Biomedical subjects

Michael D Lynch

Publications and source records attributed to Michael D Lynch.

3 recordsLinked to original sources

PubMed2006

SCALEs: multiscale analysis of library enrichment.

We report a genome-wide, multiscale approach to simultaneously measure the effect that the increased copy of each gene and/or operon has on a desired trait or phenotype. The method involves (i) growth selections on a mixture of several different plasmid-based genomic libraries of defined insert sizes or SCALEs, (ii) microarray studies of enriched plasmid DNA, and a (iii) mathematical multiscale analysis that precisely identifies the relevant genetic elements. This approach allows for identification of all single open reading frames and larger multigene fragments within a genomic library that alter the expression of a given phenotype. We have demonstrated this method in Escherichia coli by monitoring, in parallel, a population of >10(6) genomic library clones of different insert sizes, throughout continuous selections over a period of 100 generations.

DNA Fragmentation↗

PubMed2006

Broad host range vectors for stable genomic library construction.

We describe the construction of 36 stable vectors for genomic library construction in gram-negative species. These vectors contain the pBBR1 replicon that has been shown to stably replicate in every gram-negative species tested. The plasmids also contain bidirectional, rho-independent transcriptional terminators flanking the multiple cloning site, which allows for greater insert stability, and thus, greater genomic representation. Each vector varies in its antibiotic resistance cassette, mobilization function, and promoter used to express insert sequences. These vectors should prove useful in the screening of highly representational genomic libraries in a broad variety of gram-negative species.

Cloning, Molecular↗

PubMed2004

Mapping phenotypic landscapes using DNA micro-arrays.

Inverse metabolic engineering is a useful approach for engineering phenotypes in biological systems. The overarching objective of this approach is to combine the power of evolutionary engineering approaches with the precision of constructive metabolic engineering strategies. Often the difficulty in this approach is elucidating the genetic basis of the phenotypes that emerge as a result of evolutionary mechanisms. As a result of advances in genomics technologies, several techniques now exist that substantially improve researchers ability to identify such genes. Metabolic engineers now have the ability to map phenotypic landscapes of considerable genetic diversity, which should improve understanding of the relationships that exist among phenotype, genotype, and environment. In this mini-review, we will discuss several of such genomics tools that may be useful in developing inverse metabolic engineering strategies and, in particular, mapping phenotypic landscapes.

Animals↗