Predictable tuning of protein expression in bacteria.

We comprehensively assessed the contribution of the Shine-Dalgarno sequence to protein expression and used the data to develop EMOPEC (Empirical Model and Oligos for Protein Expression Changes; http://emopec.biosustain.dtu.dk). EMOPEC is a free tool that makes it possible to modulate the expression level of any Escherichia coli gene by changing only a few bases. Measured protein levels for 91% of our designed sequences were within twofold of the desired target level.

Functional mining of transporters using synthetic selections.

Only 25% of bacterial membrane transporters have functional annotation owing to the difficulty of experimental study and of accurate prediction of their function. Here we report a sequence-independent method for high-throughput mining of novel transporters. The method is based on ligand-responsive biosensor systems that enable selective growth of cells only if they encode a ligand-specific importer. We developed such a synthetic selection system for thiamine pyrophosphate and mined soil and gut metagenomes for thiamine-uptake functions. We identified several members of a novel class of thiamine transporters, PnuT, which is widely distributed across multiple bacterial phyla. We demonstrate that with modular replacement of the biosensor, we could expand our method to xanthine and identify xanthine permeases from gut and soil metagenomes. Our results demonstrate how synthetic-biology approaches can effectively be deployed to functionally mine metagenomes and elucidate sequence-function relationships of small-molecule transport systems in bacteria.

MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.

Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. At present, the change from a desired phenotype (e.g. altered expression of a specific protein) to a designed MAGE oligo, which confers the corresponding genetic change, is performed manually. To address these challenges, we have developed the MAGE Oligo Design Tool (MODEST). This web-based tool allows designing of MAGE oligos for (i) tuning translation rates by modifying the ribosomal binding site, (ii) generating translational gene knockouts and (iii) introducing other coding or non-coding mutations, including amino acid substitutions, insertions, deletions and point mutations. The tool automatically designs oligos based on desired genotypic or phenotypic changes defined by the user, which can be used for high efficiency recombineering and MAGE. MODEST is available for free and is open to all users at http://modest.biosustain.dtu.dk.

Simulation based virtual learning environment in medical genetics counseling: an example of bridging the gap between theory and practice in medical education.

BACKGROUND: Simulation based learning environments are designed to improve the quality of medical education by allowing students to interact with patients, diagnostic laboratory procedures, and patient data in a virtual environment. However, few studies have evaluated whether simulation based learning environments increase students' knowledge, intrinsic motivation, and self-efficacy, and help them generalize from laboratory analyses to clinical practice and health decision-making. METHODS: An entire class of 300 University of Copenhagen first-year undergraduate students, most with a major in medicine, received a 2-h training session in a simulation based learning environment. The main outcomes were pre- to post- changes in knowledge, intrinsic motivation, and self-efficacy, together with post-intervention evaluation of the effect of the simulation on student understanding of everyday clinical practice were demonstrated. RESULTS: Knowledge (Cohen's d = 0.73), intrinsic motivation (d = 0.24), and self-efficacy (d = 0.46) significantly increased from the pre- to post-test. Low knowledge students showed the greatest increases in knowledge (d = 3.35) and self-efficacy (d = 0.61), but a non-significant increase in intrinsic motivation (d = 0.22). The medium and high knowledge students showed significant increases in knowledge (d = 1.45 and 0.36, respectively), motivation (d = 0.22 and 0.31), and self-efficacy (d = 0.36 and 0.52, respectively). Additionally, 90 % of students reported a greater understanding of medical genetics, 82 % thought that medical genetics was more interesting, 93 % indicated that they were more interested and motivated, and had gained confidence by having experienced working on a case story that resembled the real working situation of a doctor, and 78 % indicated that they would feel more confident counseling a patient after the simulation. CONCLUSIONS: The simulation based learning environment increased students' learning, intrinsic motivation, and self-efficacy (although the strength of these effects differed depending on their pre-test knowledge), and increased the perceived relevance of medical educational activities. The results suggest that simulations can help future generations of doctors transfer new understanding of disease mechanisms gained in virtual laboratory settings into everyday clinical practice.

Direct mutagenesis of thousands of genomic targets using microarray-derived oligonucleotides.

Multiplex Automated Genome Engineering (MAGE) allows simultaneous mutagenesis of multiple target sites in bacterial genomes using short oligonucleotides. However, large-scale mutagenesis requires hundreds to thousands of unique oligos, which are costly to synthesize and impossible to scale-up by traditional phosphoramidite column-based approaches. Here, we describe a novel method to amplify oligos from microarray chips for direct use in MAGE to perturb thousands of genomic sites simultaneously. We demonstrated the feasibility of large-scale mutagenesis by inserting T7 promoters upstream of 2585 operons in E. coli using this method, which we call Microarray-Oligonucleotide (MO)-MAGE. The resulting mutant library was characterized by high-throughput sequencing to show that all attempted insertions were estimated to have occurred at an average frequency of 0.02% per locus with 0.4 average insertions per cell. MO-MAGE enables cost-effective large-scale targeted genome engineering that should be useful for a variety of applications in synthetic biology and metabolic engineering.