Synthetic Biology

Standard biological parts knowledgebase

by Michal Galdzicki

Michal Galdzicki, Cesar Rodriguez, Deepak Chandran, Herbert M. Sauro, John H. Gennari

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web... more We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

Nanobiotechnology: Scaling up synthetic gene circuits.

by Guilhem Chalancon

Mutant Malonyl-CoA Synthetases with Altered Specificity for Polyketide Synthase Extender Unit Generation

by Gavin Williams

Chembiochem, 2011

We have used structure-guided saturation mutagenesis followed by colorimetric screening to identify mutant malonyl-CoA... more We have used structure-guided saturation mutagenesis followed by colorimetric screening to identify mutant malonyl-CoA synthetases with altered substrate specificity. One particular mutant displayed a 240-fold shift in specificity (see graphic). These mutant enzymes will be useful tools for providing extender units to probe the activity of polyketide synthases.

Recombinant E. coli prototype strains for in vivo glycorandomization.

by Gavin Williams

ACS Chem Biol, 2011

In vitro glycorandomization is a powerful strategy to alter the glycosylation patterns of natural products and small... more In vitro glycorandomization is a powerful strategy to alter the glycosylation patterns of natural products and small molecule therapeutics. Yet, such in vitro methods are often difficult to scale and can be costly given the requirement to provide various nucleotides and cofactors. Here, we report the construction of several recombinant E. coli prototype strains that allow the facile production of a range of small molecule glycosides. This strategy relies on the engineered promiscuity of three key enzymes, an anomeric kinase, a sugar-1-phosphate nucleotidyltransferase, and a glycosyltransferase, as well as the ability of diverse small molecules to freely enter E. coli. Subsequently, this work is the first demonstration of "in vivo glycorandomization" and offers vast combinatorial potential by simple fermentation.

Hellsten, I. and Nerlich, B. (2011) Synthetic biology: Building the language of a new science brick by metaphorical brick. New Genetics and Society 30(4), 375-397

by Brigitte Nerlich

http://www.tandfonline.com/doi/abs/10.1080/14636778.2011.592009

Changes in the biosciences and their relations to society over the last decades provide a unique opportunity to... more Changes in the biosciences and their relations to society over the last decades provide a unique opportunity to examine whether or not such changes leave traces in the language we use to talk about them. In this article we examine metaphors used in English-speaking press coverage to conceptualise a new type of (interdisciplinary) bioscience: synthetic biology. Findings show that three central metaphors were used between 2008 and May 2010. They exploit social and cultural knowledge about books, computers and engines and are linked to knowledge of three revolutions in science and society (the printing, information and industrial revolution). These three central metaphors are connected to each other through the concepts of reading/writing, designing and mass production and they focus on science as a revolutionary process rather than on the end results or products of science. Overall, we observed the use of a complex bricolage of mixed metaphors and chains of metaphors that root synthetic biology in historical events and achievements, while at the same time extolling its promises for the future.

GeMS: an advanced software package for designing synthetic genes

by Sebastian Jayaraj

On decoding and rewriting genomes: A psychoanalytical reading of a scientific revolution

by Hub Zwart

H. Zwart (2011) Medicine, Health Care and Philosophy 15 (1) 2012

In various documents the view emerges that contemporary biotechnosciences are currently experiencing a scientific... more In various documents the view emerges that contemporary biotechnosciences are currently experiencing a scientific revolution: a massive increase of pace, scale and scope. A significant part of the research endeavours involved in this scientific upheaval is devoted to understanding and, if possible, ameliorating humankind: from our genomes up to our bodies and brains. New developments in contemporary technosciences, such as synthetic biology and other genomics and ‘‘post-genomics’’ fields, tend to blur the distinctions between prevention, therapy and enhancement. An important dimension of this development is ‘‘biomimesis’’: i.e. the tendency of novel technologies and materials to mimic or plagiarize nature on a molecular and microscopic level in order to optimize prospects for the embedding of technological artefacts in natural systems such as human bodies and brains. In this paper, these developments are read and assessed from a psychoanalytical perspective. Three key concepts from psychoanalysis are used to come to terms with what is happening in research laboratories today. After assessing the general profile of the current revolution in this manner, I will focus on a particular case study, a line of research that may serve as exemplification of the vicissitudes of contemporary technosciences, namely viral biomaterials. Viral life forms can be genetically modified (their genomes can be rewritten) in such a manner that they may be inserted in human bodies in order to produce substances at specific sites such as hormones (testosterone), neurotransmitters (dopamine), enzymes (insulin) or bone and muscle tissue. Notably, certain target groups such as top athletes, soldiers or patients suffering from degenerative diseases may become the pioneers serving as research subjects for novel applications. The same technologies can be used for various purposes ranging from therapy up to prevention and enhancement.

Dynamic control of gene expression to optimize product formation in Escherichia coli

by Nikolaos Anesiadis

Designer Biosystem with Regulated Insulin Expression and Glucose Auto-Sensing for Diabetes

by Chih-Hsien Yang

(2007) Design of an irreversible DNA memory element

by Jamie Davies

Blenkiron M, Arvind DK, Davies JA (2007) Natural Computing 6: 403-411

(2008) Synthetic morphology: prospects for engineered, self‐constructing anatomies

by Jamie Davies

Davies JA (2008) J Anat 212: 707-719

Consequences of media information uptake and deliberation: Focus groups’ symbolic coping with synthetic biology

by Wolfgang Wagner

Kronberger, N., Holtz, P., & Wagner, W. (2011). Consequences of media information uptake and deliberation: Focus groups’ symbolic coping with synthetic biology. Public Understanding of Science,. doi: 10.1177/0963662511400331

Whenever a new, potentially controversial technology enters public awareness, stakeholders suggest that education and... more Whenever a new, potentially controversial technology enters public awareness, stakeholders suggest that education and public engagement are needed to ensure public support. Both theoretical and empirical analyses suggest, however, that more information and more deliberation per se will not make people more supportive. Rather, taking into account the functions of public sense-making processes, attitude polarisation is to be expected. In a real-world experiment, this study on synthetic biology investigated the effect of information uptake and deliberation on opinion certainty and opinion valence in natural groups. The results suggest that (a) biotechnology represents an important anchor for sense-making processes of synthetic biology, that (b) real-world information uptake and deliberation make people feel more certain about their opinions, and that (c) group attitudes are likely to polarize over the course of deliberation if the issue is important to the groups.

Slides for the invited presentation of 'The Modeling and the Simulation of the Fluid Machines of Systems/Synthetic Biology'

by Jean-Louis Giavitto

See the compagnon paper. Presented at the 12th Int. Conf. on Membrane Computing (CMC 12). 23-26 august 2011, Fontainebleau.

In the past century, several conceptual and technological breakthroughs produced the digital computers and open the... more In the past century, several conceptual and technological breakthroughs produced the digital computers and open the digital in- formation age. At the very same time, the Watson – Crick model of the digital coding of the genetic information was developed. Despite this parallel development, biology as long focused in the understanding of existing systems shaped by natural evolution whilst computer science has built its own (hardware and software) objects from scratch.

This situation is no longer true: the emergence of synthetic biology opens the doors to the systematic design and construction of biological (fluid) machines. However, even if fluid machines can be based on a kind of digital information processing, they differ from the discrete dynamical systems we are used in computer science: they have a dynamical structure.

In this paper, we stress the parallel between the development of digital information processing and genetic information processing. We sketch some tools developed or appropriated in computer science that can be used to model and specify such fluid machines. We show through an example the use of MGS, a domain specific language, in the proof of concept of a “multicellular bacterium” designed at the 2007 iGEM competition.

The Modeling and the Simulation of the Fluid Machines of Systems/Synthetic Biology

by Jean-Louis Giavitto

In Proc. of CMC'2011, 12th Conf. on Membrane Computing. 23-26 august 2011, Fontainebleau.

In the past century, several conceptual and technological breakthroughs produced the digital computers and open the... more In the past century, several conceptual and technological breakthroughs produced the digital computers and open the digital information age. At the very same time, the Watson – Crick model of the digital coding of the genetic information was developed. Despite this parallel development, biology as long focused in the understanding of existing systems shaped by natural evolution whilst computer science has built its own (hardware and software) objects from scratch.

This situation is no longer true: the emergence of synthetic biology opens the doors to the systematic design and construction of biological (fluid) machines. However, even if fluid machines can be based on a kind of digital information processing, they differ from the discrete dynamical systems we are used in computer science: they have a dynamical structure.

In this paper, we stress the parallel between the development of digital information processing and genetic information processing. We sketch some tools developed or appropriated in computer science that can be used to model and specify such fluid machines. We show through an example the use of MGS, a domain specific language, in the proof of concept of a “multicellular bacterium” designed at the 2007 iGEM competition.

Chassis cells for industrial biochemical production

by Claudia Vickers

Hyper-performing whole-cell catalysts are required for the renewable and sustainable production of petrochemical... more Hyper-performing whole-cell catalysts are required for the renewable and sustainable production of petrochemical replacements. Chassis cells—self-replicating minimal machines that can be tailored for the production of specific chemicals—will provide the starting point for designing these hyper-performing 'turbo cells'.

IPBio Symposium and Summer School, Intellectual Property and the Biosciences, (Review)

by Carlos Conde

In July 2010 I had the chance to participate in the IPBio symposium, Intellectual Property and the Biosciences, and... more In July 2010 I had the chance to participate in the IPBio symposium, Intellectual Property and the Biosciences, and the IPBio summer school held the next day. Over the course of the two days I had a great time. On one hand, the international symposium was led remarkably well by Mr Berris Charnley (University of Leeds) and Professor Gregory Radick (University of Leeds). Berris and Greg managed to organise an international event with the participation of some of the most important scholars, from both the EU and the US, currently working on issues around intellectual property rights and biotechnology. The symposium papers were very interesting especially as a wide range of subjects were analysed. Topics included stem cells, synthetic biology, plant variety protection and trademarks, to name just a few.

Modification of the Genome of Rhodobacter sphaeroides and Construction of Synthetic Operons.

by Paul Jaschke

The α-proteobacterium Rhodobacter sphaeroides is an exemplary model organism for the creation and study of novel... more The α-proteobacterium Rhodobacter sphaeroides is an exemplary model organism for the creation and study of novel protein expression systems, especially membrane protein complexes that harvest light energy to yield electrical energy. Advantages of this organism include a sequenced genome, tools for genetic engineering, a well-characterized metabolism, and a large membrane surface area when grown under hypoxic or anoxic conditions. This chapter provides a framework for the utilization of R. sphaeroides as a model organism for membrane protein expression, highlighting key advantages and shortcomings. Procedures covered in this chapter include the creation of chromosomal gene deletions, disruptions, and replacements, as well as the construction of a synthetic operon using a model promoter to induce expression of modified photosynthetic reaction center proteins for structural and functional analysis.

Promoter and Coding Sequence Considerations for Caenorhabditis elegans and Other Eukaryotes

by Chris Palmer

Current ethical issues in synthetic biology: Where should we go from here?

by Ainsley Newson

Synthetic biology (SynBio) is an emerging scientific field which has quickly established momentum and visibility.... more Synthetic biology (SynBio) is an emerging scientific field which has quickly established momentum and visibility. Although no single definition of SynBio prevails, the field broadly encompasses the application of engineering principles to biology, redesigning biological materials and using them as new substrates to create products and entities not otherwise found in nature. This article first reviews SynBio, highlighting the novel aspects of this technology. It then synthesizes ethical issues highlighted in the literature to date and makes some initial claims that research on the ethical aspects of SynBio should: avoid creating a new subtype of bioethics, concentrate on novel concepts and problems, and be situated within a context of cooperative interdisciplinary investigation.

Information About the Synthesis of Life Forms: a Document-Oriented Approach

by Inna Kouper

Kouper, I. (2010). Information about the synthesis of life forms: A document-oriented approach. Journal of Documentation, 66(3), 348-369.

Purpose – This study aims to examine the forms of information about the synthesis of life forms in the public... more Purpose – This study aims to examine the forms of information about the synthesis of life forms in the public sphere.

Design/methodology/approach – A document-oriented approach was used and a wide range of documents that discuss a particular technoscientific issue was sampled. The analysis of documents involved a combination of discourse and content analysis.

Findings – The study demonstrates that there is a significant growth of the diversity of document types over time. Overall, 24 document types and 21 publication formats were identified. Web-based formats, such as blogs and news and information web sites, play a prominent role in the dissemination of information about the synthesis of life forms.

Research limitations/implications – The variety of document types identified here expands current understanding of the public documentary landscape and shows that the analysis of technoscientific debates and controversies can no longer be limited to traditional mass media documents such as news, feature articles, and editorials. However, a larger sample that includes more documents as well as non-textual objects, such as images or even lab specimens, would expand the
scope of this taxonomy and make conclusions more definitive. Further research into the specific digital types of documents identified in the study and their impact on the communication of scientific information to the public is needed.

Practical implications – Surveying and understanding the kinds of documents that circulate information about emerging technoscientific issues can help to provide better services for a variety of information users and develop better tools for access and dissemination of such information.

Originality/value – The study demonstrates that a document-oriented approach can provide valuable insight into the circulation of information about science in the public sphere. It also offers an elaborate taxonomy of documents that can be used in further research as well as in information and science literacy instruction.