Research

Transcriptionally active regions for transgene integration

transcriptional activity from RNAseq data and chromatin accessibility from ATAC sequencing graphSofie O’Brien et al. combined information on transcriptional activity from RNAseq data and chromatin accessibility from ATAC sequencing to identify desirable sites for transgene integration. This approach streamlines the development of new product producing cell lines.

(Biotechnol. J. 13: 1800226. DOI 10.1002/biot.201800226)

 

 

 

 

 

 

Stochasticity in the transfer of antibiotic resistance plasmids

pictureA collaboration between Gary Dunny (Microbiology UMN) and the Hu lab combined modeling and HCR FISH to demonstrate stochasticity in the transfer of antibiotic resistance plasmids in Enterrococcus faecalis, where transfer can occur despite unfavorable pheromone conditions.  

(Breuer, Bandyopadhyay, et al. PLoS Genet., 13:e1006878, DOI 10.1371/journal. pgen.1006878)

 

 

 

 

 

Meta-analysis of transcriptomes for hepatocyte cell differentiation

pictureRavali Raju et al. described a meta-analysis approach that enabled gene expression data of in vitrodifferentiation of hepatocyte-like cells from stem cells and mouse embryonic liver development to be integrated for analysis. Through aligning the metadata chronologically they concluded that the current HLC derived from pluripotent stem cells all reached an immature stage that is equivalent to mouse embryo liver at ~E14.

(Stem Cells and Development, 27:910-921, DOI 10.1089/scd.2017.0270)

 

 

 

Assessment of genomic instability of CHO cells

pictureCell line stability is an important issue for cell line development. Arpan Bandyopadhyay, Sofie O’Brien, et al. demonstrate regions in the genome may be prone to structural variability or copy number loss. Furthermore, heterogeneity at chromosome number, karyotype, and structure were quickly reestablished quickly after “homogenization” by single cell cloning. This work will impact current understanding of the utility of single cell cloning.  

(Biotechnol. Bioeng. DOI 10.1002/bit.26823)