SynBioFromLeukipposInstitute

"Synthetic Biology Open Language (SBOL) is a software standard for the electronic exchange of specifications and descriptions of genetic parts, devices, modules, systems, and engineered genomes.

For a general introduction and the motivation for SBOL, readers can go to the Get Started Page
To learn more about SBOL, follow one of the links below."

Engineering Molecular Circuits Using Synthetic Biology in Mammalian Cells - review

by
Wieland M, Fussenegger M.
"Synthetic biology has made significant leaps over the past decade, and it now enables rational and predictable reprogramming of cells to conduct complex physiological activities. The bases for cellular reprogramming are mainly genetic control components affecting gene expression. A huge variety of these modules, ranging from engineered fusion proteins regulating transcription to artificial RNA devices affecting translation, is available, and they often feature a highly modular scaffold. First endeavors to combine these modules have led to autoregulated expression systems and genetic cascades. Analogous to the rational engineering of electronic circuits, the existing repertoire of artificial regulatory elements has further enabled the ambitious reprogramming of cells to perform Boolean calculations or to mimic the oscillation of circadian clocks. Cells harboring synthetic gene circuits are not limited to cell culture, as they have been successfully implanted in animals to obtain tailor-made therapeutics that have made it possible to restore urea or glucose homeostasis as well as to offer an innovative approach to artificial insemination. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering Volume 3 is June 07, 2012. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates."

by

Cole J.

N. Biotechnol.

by

Natalie de Souza

"Manipulating either culture conditions or genes can precipitate iron particles in yeast cells and render them magnetic.

Yeast are not necessarily known for their magnetic personalities (although some scientists might disagree). Migrating birds, monarch butterflies and other types of migratory or homing animals, by contrast, perform some of the more awe-inspiring feats in the animal world, moving in a precise and directional fashion across vast distances in a process that involves sensing the Earth's magnetic field. Magneto-sensing depends in part on the presence of magnetic particles in the bodies of these organisms. Now, in recently published work, Keiji Nishida and Pam Silver at Harvard Medical School show a proof of concept that laboratory strains of yeast, too, can be magnetized......"

ref Nishida, K. & Silver, P.A. Induction of biogenic magnetization and redox control by a component of the target of rapamycin complex 1 signaling pathway. PLoS Biol. 10, e1001269 (2012).

 http://bit.ly/HT7oUR

MIT do it, Stanford do it..... It is time for new form of courses......

A friend of mine, +Pedro Fernandes had the idea that it would be great to have a bioinformatic course especially aimed for the needs of the synthetic biologist. It would be great if we could use joint forces and find people on the net who would like to build the course material in collaboration.
You are welcome to join the FB group Leukippos - Synthetic Biology Dry Lab http://on.fb.me/xHvMAZ in order to discuss this project.

Pedro posted
"Dear SynBio, I propose that we create, by joining forces, a set of materials to build (synthesize) a training course on the bioinformatics that is needed for Synthetic Biology projects. I propose to brainstorm some ideas here and then to start a shared pool of the materials in a separate electronic forum. When we are happy with the result I can launch a training course in the GTPB programme that I run in Oeiras, Portugal. At that time two of the main contributors will get invited to travel here and teach the course with me. Please drop your comments under this post."

He has my full support and I hope as many as possible can join.

#syntheticbiology #synbio #syntheticbio #bioinformatics

"With this first "regular" issue of Biotechnology Journal we would like to highlight that we invite you all to send us your best articles in the focus areas of BTJ - systems and synthetic biology, nanobiotech and medicine. It features the best of the latest in biotechnology, with several articles on established and new productions hosts, such as Chinese hamster ovary (CHO) cells and plant and algae cultures."

by 

Yanjun Qi, Merja Oja, Jason Weston, William Stafford Noble

"A variety of functionally important protein properties, such as secondary structure, transmembrane topology and solvent accessibility, can be encoded as a labeling of amino acids. Indeed, the prediction of such properties from the primary amino acid sequence is one of the core projects of computational biology. Accordingly, a panoply of approaches have been developed for predicting such properties; however, most such approaches focus on solving a single task at a time. Motivated by recent, successful work in natural language processing, we propose to use multitask learning to train a single, joint model that exploits the dependencies among these various labeling tasks. We describe a deep neural network architecture that, given a protein sequence, outputs a host of predicted local properties, including secondary structure, solvent accessibility, transmembrane topology, signal peptides and DNA-binding residues. The network is trained jointly on all these tasks in a supervised fashion, augmented with a novel form of semi-supervised learning in which the model is trained to distinguish between local patterns from natural and synthetic protein sequences. The task-independent architecture of the network obviates the need for task-specific feature engineering. We demonstrate that, for all of the tasks that we considered, our approach leads to statistically significant improvements in performance, relative to a single task neural network approach, and that the resulting model achieves state-of-the-art performance...."

by
Tsvetanova B, Peng L, Liang X, Li K, Hammond L, Peterson TC, Katzen F.

"Recombinant DNA technologies have had a fundamental impact on drug discovery. The continuous emergence of unique gene assembly techniques resulted in the generation of a variety of therapeutic reagents such as vaccines, cancer treatment molecules and regenerative medicine precursors. With the advent of synthetic biology there is a growing need for precise and concerted assembly of multiple DNA fragments of various sizes, including chromosomes. In this article, we summarize the highlights of the recombinant DNA technology since its inception in the early 1970s, emphasizing on the most recent advances, and underscoring their principles, advantages and shortcomings. Current and prior cloning trends are discussed in the context of sequence requirements and scars left behind. Our opinion is that despite the remarkable progress that has enabled the generation and manipulation of very large DNA sequences, a better understanding of the cell's natural circuits is needed in order to fully exploit the current state-of-the-art gene assembly technologies."

by

Smolke CD, Tyo KE.

I totally disagree with this. Regulations are the wrong way to go. Saftey is engineerable. We will never catch the bad guys. For this case we need a bio defense system. Political regulations have a tendency to are way behind the scientific development. It is the responsibility of the single scientist to engeneer saftey in his system. Scientists are responsible people. They do this. 

"Call for moratorium on synthetic biology

02 April 2012

By Louisa Petchey

Appeared in BioNews 651
Synthetic biology, which uses genetic engineering to build new genomes and organisms, has come under attack in a report published by Friends of the Earth and supported by over 100 other 'public interest' groups.

The report, 'Principles for the oversight of synthetic biology', calls for a suspension on the release and commercial use of all synthetic organisms and products until more stringent regulation is in place.

Describing current laws regulating biotechnology as 'outdated and inadequate', the report outlines seven guiding principles to be applied in order to place 'the health of people and the environment above corporate profits' and protect against the 'novel risks of synthetic biology'. Chief among these risks, the report says, are the possible impact on delicate ecosystems and the potential of synthetic organisms to develop into human pathogens.

The report also recommends a complete ban on the use of synthetic biology to manipulate human genomes or the microorganisms found in and on the human body, calling this research 'risky' and 'fraught with ethical concerns'...."

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature

by

Li GW, Oh E, Weissman JS.

"Protein synthesis by ribosomes takes place on a linear substrate but at non-uniform speeds. Transient pausing of ribosomes can affect a variety of co-translational processes, including protein targeting and folding. These pauses are influenced by the sequence of the messenger RNA. Thus, redundancy in the genetic code allows the same protein to be translated at different rates. However, our knowledge of both the position and the mechanism of translational pausing in vivo is highly limited. Here we present a genome-wide analysis of translational pausing in bacteria by ribosome profiling-deep sequencing of ribosome-protected mRNA fragments. This approach enables the high-resolution measurement of ribosome density profiles along most transcripts at unperturbed, endogenous expression levels. Unexpectedly, we found that codons decoded by rare transfer RNAs do not lead to slow translation under nutrient-rich conditions. Instead, Shine-Dalgarno-(SD)-like features within coding sequences cause pervasive translational pausing. Using an orthogonal ribosome possessing an altered anti-SD sequence, we show that pausing is due to hybridization between the mRNA and 16S ribosomal RNA of the translating ribosome. In protein-coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites. Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes...."

"Embryonic development is controlled by networks of interacting regulatory genes. The individual linkages of gene regulatory networks (GRNs) are customarily validated by functional cis-regulatory analysis, but an additional approach to validation is to rewire GRN circuitry to test experimentally predictions derived from network structure. Here we use this synthetic method to challenge specific predictions of the sea urchin embryo endomesoderm GRN. Expression vectors generated by in vitro recombination of exogenous sequences into BACs were used to cause elements of a nonskeletogenic mesoderm GRN to be deployed in skeletogenic cells and to detect their effects. The result of reengineering the regulatory circuitry in this way was to divert the developmental program of these cells from skeletogenesis to pigment cell formation, confirming a direct prediction of the GRN. In addition, the experiment revealed previously undetected cryptic repression functions."

"The one-day meeting on Synthetic DNA (January 24, 2012) organized by and held at the DECHEMA in Frankfurt attracted about 100 participants from academia and industry interested in synthesizing DNA and its applications in synthetic biology. In recent years the cost for synthetic DNA reduced from 7€/bp to 0.35€/bp which has opened up many new possibilities for molecular biology. (Image: © Spectral-Design - Fotolia.com)."