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Literature DB >> 24781325

Programming biological operating systems: genome design, assembly and activation.

Abstract

The DNA technologies developed over the past 20 years for reading and writing the genetic code converged when the first synthetic cell was created 4 years ago. An outcome of this work has been an extraordinary set of tools for synthesizing, assembling, engineering and transplanting whole bacterial genomes. Technical progress, options and applications for bacterial genome design, assembly and activation are discussed.

Mesh：

Substances：
DNA
Deoxyribonucleases

Year: 2014 PMID： 24781325 DOI： 10.1038/nmeth.2894

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

48 in total

Review 1. Computational tools for the synthetic design of biochemical pathways.

Authors: Marnix H Medema; Renske van Raaphorst; Eriko Takano; Rainer Breitling
Journal: Nat Rev Microbiol Date: 2012-01-23 Impact factor: 60.633

Review 2. Synthetic biology projects in vitro.

Authors: Anthony C Forster; George M Church
Journal: Genome Res Date: 2006-12-06 Impact factor: 9.043

3. Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome.

Authors: Mitsuhiro Itaya; Kenji Tsuge; Maki Koizumi; Kyoko Fujita
Journal: Proc Natl Acad Sci U S A Date: 2005-10-18 Impact factor: 11.205

4. A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast.

Authors: Paul R Jaschke; Erica K Lieberman; Jon Rodriguez; Adrian Sierra; Drew Endy
Journal: Virology Date: 2012-10-15 Impact factor: 3.616

5. Synthetic generation of influenza vaccine viruses for rapid response to pandemics.

Authors: Philip R Dormitzer; Pirada Suphaphiphat; Daniel G Gibson; David E Wentworth; Timothy B Stockwell; Mikkel A Algire; Nina Alperovich; Mario Barro; David M Brown; Stewart Craig; Brian M Dattilo; Evgeniya A Denisova; Ivna De Souza; Markus Eickmann; Vivien G Dugan; Annette Ferrari; Raul C Gomila; Liqun Han; Casey Judge; Sarthak Mane; Mikhail Matrosovich; Chuck Merryman; Giuseppe Palladino; Gene A Palmer; Terika Spencer; Thomas Strecker; Heidi Trusheim; Jennifer Uhlendorff; Yingxia Wen; Anthony C Yee; Jayshree Zaveri; Bin Zhou; Stephan Becker; Armen Donabedian; Peter W Mason; John I Glass; Rino Rappuoli; J Craig Venter
Journal: Sci Transl Med Date: 2013-05-15 Impact factor: 17.956

Programming biological operating systems: genome design, assembly and activation.

Review 1. Computational tools for the synthetic design of biochemical pathways.

Review 2. Synthetic biology projects in vitro.

3. Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome.

4. A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast.

5. Synthetic generation of influenza vaccine viruses for rapid response to pandemics.

6. A whole-cell computational model predicts phenotype from genotype.

7. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca.

Review 8. DNA synthesis, assembly and applications in synthetic biology.

9. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis.

Review 10. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering.

1. Synthetic biology advances and applications in the biotechnology industry: a perspective.

Review 2. Synthetic Biology of Natural Products.

Review 3. Codon Bias as a Means to Fine-Tune Gene Expression.

4. Exponential propagation of large circular DNA by reconstitution of a chromosome-replication cycle.

Review 5. Strategies for cloning and manipulating natural and synthetic chromosomes.

6. Vibrio natriegens as a fast-growing host for molecular biology.

7. Reinvigorating natural product combinatorial biosynthesis with synthetic biology.

Review 8. Transformation-associated recombination (TAR) cloning for genomics studies and synthetic biology.

Review 9. Rewriting the blueprint of life by synthetic genomics and genome engineering.

10. Artificially designed pathogens - a diagnostic option for future military deployments.