Oligomeric proanthocyanidins (OPCs) target cancer stem-like cells and suppress tumor organoid formation in colorectal cancer
February 2018
Authors:
Shusuke Toden, Preethi Ravindranathan, Jinghua Gu, Jacob Cardenas, Madelaine Yuchang &
Ajay Goel
Info:
Scientists from Baylor University Medical Center studied the chemoprotective role of oligomeric proanthocyanidins, finding that they inhibited cellular proliferation and spurred apoptosis. RNA sequencing data showed that these elements disrupted self-renewal pathways. The team used PippinHT to size-select pooled libraries prior to RNA sequencing.
Citation:
Scientific Reports
Vol 8, Article number: 3335(2018)
doi:10.1038/s41598-018-21478-8
Identification of a precursor processing protease from the spider Cupiennius saleiessential for venom neurotoxin maturation
February 2018
Authors:
Nicolas Langenegger, Dominique Koua, Stefan Schürch, Manfred Heller, Wolfgang Nentwig and Lucia Kuhn-Nentwig
Info:
In this paper, scientists from the University of Bern and collaborators report the identification and purification of a protease that’s an important neurotoxin element in spider venom. PippinHT was used to size-select cDNAs prior to sequencing.
Citation:
The Journal of Biological Chemistry
doi: 10.1074/jbc.M117.810911
Transcription-associated mutation promotes RNA complexity in highly expressed genes — a major new source of selectable variation
February 2018
Authors:
Shengkai Pan, Michael Bruford, Yusong Wang, Zhenzhen Lin, et al.
Info:
In this project, researchers studied transcriptomes in falcons, mice, and chickens and found that highly expressed genes are more likely to alternatively spliced. They also studied methylation patterns and its effect on alternative splicing. For this work, the team used SageELF to size and separate fractions for Iso-Seq analysis on the PacBio RS II system.
Citation:
Molecular Biology and Evolution
doi: 10.1093/molbev/msy017
Assembly and RNA‐free annotation of highly heterozygous genomes: The case of the thick‐billed murre (Uria lomvia)
January 2018
Authors:
Anna Tigano, Timothy Sackton, and Vicki Friesen
Info:
Researchers at Queen’s University and Harvard teamed up for an effort to assemble the highly heterozygous genome of an arctic colonial seabird. The found that the platanus assembler outperformed other methods, producing an assembly with an impressive 15.8 Mb N50. DNA integrity was evaluated using the Pippin Pulse.
Citation:
Molecular Ecology Resources
doi.org: 10.1111/1755-0998.12712
Genomics of Corynebacterium striatum, an emerging multidrug-resistant pathogen of immunocompromised patients
January 2018
Authors:
K. Nudel, X. Zhao, S. Basu, X. Dong, et al.
Info:
Scientists from Harvard Medical School and other institutions used whole genome sequencing and MALDI/TOF to analyze seven C. striatum infections, all resistant to multiple drugs. They found that three of the pathogens were related, and that complex resistance profiles could be spread by a single recombination event. BluePippin was used for size-selecting libraries prior to PacBio sequencing.
Citation:
Clinical Microbiology and Infection