SynBioFromLeukipposInstitute

SB6.0 Digital Conference Registration Open Now http://bit.ly/10EGES8

*3D-printing synthetic tissues*

credit
G Villar

"A custom-built programmable 3D printer can create materials with some the properties of living tissues, Oxford University scientists have demonstrated.

 The new type of material consists of tens of thousands of picoliter connected water droplets encapsulated within lipid films, which can perform some of the functions of the cells inside our bodies. These printed “droplet networks” might be interfaced with tissues, used as tissue engineering substrates, or developed as mimics of living tissue. The droplet networks could be the building blocks of a new kind of technology for delivering drugs to places where they are needed, and potentially could one day replace or interface with damaged human tissues. The droplet networks are entirely synthetic, so they avoid some of the problems associated with other approaches to creating artificial tissues, such as those that use stem cells>>>"

http://bit.ly/1cJKb45

*GAMIFICATION OF IN SILICO OPEN SYNTHETIC BIOLOGY: A GAME-CHANGER* 

by
+Eugenio Battaglia 

"Fancy doing some Synthetic Biology but you don’t have access to a lab or expensive equipments?

Don’t worry. Synthetic biology is a sub-field of life sciences that requires a lot of in silico tests before eventually create life.And even if you’re not able to code, again no prob.Leukippos is a DIY synthetic biology lab in the cloud. This non profit group gives to everyone who can access to a web browser, the opportunity to collaborate on exiting synthetic biology projects. For this reason, Leukippos focus especially on in silico works, so that people can do science independently from their location. The spirit is similar to the OpenWorm project.  A great mission, Big issues, Collaborative simple models. This gives many people an awesome opportunity, although if they live in low-income countries, or in areas where access to a scientific carrer is constrained. People form all over the world (e.g. India, Canada, Colombia, Germany, Portugal) who share a passion for synthetic biology and computer science have teamed-up together. Recently, two projects are in progress. The first, is a mashup app of all synthetic biology related softwares, on enlace to find everything you need to do your synthetic biology computer work. The other is a synthetic biology related game modeled after FoldIt. Teams can play online together to solve real world problems with help of synthetic biology. The work of the Leukippos project resulted in several publications. They submitted two papers produced by their synthetic biology lab to the International Workshop on Bio Design Automation that will take place this July in London, and got accepted. They have started a crowd sourcing campaign on Microryza to get the money they need for participation at this conference. So, you got the chance to join as a member to develop the apps, or you could wait the app to play… I assure you that you won’t need skills in biology, but only a good attitude to play videogames!  Or, if you believe in this open-project please give your contributions, also a dollar worth! Moreover, Leukippos published two reviews. One is about security and safety in synthetic biology, an important topic to keep in mind. The other is about biological computing. see references. You can find other information on Leukippos and how to join are here.   Gerd H. G. Moe-Behrens, Rene Davis, & Karmella A. Haynes (2013). Preparing synthetic biology for the world Frontiers in MICROBIOTECHNOLOGY, ECOTOXICOLOGY AND BIOREMEDIATION DOI: 10.3389/fmicb.2013.00005 Gerd HG Moe-Behrens (2013). The biological microprocessor, or how to build a computer with biological parts Computational and Structural Biotechnology Journal DOI: 10.5936/csbj.201204003 "

http://bit.ly/14DbVV2

by
Ulrike Scheib, Sooruban Shanmugaratnam, José Arcadio Farías-Rico, Birte Höcker

"Recognition and discrimination of small molecules are crucial for biological processes in living systems. Understanding the mechanisms that underlie binding specificity is of particular interest to synthetic biology, e.g. the engineering of biosensors with de novo ligand affinities. Promising scaffolds for such biosensors are the periplasmic binding proteins (PBPs) due to their ligand-mediated structural change that can be translated into a physically measurable signal.

 In this study we focused on the two homologous polyamine binding proteins PotF and PotD. Despite their structural similarity, PotF and PotD have different binding specificities for the polyamines putrescine and spermidine. To elucidate how specificity is determined, we grafted the binding site of PotD onto PotF. The introduction of 7 mutations in the first shell of the binding pocket leads to a swap in the binding profile as confirmed by isothermal titration calorimetry. Furthermore, the 1.7 Å crystal structure of the new variant complexed with spermidine reveals the interactions of the specificity determining residues including a defined water network. Altogether our study shows that specificity is encoded in the first shell residues of the PotF binding pocket and that transplantation of these residues allows the swap of the binding specificity."

http://bit.ly/17h0zbN

by
Ulrike Scheib, Sooruban Shanmugaratnam, José Arcadio Farías-Rico, Birte Höcker

"Recognition and discrimination of small molecules are crucial for biological processes in living systems. Understanding the mechanisms that underlie binding specificity is of particular interest to synthetic biology, e.g. the engineering of biosensors with de novo ligand affinities. Promising scaffolds for such biosensors are the periplasmic binding proteins (PBPs) due to their ligand-mediated structural change that can be translated into a physically measurable signal.

 In this study we focused on the two homologous polyamine binding proteins PotF and PotD. Despite their structural similarity, PotF and PotD have different binding specificities for the polyamines putrescine and spermidine. To elucidate how specificity is determined, we grafted the binding site of PotD onto PotF. The introduction of 7 mutations in the first shell of the binding pocket leads to a swap in the binding profile as confirmed by isothermal titration calorimetry. Furthermore, the 1.7 Å crystal structure of the new variant complexed with spermidine reveals the interactions of the specificity determining residues including a defined water network. Altogether our study shows that specificity is encoded in the first shell residues of the PotF binding pocket and that transplantation of these residues allows the swap of the binding specificity."

http://bit.ly/14Y5bTN

*Synthetic-biology company pushes open-source models*

by
Heidi Ledford

"When DNA2.0, a company that synthesizes made-to-order genes, needed to conduct a few routine experiments using a fluorescent protein, its lawyers dug up more than 1,000 US patents covering their use. DNA2.0 decided to avoid the legal thicket by engineering several dozen fluorescent proteins from scratch. But the company, based in Menlo Park, California, was convinced that something had to change.

 Last month, DNA2.0 deposited gene sequences encoding three of its fluorescent proteins into an open-access collection of recipes for DNA ‘parts’, molecular building blocks used to engineer organisms — often bacteria — to carry out specific functions. The company vows not to pursue its patent rights against anyone using the sequences...."

.http://bit.ly/125Xszg

By
Bryan Le

"3D printing is a highly-anticipated new technology that could soon "revolutionize" the drug market. This technology, now in development, could soon allow us to design and print everything from toys and tools to human hearts—and, inevitably, drugs. Lee Cronin, a chemist from the University of Glasgow, says he has created a prototype 3D "Chemputer" that can create medicine by assembling chemical compounds on a molecular level. “What Apple did for music, I'd like to do for the discovery and distribution of prescription drugs,” says Cronin. Prescription patients would be able to purchase a "blueprint" and chemical "ink" at an online version of a pharmacy, and could then print the drug at home with software and a 3D molecular printer. Chemicals and dosages could be tailored to meet each individual's specific needs, and certain allergies and other health concerns could be "edited out." If successful, this new prescription method could radically alter the entire pharmaceutical industry, taking control away from Big Pharma and placing it in the hands of the consumers. “In the future, we will not sell drugs, but blueprints or apps,” says Cronin.

 But just like music on iTunes, the technology will also open up avenues for consumers to evade the rules. Mike Power, author of Drugs 2.0: The Web Revolution That's Changing How the World Gets High, predicts ambitious DIY chemists will eventually control the drug market—making the very notion of "controlled substances" a thing of the past. Power says this could be a good thing: free production and distribution of drugs like LSD and MDMA, he claims, would eliminate the need for “designer drugs" (unregulated substitutes for illicit street drugs, with often-unpredictable and harmful effects). But downloading illegal drug blueprints from unknown sites could also create the same problems as downloading music: Without any official standards or regulation, the blueprints could be mislabeled (the same problem, Powers points out, that currently plagues the illegal drug market). And chemically sloppy medicines could have far more harmful consequences than sloppily-recorded songs. But for better or for worse, the technology is on the horizon. When, exactly? “Maybe 10 to 15 years? Who knows?” says Cronin. “Maybe five to 10.”..."

http://bit.ly/12DrIVa

My Group submission: Heart Disease and the Internet of Me - Mobile Health Without Borders (Stanford  University - Venture Lab) http://bit.ly/18qrJA4

*Materials Manufactured from 3D Printed Synthetic Biology Arrays*

by

Gentry, DianaMicks, Ashley

"Many complex, biologically-derived materials have extremely useful properties (think wood or silk), but are unsuitable for space-related applications due to production, manufacturing, or processing limitations. Large-scale ecosystem-based production, such as raising and harvesting trees for wood, is impractical in a self-contained habitat such as a space station or potential Mars colony. Manufacturing requirements, such as the specialized equipment needed to harvest and process cotton, add too much upmass for current launch technology. Cells in nature are already highly specialized for making complex biological materials on a micro scale. We envision combining these strengths with the recently emergent technologies of synthetic biology and 3D printing to create 3D-structured arrays of cells that are bioengineered to secrete different materials in a specified three-dimensional pattern..."

http://1.usa.gov/14HbvwI

by
Michael C Jewett, Brian R Fritz, Laura E Timmerman & George M Church

"This report describes an integrated method for in vitro construction of Escherichia coli ribosomes under near-physiological conditions. This method enables coupling of ribosome synthesis and assembly in a single, integrated system.

An integrated synthesis, assembly, and translation technology (termed iSAT) was developed to construct ribosomes in vitro.iSAT mimics co-transcription of rRNA and ribosome assembly as it occurs in vivo.iSAT makes possible the in vitro construction of modified ribosomes.iSAT is expected to aid studies of ribosome assembly and open new avenues for making ribosomes with altered capabilities.Top of pageAbstractPurely in vitro ribosome synthesis could provide a critical step towards unraveling the systems biology of ribosome biogenesis, constructing minimal cells from defined components, and engineering ribosomes with new functions. Here, as an initial step towards this goal, we report a method for constructing Escherichia coli ribosomes in crude S150 E. coli extracts. While conventional methods for E. coli ribosome reconstitution are non-physiological, our approach attempts to mimic chemical conditions in the cytoplasm, thus permitting several biological processes to occur simultaneously. Specifically, our integrated synthesis, assembly, and translation (iSAT) technology enables one-step co-activation of rRNA transcription, assembly of transcribed rRNA with native ribosomal proteins into functional ribosomes, and synthesis of active protein by these ribosomes in the same compartment. We show that iSAT makes possible the in vitro construction of modified ribosomes by introducing a 23S rRNA mutation that mediates resistance against clindamycin. We anticipate that iSAT will aid studies of ribosome assembly and open new avenues for making ribosomes with altered properties."

http://bit.ly/13epFKk

by
Gerd Moe-Behrens

"Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor.  Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system."

http://bit.ly/1cwM43X