Biotechnology Journal

Cover image for Vol. 7 Issue 7

Special Issue: Focus: Synthetic biology

July 2012

Volume 7, Issue 7

Pages 825–932, A1–A8

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      Focus: Synthetic biology

      Article first published online: 2 JUL 2012 | DOI: 10.1002/biot.201290035

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      Focus: Synthetic biology. Synthetic biology (SynBio) can be defined as the design and construction of new biological parts, devices and systems. The field has now advanced from first-generation understanding to smarter engineering. This focus issue of BTJ gives several examples; e.g. Morey et al. review the current status of plant synthetic biology and the crosstalk between endogenous and synthetic components. (Image: © James Thew – Fotolia.com)

  2. Editorial Board

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      Editorial Board: Biotechnology Journal 7/2012 (page 825)

      Article first published online: 2 JUL 2012 | DOI: 10.1002/biot.201290039

  3. Editorial

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      Editorial: NextGen SynBio has arrived... (page 827)

      Prof. Anthony C. Forster and Prof. Sang Yup Lee

      Article first published online: 2 JUL 2012 | DOI: 10.1002/biot.201200211

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      This Focus issue edited by Anthony C. Forster (Uppsala University, Sweden) and Sang Yup Lee (KAIST, Korea) features articles from the inaugural Annual Symposium of Cold Spring Harbor Asia, entitled “Design and Synthesis of Biological Systems”, which are summarized in this editorial.

  4. In this issue

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      In this issue (page 828)

      Article first published online: 2 JUL 2012 | DOI: 10.1002/biot.201290036

  5. Contents

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      Contents: Biotechnology Journal 7/2012 (pages 829–830)

      Article first published online: 2 JUL 2012 | DOI: 10.1002/biot.201290037

  6. BiotecVisions

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  7. Forum

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      3D cell culture systems – towards primary drug discovery platforms: An interview with Heinz Ruffner (Novartis) and Jan Lichtenberg (InSphero) (pages 833–834)

      Uta Göbel

      Article first published online: 22 MAY 2012 | DOI: 10.1002/biot.201200176

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      Advanced cell culture systems for regenerative medicine, drug efficacy and toxicity testing, enabling technologies to create and analyze 3D cell culture systems were the topics of the 3D cell culture meeting taking place in March 14–16, 2012 at the Technopark in Zurich, Switzerland. At this meeting Biotechnology Journal had the pleasure to talk to Dr. Heinz Ruffner, Novartis AG, and Dr. Jan Lichtenberg, co-founder and CEO of InSphero AG, about challenges and perspectives in using 3D cell culture systems as primary drug discovery platforms.

  8. Reviews

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    1. Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription (pages 835–845)

      Prof. Anthony C. Forster

      Article first published online: 14 JUN 2012 | DOI: 10.1002/biot.201200002

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      Synthetic biology not only enables new applications in biotechnology, but also challenges hypotheses in basic biological science. Examples are reviewed here from Escherichia coli translation, codon bias and transcription.

    2. Crosstalk between endogenous and synthetic components – synthetic signaling meets endogenous components (pages 846–855)

      Kevin J. Morey, Mauricio S. Antunes, Matt J. Barrow, Fernando A. Solorzano, Keira L. Havens, J. Jeff Smith and Prof. June Medford

      Article first published online: 31 MAY 2012 | DOI: 10.1002/biot.201100487

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      Unwanted and nonspecific interactions between artificial and native signaling components in a cell can interfere with the desired signal output: The field of synthetic biology looks to the predictable behavior of electronic devices when using biological parts to engineer novel functions in living organisms. However, native signaling systems can and do interfere with synthetic systems. This review article discusses the impact of these interactions in two partial synthetic signaling systems in plants, and reviews current research that applies to the design of synthetic signaling systems with regards to improved signaling specificity.

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      Contextualizing context for synthetic biology – identifying causes of failure of synthetic biological systems (pages 856–866)

      Stefano Cardinale and Prof. Adam Paul Arkin

      Article first published online: 31 MAY 2012 | DOI: 10.1002/biot.201200085

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      Identifying sources of failure of synthetic biological devices: In this review, the authors explore a variety of factors that unpredictably affect the function of synthetic devices once transferred in a cellular environment. These sources of failure are obviously interconnected from the direct molecular interactions within the device, the interaction among devices within cells, and the external environment, which can affect either class of contextual effects directly or indirectly through the host. This analysis will certainly help improve the rational design of synthetic biological systems.

  9. Research Articles

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    1. Serial assembly of Thermus megaplasmid DNA in the genome of Bacillus subtilis 168: A BAC-based domino method applied to DNA with a high GC content (pages 867–876)

      Naoto Ohtani, Miki Hasegawa, Mitsuru Sato, Masaru Tomita, Shinya Kaneko and Prof. Mitsuhiro Itaya

      Article first published online: 16 MAY 2012 | DOI: 10.1002/biot.201100396

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      Bacillus subtilis is the most optimal bacterium-based host which allows cloning of giant DNAs. DNA previously cloned with this host was limited to that with GC content similar to or lower than that of the B. subtilis genome. In this study, a pTT27 megaplasmid from T. thermophilus was cloned in BGM (B. subtilis genome) vector through three intermediary lengths by a BAC-based Domino method. The shorter two pTT27 segments were retrieved in plasmid form by a CReT method with a conjugational plasmid, whereas the longer ones were not. The B. subtilis genome was demonstrated to accommodate large DNA with high GC content but may be restricted to less than 200 kbp by unidentified mechanisms.

    2. Engineering of self-sustaining systems: Substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system in a Lactococcus lactis network in silico (pages 877–883)

      Malgorzata Adamczyk and Prof. Hans V. Westerhoff

      Article first published online: 14 JUN 2012 | DOI: 10.1002/biot.201100314

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      Living cells are bound to notice that metabolic engineering is being effected through changes in metabolite concentrations. In this study, the authors asked whether one could engage in such engineering without changing metabolite concentrations. The authors demonstrate in the computer that one can engineer the sugar uptake system (blue) from yeast that helps make bread, into the bacterium Lactococcus lactis that can make buttermilk and help to make cheese. One can do this in such a way that the bacterium organism does not notice, i.e. by also introducing hexokinase (green) and increasing pyruvate kinase (red) precisely to the extents that ensure that the metabolite concentrations (e.g. that of phosphoenolpyruvate, PEP) remain constant. This method should open up new and perhaps betters ways of making more or better buttermilk and (Gouda) cheeses as well as improved metabolic engineering strategies.

  10. Technical Reports

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    1. Virus-induced multiple gene silencing to study redundant metabolic pathways in plants: Silencing the starch degradation pathway in Nicotiana benthamiana (pages 884–890)

      Dr. Gavin M. George, Rolene Bauer, Andreas Blennow, Jens Kossmann and James R. Lloyd

      Article first published online: 7 MAR 2012 | DOI: 10.1002/biot.201100469

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      Virus-Induced Gene Silencing (VIGS) is an effective tool for ‘loss-of-function’ studies when multiple genes are targeted. To advance the understanding of starch degradation, in this article, the authors show the application of multiple gene VIGS repression for the study of the redundant biological pathways in the leaf metabolism of Nicotiana benthamiana. They demonstrate the feasibility for multiple VIGS to be used as reverse genetics tool, which can assess redundant enzyme systems typical for the plant kingdom.

    2. Gateway-compatible transposon vector to genetically modify human embryonic kidney and adipose-derived stromal cells. (pages 891–897)

      Dr. Spyros Petrakis, Tamas Raskó, Lajos Mátés, Zoltan Ivics, Zsuzsanna Izsvák, Kokkona Kouzi-Koliakou and George Koliakos

      Article first published online: 7 MAR 2012 | DOI: 10.1002/biot.201100471

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      Novel Gateway Technology compatible transposon plasmid combines the advantages of the Gateway recombination cloning with the Sleeping Beauty (SB) transposon-mediated transgene integrations. With this technique HEK293 or adipose-derived stromal cell lines were stably transfected to express and secrete human interferon-beta. The generated Gateway compatible transposon plasmid may be used for gene therapy or high-throughput screening methods in primary cells representing a valuable molecular tool for laboratory applications.

  11. Research Articles

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    1. Using the Cre/lox system for targeted integration into the human genome: loxFAS-loxP pairing and delayed introduction of Cre DNA improve gene swapping efficiency (pages 898–908)

      Amanda M. Lanza, Timothy J. Dyess and Prof. Hal S. Alper

      Article first published online: 16 MAY 2012 | DOI: 10.1002/biot.201200034

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      Cre recombinase is a widely used genomic editing tool for mammalian cells; however, the efficiency of transgenic swapping events compared to excision remains limited. In this article, authors describe and validate a dual fluorescent assay that facilitates real-time measurements of the swapping and excision processes, which cannot be assessed using standard antibiotic selection techniques. The swapping frequencies identified here can greatly improve the prospects of using this genome-editing tool in mammalian cell systems.

    2. Use of high-gradient magnetic fishing for reducing proteolysis during fermentation (pages 909–918)

      Trine L. Maury, Kim E. Ottow, Jesper Brask, John Villadsen and Prof. Timothy J. Hobley

      Article first published online: 14 FEB 2012 | DOI: 10.1002/biot.201100376

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      Degradation or modification of products during fermentation and downstream processing complicates both laboratory and industrial scale production, which is often a side-effect extracellular enzyme by-products. In this article, authors from the Technical University of Denmark, demonstrate the use of high-gradient magnetic fishing (HGMF) as an efficient alternative to the more conventional methods of preventing proteolytic degradation.

    3. High-throughput screening for cellobiose dehydrogenases by Prussian Blue in situ formation (pages 919–930)

      Liliya G. Vasilchenko, Roland Ludwig, Olga P. Yershevich, Dietmar Haltrich and Prof. Mikhail L. Rabinovich

      Article first published online: 14 FEB 2012 | DOI: 10.1002/biot.201100480

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      Cellobiose dehydrogenases (CDHs) are extracellular fungal flavocytochromes which, owing to their unique electron transfer properties, are extensively studied in bioelectronics. Neutral CDHs from ascomycetes are of particular interest because of their possible application in the physiologically compatible nanobiodevices. In this article, the authors present a new selective and high-throughput screening assay for these enzymes based on in situ Prussian Blue formation.

  12. Meetings

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      Meetings and Conferences: Biotechnology Journal 7/2012 (pages 931–932)

      Article first published online: 2 JUL 2012 | DOI: 10.1002/biot.201290038

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