudoalteromonas luteoviolacea, a marine bacterium. They determined that the compounds, suspected to have antibacterial activity, were not effective in that role and that the bacterium may be producing other undiscovered compounds that achieve this function. Sequencing was conducted with PacBio after size-selection with BluePippin for 10 kb libraries.
Citation:
Front Microbiol. 2016; 7: 1461.
doi: 10.3389/fmicb.2016.01461
The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads
August 2016
Authors:
Jeremy R. Shearman, Chutima Sonthirod, Chaiwat Naktang, Wirulda Pootakham, Thippawan Yoocha, Duangjai Sangsrakru, Nukoon Jomchai, Somvong Tragoonrung, and Sithichoke Tangphatsornruang
Info:
Scientists in Thailand used long-read sequencing to assemble the mitochondrial genome of a sugarcane cultivar from southeast Asia, producing two circular chromosomes. The project supports theories that all modern commercial hybrid plants descend from S. officinarum plants in New Guinea. BluePippin size selection was used to produce 20 kb libraries for PacBio sequencing.
Citation:
Sci Rep. 2016; 6: 31533.
doi: 10.1038/srep31533
A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of ‘mozuku’ biology
August 2016
Authors:
Koki Nishitsuji, Asuka Arimoto, Kenji Iwai, Yusuke Sudo, Kanako Hisata, Manabu Fujie, Nana Arakaki, Tetsuo Kushiro, Teruko Konishi, Chuya Shinzato, Noriyuki Satoh and Eiichi Shoguchi
Info:
Scientists from Japan sequenced the genome of Cladosiphon okamuranus, an edible seaweed popular in markets in Okinawa. Their analysis found more than 13,000 protein-coding genes in the 140 Mb genome. Libraries were purified with BluePippin before sequencing on Illumina MiSeq and HiSeq instruments
Citation:
Nature Methods (2016)
doi: 10.1093/dnares/dsw039
DSBCapture: in situ capture and sequencing of DNA breaks
August 2016
Authors:
Stefanie V Lensing, Giovanni Marsico, Robert Hänsel-Hertsch, Enid Y Lam, David Tannahill & Shankar Balasubramanian
Info:
Scientists at Cancer Research UK developed and validated a new sequencing-based protocol to spot double-stranded DNA breaks in situ; these regions are important for study because they contribute to mutations and chromosomal rearrangements. The method includes performing size selection on a BluePippin prior to sequencing
Citation:
Nature Methods (2016)
doi:10.1038/nmeth.3960
Association of MicroRNAs with Antibody Response to Mycoplasma bovis in Beef Cattle
August 2016
Authors:
Eduardo Casas, Guohong Cai, Larry A. Kuehn, Karen B. Register, Tara G. McDaneld, John D. Neill
Info:
USDA scientists performed a longitudinal study of young cows to identify microRNAs linked to a serum antibody produced after exposure to a common pathogen. Their analysis detected miRNAs that may have diagnostic value, as well as ones that may help boost productivity in cattle. MiRNAs were sequenced on an Illumina HiSeq after being size-selected with Pippin Prep.
Citation:
PLoS One 11(8): e0161651
doi:10.1371/journal.pone.0161651