'Transfer of a biosynthetic pathway between evolutionary distant organisms can create a metabolic shunt capable of bypassing the native regulation of the host organism, hereby improving the production of secondary metabolite precursor molecules for important natural products. Here, we report the engineering of Escherichia coli genes encoding the 2-C-methyl-D-erythritol-4-phosphate (MEP) ... More
Generation of human cell lines using lentiviral-mediated genetic engineering.
AuthorsSalmon P
JournalMethods Mol Biol
PubMed ID23097121
'Even now, most human cell lines used in research are derived from tumor cells. They are still widely used because they grow well in vitro and so far have helped answering several basic biological questions. However, as modern biology moves into more sophisticated areas, scientists now need human cell lines ... More
Construction and analysis of randomized protein-encoding libraries using error-prone PCR.
AuthorsHanson-Manful P, Patrick WM
JournalMethods Mol Biol
PubMed ID23504429
'In contrast to site-directed mutagenesis and rational design, directed evolution harnesses Darwinian principles to identify proteins with new or improved properties. The critical first steps in a directed evolution experiment are as follows: (a) to introduce random diversity into the gene of interest and (b) to capture that diversity by ... More
Large-scale sequencing of plant small RNAs.
AuthorsDonovan WP, Zhang Y, Howell MD
JournalMethods Mol Biol
PubMed ID21533692
'Deep sequencing technologies have become very powerful tools in the identification and quantification of small RNAs involved in gene regulation. Small interfering RNA (siRNA) and miRNA are two classes of DCL-dependent small RNAs known to affect phenotype, developmental regulation, and various traits in plants. These small RNAs function by selectively ... More
Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing.
AuthorsHarakalova M, Mokry M, Hrdlickova B, Renkens I, Duran K, van Roekel H, Lansu N, van Roosmalen M, de Bruijn E, Nijman IJ, Kloosterman WP, Cuppen E
JournalNat Protoc
PubMed ID22051800
The unprecedented increase in the throughput of DNA sequencing driven by next-generation technologies now allows efficient analysis of the complete protein-coding regions of genomes (exomes) for multiple samples in a single sequencing run. However, sample preparation and targeted enrichment of multiple samples has become a rate-limiting and costly step in ... More
InfoBiology by printed arrays of microorganism colonies for timed and on-demand release of messages.
AuthorsPalacios MA, Benito-Peña E, Manesse M, Mazzeo AD, Lafratta CN, Whitesides GM, Walt DR
JournalProc Natl Acad Sci U S A
PubMed ID21949364
This paper presents a proof-of-principle method, called InfoBiology, to write and encode data using arrays of genetically engineered strains of Escherichia coli with fluorescent proteins (FPs) as phenotypic markers. In InfoBiology, we encode, send, and release information using living organisms as carriers of data. Genetically engineered systems offer exquisite control ... More