SynBioFromLeukipposInstitute

by

Richard Kitney, Paul Freemont
"It is now just over two years since the article 5 Hard Truths for Synthetic Biology was published [1]. The article looked at some of the issues relating to synthetic biology at that time. As we will show, many things have changed in the interim period. Two years ago there was still considerable doubt about whether or not synthetic biology was likely to have significant industrial impact. It is now pretty clear that the case has been made and that synthetic biology will have very significant impact in a range of fields - leading to the development of new, major industries. The evidence for this statement can be found in a number of sources. For example the bcc report [2] which predicts that:
 The global value of the synthetic biology market reached $1.1 billion in 2010. It is expected to reach $1.6 billion in 2011 and it will further grow to $10.8 billion by 2016, increasing at a compound annual growth rate (CAGR) of 45.8.%
 The global value of the enabled products segment reached $944.7 million in 2010. It is expected to reach $1.4 billion in 2011 and will further grow to nearly $9.5 billion by 2016 at a CAGR of 46.5%.
 The global value of the core products segment reached $109.4 million in 2010. It is expected to reach $126.8 million in 2011 and to grow to $698.8 million by 2016 at a CAGR of 40.7%.
There is, in some quarters, still doubt about the definition of synthetic biology......"
http://bit.ly/MICe28

by

Yaakov Benenson
"The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing."
http://bit.ly/Ll8Lg2

http://bit.ly/Ny8Kss

*Genome-based microbiology-From -omics research to systems and synthetic biology*

by
Pühler A.
http://1.usa.gov/Kn2OBF

*Increasing the success rate of lantibiotic drug discovery by Synthetic Biology*

by
Montalbán-López M, Zhou L, Buivydas A, van Heel AJ, Kuipers OP.
"Introduction: Lantibiotics are post-translationally modified antimicrobial peptides produced by bacteria from diverse environments that exhibit an activity against pathogenic bacteria comparable to that of medically used antibiotics. The actual need for new antimicrobials in therapeutics has placed them in the pipeline of antibiotic research, due not only to their high antimicrobial activity but also to the fact that they are directed to novel targets. Areas covered: This review covers the different approaches traditionally used in bacteriocin discovery, based on the isolation of bacteria from different habitats and determining their inhibitory spectrum against a set of relevant strains. It also elaborates on more recent approaches covering organic synthesis and semi-synthesis of lantibiotics, genomic and proteomic approaches and the application of Synthetic Biology to the field of antimicrobial drug discovery. Expert opinion: Lantibiotics show a great potential in fulfilling the requirements for new antimicrobials. Culture-dependent techniques are still applied to lantibiotic discovery producing successful results that can be furthered by employing high-throughput screening techniques and peptidogenomics. The necessity of culturing bacteria and growing them in specific conditions for lantibiotic expression, can hamper the discovery rate, especially in exotic or unculturable bacteria. Thus, a combination of genome mining procedures, to detect novel lantibiotic-related sequences, with heterologous production systems and high-throughput screening, offers a promising strategy. Furthermore, the characterization of the mechanism of action of many lantibiotics, and the development of "plug and play" peptide biosynthesis systems, offers the possibility of initiating the rational design of non-natural lantibiotics based on structure-activity relationships."
http://1.usa.gov/LR4W1c

June 12-13, 2012
Washington, DC

Follow on Twitter: #synbioLEAP

http://bit.ly/Mp5Lk2

by

Hockenberry AJ, Jewett MC.

"Inspired by advances in the ability to construct programmable circuits in living organisms, in vitro circuits are emerging as a viable platform for designing, understanding, and exploiting dynamic biochemical circuitry. In vitro systems allow researchers to directly access and manipulate biomolecular parts without the unwieldy complexity and intertwined dependencies that often exist in vivo. Experimental and computational foundations in DNA, DNA/RNA, and DNA/RNA/protein based circuitry have given rise to systems with more than 100 programmed molecular constituents. Functionally, they have diverse capabilities including: complex mathematical calculations, associative memory tasks, and sensing of small molecules. Progress in this field is showing that cell-free synthetic biology is a versatile testing ground for understanding native biological circuits and engineering novel functionality."

by

Mary Ann Blätke, Anna Dittrich2, Christian Rohr, Monika Heiner, Fred Schaper, Wolfgang Marwan
"We describe a molecule-oriented modelling approach based on a collection of Petri net models organized in the form of modules into a prototype database accessible through a web interface. The JAK/STAT signalling pathway with the extensive cross- talk of its components is selected as case study. Each Petri net module represents the reactions of an individual protein with its specific interaction partners. These Petri net modules are graphically displayed, can be executed individually, and allow the automatic composition into coherent models containing an arbitrary number of molecular species chosen ad hoc by the user. Each module contains metadata for documentation purposes and can be extended to a wiki-like minireview. The database can manage multiple versions of each module. It supports the curation, documentation, version control, and update of individual modules and the subsequent automatic composition of complex models, without requiring mathematical skills. Modules can be (semi-) automatically recombined according to user defined scenarios e.g. gene expression patterns in given cell types, under certain physiological conditions, or states of disease. Adding a localisation component to the module database would allow to simulate models with spatial resolution in the form of coloured Petri nets. As synthetic biology application we propose the fully automated generation of synthetic or synthetically rewired network models by composition of metadata-guided automatically modified modules representing altered protein binding sites. Petri nets composed from modules can be executed as ODE system, stochastic, hybrid, or merely qualitative models and exported in SMBL format."
http://bit.ly/LFjfb9

*FEBS Lett. Special Issue - Synthetic Biology*

Introduction by
Reiss T.
"Already 100 years ago the concept of synthetic biology emerged
when Stéphane Leduc [6] and Jacques Loeb [7] speculated over
possibilities to create artificial living systems. Since then the idea
of synthetic biology has evolved mainly as an approach of analys-
ing, understanding, and improving biological processes for the pro-
duction of desirable goods and functions. The introduction of
recombinant DNA technology in the early 1970s added completely
new options to such approaches. Since about 10 years the original
concept of synthetic biology returned with a new orientation and
an extraordinary dynamics [1–5]. Main drivers for this revival were
the results of whole genome sequencing, which provided abundant
information about the building blocks of living systems, and the
concept of systems biology, which offered a new way for the
understanding of how biological components function and interact
in reality trying to explain structures and functions of biological
systems........"
http://bit.ly/M6QjF6

by

Lindblad P, Lindberg P, Oliveira P, Stensjö K, Heidorn T.
"There is an urgent need to develop sustainable solutions to convert solar energy into energy carriers used in the society. In addition to solar cells generating electricity, there are several options to generate solar fuels. This paper outlines and discusses the design and engineering of photosynthetic microbial systems for the generation of renewable solar fuels, with a focus on cyanobacteria. Cyanobacteria are prokaryotic microorganisms with the same type of photosynthesis as higher plants. Native and engineered cyanobacteria have been used by us and others as model systems to examine, demonstrate, and develop photobiological H(2) production. More recently, the production of carbon-containing solar fuels like ethanol, butanol, and isoprene have been demonstrated. We are using a synthetic biology approach to develop efficient photosynthetic microbial cell factories for direct generation of biofuels from solar energy. Present progress and advances in the design, engineering, and construction of such cyanobacterial cells for the generation of a portfolio of solar fuels, e.g., hydrogen, alcohols, and isoprene, are presented and discussed. Possibilities and challenges when introducing and using synthetic biology are highlighted."
http://1.usa.gov/Ny7N3s

by

Brune KD, Bayer TS.
"In natural environments microorganisms commonly exist as communities of multiple species that are capable of performing more varied and complicated tasks than clonal populations. Synthetic biologists have engineered clonal populations with characteristics such as differentiation, memory, and pattern formation, which are usually associated with more complex multicellular organisms. The prospect of designing microbial communities has alluring possibilities for environmental, biomedical, and energy applications, and is likely to reveal insight into how natural microbial consortia function. Cell signaling and communication pathways between different species are likely to be key processes for designing novel functions in synthetic and natural consortia. Recent efforts to engineer synthetic microbial interactions will be reviewed here, with particular emphasis given to research with significance for industrial applications in the field of biomining and bioremediation of acid mine drainage."
http://1.usa.gov/LKHeUm

by

JURIJS MEITALOVS, NATALJA BULIPOPA, OLESJA KOVALONOKA

"The aim of this paper is to review several computational tools for application in synthetic biology. Recently developed computational tools, for instance, for gap-filling, orphan reaction searching, metabolic engineering, pathway analysing, gene engineering, metabolic reconstruction and others, were reviewed and their functionality was described. Some tools have similar functionality and some tools can be used for different tasks. Tools for comparison were chosen from the most cited scientific literature."
http://bit.ly/KTbIaG

by

Stephen Hilgartner
"Synthetic biology is typically described as an arena in which new kinds of biological entities are being created via novel ‘engineering-based’ means of tinkering with life and its component parts. This research domain is also an arena of social experimentation, in that some advocates of synthetic biology are actively promoting new property regimes aimed at establishing various forms of ‘open biology’. This article considers how these emerging visions of open biology are implicated in the construction of political subjects and the relations among them. The article contrasts two policy discourses for understanding intellectual property: the traditional innovation perspective and the less well-institutionalized but clearly emerging politics-of-technology perspective. These discourses serve as heuristic devices that offer different perspectives from which to view emerging property regimes in the synthetic biology arena. As a concrete example of an open biology regime, the article then turns to the BioBricks initiative and examines the regime being imagined and constituted in its vision of open synthetic biology. In this way, the article explores the question of whether and in what ways the open source regimes currently being proposed actually address increasingly pressing questions about how property rights in emerging technology impinge on democratic decision making."
http://bit.ly/Kagq35