SynBioFromLeukipposInstitute

Video 28min

Jim Collins' talk "Mammalian Synthetic Biology & Biomedical Applications" from the First International Workshop on Mammalian Synthetic Biology, May 11-12, 2013 at the Strata Center, MIT.

http://bit.ly/16Qj5sg

*Engineered Ion Channels as Emerging Tools for Chemical Biology*

by
Michael Mayer and Jerry Yang

"Over the last 25 years, researchers have developed exogenously expressed, genetically engineered, semi-synthetic, and entirely synthetic ion channels. These structures have sufficient fidelity to serve as unique tools that can reveal information about living organisms. One of the most exciting success stories is optogenetics: the use of light-gated channels to trigger action potentials in specific neurons combined with studies of the response from networks of cells or entire live animals.

 Despite this breakthrough, the use of molecularly engineered ion channels for studies of biological systems is still in its infancy. Historically, researchers studied ion channels in the context of their own function in single cells or in multicellular signaling and regulation. Only recently have researchers considered ion channels and pore-forming peptides as responsive tools to report on the chemical and physical changes produced by other biochemical processes and reactions. This emerging class of molecular probes has a number of useful characteristics. For instance, these structures can greatly amplify the signal of chemical changes: the binding of one molecule to a ligand-gated ion channel can result in flux of millions of ions across a cell membrane. In addition, gating occurs on sub-microsecond time scales, resulting in fast response times. Moreover, the signal is complementary to existing techniques because the output is ionic current rather than fluorescence or radioactivity. And finally, ion channels are also localized at the membrane of cells where essential processes such as signaling and regulation take place. This Account highlights examples, mostly from our own work, of uses of ion channels and pore-forming peptides such as gramicidin in chemical biology. We discuss various strategies for preparing synthetically tailored ion channels that range from de novo designed synthetic molecules to genetically engineered or simply exogenously expressed or reconstituted wild-type channels. Next we consider aspects of experimental design by comparing various membrane environments or systems that make it possible to quantify the response of ion channels to biochemical processes of interest. We present applications of ion channels to answer questions in chemical biology, and propose potential future developments and applications of these single molecule probes. Finally we discuss the hurdles that impede the routine use of ion channel probes in biochemistry and cell biology laboratories and developments and strategies that could overcome these problems. Optogenetics has facilitated breakthroughs in neuroscience, and these results give a dramatic idea of what may lie ahead for designed ion channels as a functional class of molecular probes. If researchers can improve molecular engineering to increase ion channel versatility and can overcome the barriers to collaborating across disciplines, we conclude that these structures could have tremendous potential as novel tools for chemical biology studies."

 http://bit.ly/1a2Aktp

http://onforb.es/139MONy

Leeds iGEM Team @microryza: detecting of lethal pathogens within a water supply http://bit.ly/179S4xU

http://blogs.nature.com/news/2013/08/university-of-california-adopts-open-access-publishing-policy.html

*Systems & synthetic industrial biotechnology* 

Cover illustration This Special Issue on “Systems and Synthetic Approaches to Industrial Biotechnology” compiles the outcomes of the minisymposiumat the 31st General Assembly of the International Union of Biological Sciences (IUBS). Implementation of systems biology and synthetic biology approaches in engineering industrial microbes and processes provides a promising and straight-forward approach to linking basic and application-inspired research. The cover represents the various concepts involved in systems and synthetic biotechnology. Image: © kytalpa – Fotolia.com.

http://bit.ly/15LBlBQ

by
Alok Jha,

"All it took was a little butter and sunflower oil and, in less than 10 minutes, the world's most expensive burger, grown from muscle stem cells in a lab, was ready to eat.

 "I was expecting the texture to be more soft," said Hanni Rützler of the Future Food Studio, who researches food trends and was the first to get a taste of the synthetic beef hamburger at a lavish event in London on Monday that bore more resemblance to a TV set than a scientific press conference. The lack of fat was noticeable, she added, which meant a lack of juiciness in the centre of the burger. If she had closed her eyes, however, she would have thought the cultured beef was definitely meat rather than a vegetable-based substitute."

http://bit.ly/18624t9

see also:

Google burger: +Sergey Brin  explains why he funded world's first lab-grown beef hamburger - video http://bit.ly/15Bf2kE

*Design and Construction of Synthetic Species*

by
Eduardo Moreno

"Synthetic biology is an area of biological research that combines science and engineering. Here, I merge the principles of synthetic biology and regulatory evolution to create a new species with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfils the criteria of a new species according to Mayr’s Biological Species Concept. The population described here is the first transgenic organism that cannot hybridize with the original wild type population but remains fertile when crossed with other identical transgenic animals. I therefore propose the term “synthetic species” to distinguish it from “natural species”, not only because it has been created by genetic manipulation, but also because it may never be able to survive outside the laboratory environment. The use of genetic engineering to design artificial species barriers could help us understand natural speciation and may have practical applications. For instance, the transition from transgenic organisms towards synthetic species could constitute a safety mechanism to avoid the hybridization of genetically modified animals with wild type populations, preserving biodiversity."


http://bit.ly/17LTugU

by

Guillermo Rodrigo, Thomas E. Landrain, Eszter Majer, José-Antonio Daròs,  Alfonso Jaramillo

"Small RNAs (sRNAs) can operate as regulatory agents to control protein expression by interaction with the 5′ untranslated region of the mRNA. We have developed a physicochemical framework, relying on base pair interaction energies, to design multi-state sRNA devices by solving an optimization problem with an objective function accounting for the stability of the transition and final intermolecular states. Contrary to the analysis of the reaction kinetics of an ensemble of sRNAs, we solve the inverse problem of finding sequences satisfying targeted reactions. We show here that our objective function correlates well with measured riboregulatory activity of a set of mutants. This has enabled the application of the methodology for an extended design of RNA devices with specified behavior, assuming different molecular interaction models based on Watson-Crick interaction. We designed several YES, NOT, AND, and OR logic gates, including the design of combinatorial riboregulators. In sum, our de novo approach provides a new paradigm in synthetic biology to design molecular interaction mechanisms facilitating future high-throughput functional sRNA design."

http://bit.ly/17n4u5I

by
Yoo SM, Na D, Lee SY.

"Gene knockout experiments are often essential in functional genomics and metabolic engineering studies. However, repeated multiple gene knockout experiments are laborious, time consuming and sometimes impossible to perform for those genes that are essential for cell function. Small regulatory RNAs (sRNAs) are short noncoding RNAs in prokaryotes that can finely control the expression of target genes in trans at the post-transcriptional level. Here we describe the protocol for synthetic sRNA-based gene expression control, including sRNA design principles. Customized synthetic sRNAs consist of a scaffold and a target-binding sequence, and they can be created by simply replacing an existing target-binding sequence with one that is complementary to the target mRNA to be repressed, while retaining the scaffold. Our plasmid-based synthetic sRNA system does not require chromosomal modifications, and it enables one to perform high-throughput studies on the effects of knockdowns on host cell physiology, and it further allows the simultaneous screening of target genes in different Escherichia coli strains for applications in metabolic engineering and synthetic biology. Once an sRNA scaffold-harboring plasmid is constructed, customized synthetic sRNAs can be made within 3-4 d; after this time, the synthetic sRNAs can be applied to the desired experiments."

http://bit.ly/14i3mx8

#SynBio on indiegogo: WormBoys iGEM 2013 http://bit.ly/13O9kX5

by Sam Wong

"In the latest edition of the Imperial Podcast, we hear from leading researchers in synthetic biology and fetal development.

The podcast is presented by Gareth Mitchell, a lecturer on Imperial'sScience Communication MSc course and the presenter of Click Radio on the BBC World Service, with contributors from the Communications and Public Affairs Division.
.."

http://bit.ly/14l05B6

http://bit.ly/13ZRsrv

Book: Synthetic Biology and Morality: Artificial Life and the Bounds of Nature

 edited by Gregory E. Kaebnick, Thomas H. Murray



 http://bit.ly/14eeuit

We need to take the public discussion more seriously...

*Kickstarter bans project creators from giving away genetically-modified organisms*

by
Duncan Geere 

"Kickstarter is clamping down on genetically-modified organisms following the success of a project to genetically engineer glowing plants for use as additional lighting in people's homes. Earlier this week and without explanation, the crowdfunding website quietly altered its guidelines for project creators, introducing a new term that bans creators from giving away genetically-modified organisms (GMOs) as rewards to their online backers. "Projects cannot offer genetically modified organisms as a reward," the new language states. The prohibition is effective July 31st, meaning that the popular glow-in-the-dark plant project is safe, but that any future projects like it can't offer GMOs to their backers.

  When asked about the change by The Verge, the company provided only the following canned statement: "we aim to be as open as possible while protecting the health and creative spirit of Kickstarter for the long term." Yet the move comes just days after a project called "Glowing Plants" successfully raised nearly half-a-million dollars..."

http://bit.ly/17r1tzS