SynBioFromLeukipposInstitute

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Erhan Bilal et al

"Animal models are very important tools in drug discovery and for understanding human biology in general. However many drugs that initially show promising results in rodents fail in later stages of clinical trials. Understanding the commonalities and differences between human and rat cell signaling networks can lead to better experimental designs, improved allocation of resources and ultimately better drugs.

 http://bit.ly/1w4adti

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Filippo Caschera, Vincent Noireaux 

"Various approaches are taken to construct synthetic cells in the laboratory, a challenging goal that became experimentally imaginable over the past two decades. The construction of protocells, which explores scenarios of the origin of life, has been the original motivations for such projects. With the advent of the synthetic biology era, bottom-up engineering approaches to synthetic cells are now conceivable. The modular design emerges as the most robust framework to construct a minimal cell from natural molecular components. Although significant advances have been made for each piece making this complex puzzle, the integration of the three fundamental parts, information–metabolism–self-organization, into cell-sized liposomes capable of sustained reproduction has failed so far. Our inability to connect these three elements is also a major limitation in this research area. New methods, such as machine learning coupled to high-throughput techniques, should be exploited to accelerate the cell-free synthesis of complex biochemical systems."


http://bit.ly/ZQe6IT

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Kennedy AB, Vowles JV, d'Espaux L, Smolke C

"Genetic devices that directly detect and respond to intracellular concentrations of proteins are important synthetic biology tools, supporting the design of biological systems that target, respond to or alter specific cellular states. Here, we develop ribozyme-based devices that respond to protein ligands in two eukaryotic hosts, yeast and mammalian cells, to regulate the expression of a gene of interest. Our devices allow for both gene-ON and gene-OFF response upon sensing the protein ligand. As part of our design process, we describe an in vitro characterization pipeline for prescreening device designs to identify promising candidates for in vivo testing. The in vivo gene-regulatory activities in the two types of eukaryotic cells correlate with in vitro cleavage activities determined at different physiologically relevant magnesium concentrations. Finally, localization studies with the ligand demonstrate that ribozyme switches respond to ligands present in the nucleus and/or cytoplasm, providing new insight into their mechanism of action. By extending the sensing capabilities of this important class of gene-regulatory device, our work supports the implementation of ribozyme-based devices in applications requiring the detection of protein biomarkers."


http://bit.ly/1nXDE1v

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Christian Pade, Bernd Giese, Stefan Koenigstein, Henning Wigger, Arnim von Gleich

"What distinguishes synthetic biology from earlier approaches in biology and biotechnology? What are future applications that may possibly be realized through synthetic biology? What can be expected from synthetic biology with respect to the benefits it may provide as well as the risks it may pose? This chapter puts forward the idea that these questions, among others that regard the promises and threats of this new and emerging field of science and technology, can be explored by applying the concept of functionality to synthetic-biological structures and systems. Functionality, in this respect, is defined as a certain physicochemical or biological effect that can be brought about by a (synthetic-) biological object. This effect, in turn, has repercussions on the wider systems context the respective object appears in. Looking at the various hierarchical levels of biological life, functionalities that have already been realized through synthetic-biological approaches, as well as those that may be realized through future research and development, are systematically analyzed. Based on this analysis, applications that make use of these functionalities thus far, or may do so in the future, are presented. Furthermore, it is investigated how the functionalities may change the hazardous properties or exposure behavior of the respective structures or systems and thus potentially increase the risk associated with them."

 http://bit.ly/1vIl5wX

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Kitaoka N, Lu X, Yang B, Peters RJ.

"Plants synthesize a huge variety of terpenoid natural products, including photosynthetic pigments, signaling molecules and defensive substances. These are often produced as complex mixtures, presumably shaped by selective pressure over evolutionary timescales, some of which have been found to have pharmaceutical and other industrial uses. Elucidation of the relevant biosynthetic pathways can provide increased access (e.g., via molecular breeding or metabolic engineering), and enable reverse genetic approaches towards understanding the physiological role of these natural products in plants as well. While such information can be obtained via a variety of approaches, this review describes the emerging use of synthetic biology to recombinantly reconstitute plant terpenoid biosynthetic pathways in heterologous host organisms as a functional discovery tool, with a particular focus on incorporation of the historically problematic cytochrome P450 mono-oxygenases. Also falling under the synthetic biology rubric and discussed here is the nascent application of genome-editing tools to probe physiological function."

 http://bit.ly/1mRVcLM

From BioCoder 4:

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Pablo Cárdenas, Maaruthy Yelleswarapu, Sayane Shome, Jitendra Kumar Gupta, Eugenio Maria Battaglia, Pedro Fernandes, Alioune Ngom, and Gerd Moe-Behrens

"As we move deeper into the digital age, the social praxis of science undergoes fundamental changes, driven by new tools provided by information and communication technologies. Specifically, social networks and computing resources such as online cloud-based infrastructures and applications provide the necessary context for unprecedented innovations in modern science. These tools are leading to a planetary-scale connectivity among researchers and enable the organization of in silico research activities entirely through the cloud.

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Philip D. Howes, Rona Chandrawati, Molly M. Stevens

"Nanoparticle biosensors have the potential to enhance or supersede current analytical techniques, and their introduction could have a great impact in research and clinical practice. The unique optical properties of many nanomaterials make them ideal for biosensing. Colloidal fluorescent and plasmonic nanoparticles are particularly interesting, as they produce intense responses to incident light, and linking this response to the presence of a target analyte yields extremely sensitive detection in solution."

 http://bit.ly/1xXcZ8d

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Diego Barcena MenendezVivek Raj Senthivel Mark Isalan

+Sender–receiver (S–R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S–R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning."

http://bit.ly/1vJxH93