SynBioFromLeukipposInstitute

"PUTTING THE SIN — AND THE PROZAC YOGURT — INTO SYNTHETIC BIOLOGY. Synthetic biology has as yet no agreed-upon definition even among synthetic biologists. But it already has a nickname, as an event this week is making clear, that is somewhat unfortunate from the standpoint of public relations. The nickname: synbio.

The event was a report issued by 111 environmental and other organizations. They argue that synthetic biology is potentially dangerous and needs more oversight. At ScienceInsider, Elizabeth Pennisi summarizes the call they issued this week. At Patent Docs, Kevin Noonan goes into more detail about the organizations' press conference, the report they issued, and even lists all the participating organizations.

If you're not sure what the term "synthetic biology" means either, you won't get much help. The new report calls it "an extreme form of genetic engineering." Read on, but for now let's go with Pennisi, who says synthetic biology comprises..."

"Although the field of synthetic biology is still in its infancy, there are expectations for great advances in the coming decades, both on Earth and potentially in space. Promising applications for long duration space missions include a variety of biologically engineered products and biologically aided processes and technologies, which will undoubtedly be scrutinized for risks and benefits in the broad context of ethical, legal and social realms. By comparing and contrasting features of Earth-based and space-applied synthetic biology, it is possible to identify the likely similarities and differences, and to identify possible challenges ahead for space applications that will require additional research, both in the short and long terms. Using an analytical framework associated with synthetic biology and new technologies on Earth, this paper analyses the kinds of issues and concerns ahead, and identifies those areas where space applications may require additional examination. In general, while Earth- and space-based synthetic biology share many commonalities, space applications have additional challenges such as those raised by space microbiology and environmental factors, legal complications, planetary protection, lack of decision-making infrastructure(s), long duration human missions, terraforming and the possible discovery of extraterrestrial (ET) life. For synthetic biology, the way forward offers many exciting opportunities, but is not without legitimate concerns - for life, environments and society, both on Earth and beyond...."

 

CALL FOR SUBMISSIONS

SPECIAL INTEREST GROUP ON BIOLOGICAL SYSTEMS DESIGN (BSD-SIG 2012)

Intelligent Systems for Molecular Biology (ISMB 2012)
July 13, 2012 - Long Beach, CA USA

Homepage: http://bsd2012.bme.jhu.edu/
Submission site: https://www.easychair.org/conferences/?conf=bsdsig2012
Email: bsd2012@jhu.edu

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Important Dates:
Paper submission: April 20, 2012
Author notification: May 4, 2012
Workshop: July 13, 2012

 

**Keynote Speakers**

- Jef D. Boeke, Johns Hopkins University
- Christodoulos A. Floudas, Princeton
- Dan Gusfield, UC Davis
- Nathan J. Hillson, Joint BioEnergy Institute

**Invited Speakers**

- Jake Beal, BBN Technologies
- Michal Galdzicki, University of Washington School of Medicine
- Sarah Richardson, Joint Genome Institute

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**Sessions**

BSD-SIG is structured in four sessions:

* Genome Design
* Protein Design
* Computer Aided Design Tools
* Data management & standards

**Genome Design**
The availability of high-fidelity techniques for the synthesis of long DNA strands constitutes the
starting point for effective pathway engineering. The aim of this session is to present state-of-the-art
methods for genome design, focusing, but not limited to, on the following topics: oligo-nucleotides
design, Probe and watermark design, High-throughput techniques, theoretical aspects of DNA design.

**Protein Design**
An important purpose of synthetic DNA is to express non-native or human-designed proteins.
Protein expression and design introduce additional complexities. This session provides a forum
to discuss the recent advances in this field, with particular emphasis on the design of
therapeutic peptides and proteins.

**Computer Aided Design Tools**
The design of biological systems is often characterized by ad hoc, human-centric procedures,
which limit applications to small-scale problems. While Computer-Aided-Design (CAD) tools are
standard in many engineering fields, CAD capabilities for synthetic biology are at a
very early stage. This session gives a broad view of some emerging approaches in Biological
Design Automation (BDA), with the aim of finding and discussing new areas where CAD tools can
improve and accelerate the synthesis of living matter.

**Data management & standards**
The enormous amount of data generated by high-throughput techniques and synthesis processes
requires the introduction of new and specific representation schemes, along with efficient and
open standards for interfacing different data sources. New systems are also required to collect
information and performing on-line data analysis. The aim of this session is twofold: first,
exploring data structures and representations for synthetic biology; second, promoting and
discussing use-case scenarios for the Synthetic Biology Open Language (SBOL).

"Synthetic nanotubes that have the ability to broadly mimic the function of biological ion channels have extraordinary potential for various applications, from ultrasensitive biosensors to efficient water purification devices. As a result of their immense potential, the design and fabrication of such synthetic nanotubes is rapidly gaining momentum. We briefly review recent theoretical and experimental studies on nanoscale cylindrical hollow tubes constructed from carbon, boron, and nitrogen atoms that are able to selectively transport water molecules, cations (positively charged ions), or anions (negatively charged ions) similar to various biological ion channels. FROM THE CLINICAL EDITOR: This review discusses the current status of synthetic nanotube research, including recent theoretical and experimental studies on nanoscale cylindrical hollow tubes constructed from carbon, boron, and nitrogen atoms that are able to selectively transport water molecules, cations or anions similar to biological ion channels..."

"Synthetic biology applications call for efficient methods to generate large gene cassettes that encode complex gene circuits in order to avoid simultaneous delivery of multiple plasmids encoding individual genes. Multiple methods have been proposed to achieve this goal. Here, we describe a novel protocol that allows one-step cloning of up to four gene-size DNA fragments, followed by a second assembly of these concatenated sequences into large circular DNA. The protocols described here comprise a simple, cheap and fast solution for routine construction of cassettes with up to 10 gene-size components...."

Agent-based Models in Synthetic Biology: Tools for Simulation and Prospects

"We describe a multiset of agents based modeling and simulation paradigm for synthetic biology. The multiset of agents –based programming paradigm, can be interpreted as the outcome arising out of deterministic, nondeterministic or stochastic interaction among elements in a multiset object space, that includes the environment. These interactions are like chemical reactions and the evolution of the multiset can emulate the system biological functions. Since the reaction rules are inherently parallel, any number of actions can be performed cooperatively or competitively among the subsets of elements, so that the elements evolve toward equilibrium or emergent state. Practical realization of this paradigm for system biological simulation is achieved through the concept of transactional style programming with agents, as well as soft computing (neural- network) principles. Also we briefly describe currently available tools for agent-based-modeling, simulation and animation..."

DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response

 

Very interesting Nature paper:

by

Anton Kuzyk, Robert Schreiber, Zhiyuan Fan, Günther Pardatscher, Eva-Maria Roller, Alexander Högele, Friedrich C. Simmel, Alexander O. Govorov & Tim Liedl

Nature 483, 311–314 (15 March 2012)

 

"Matter structured on a length scale comparable to or smaller than the wavelength of light can exhibit unusual optical properties1. Particularly promising components for such materials are metal nanostructures, where structural alterations provide a straightforward means of tailoring their surface plasmon resonances and hence their interaction with light2, 3. But the top-down fabrication of plasmonic materials with controlled optical responses in the visible spectral range remains challenging, because lithographic methods are limited in resolution and in their ability to generate genuinely three-dimensional architectures4, 5. Molecular self-assembly6, 7 provides an alternative bottom-up fabrication route not restricted by these limitations, and DNA- and peptide-directed assembly have proved to be viable methods for the controlled arrangement of metal nanoparticles in complex and also chiral geometries8, 9, 10, 11, 12, 13, 14. Here we show that DNA origami15, 16 enables the high-yield production of plasmonic structures that contain nanoparticles arranged in nanometre-scale helices. We find, in agreement with theoretical predictions17, that the structures in solution exhibit defined circular dichroism and optical rotatory dispersion effects at visible wavelengths that originate from the collective plasmon–plasmon interactions of the nanoparticles positioned with an accuracy better than two nanometres. Circular dichroism effects in the visible part of the spectrum have been achieved by exploiting the chiral morphology of organic molecules and the plasmonic properties of nanoparticles18, 19, 20, or even without precise control over the spatial configuration of the nanoparticles12, 21, 22. In contrast, the optical response of our nanoparticle assemblies is rationally designed and tunable in handedness, colour and intensity—in accordance with our theoretical model."

 

http://bit.ly/FOsNto PDF can be found here http://bit.ly/wjk296

 

 

 

"● The impetus for a popular annual contest for students learning synthetic biology traces to an introductory course in engineering and design at MIT.
● The first chapter of iGEM involved a group of 16 undergraduate students at MIT in 2003 trying to make bacterial cells into a "living lighthouse" using standardized DNA "parts."
● The annual iGEM contest now includes students from four continents who compete regionally, with those winners gathering in November for a Jamboree.
● Formal educational modules at BioBuilder harness the iGEM approach for teaching engineering in the context of high school and college biology, an approach that may be adapted for teaching other scientific disciplines.

If you were a new student arriving at Massachusetts Institute of Technology (MIT) in Cambridge during the early 1970s with an expressed interest in mechanical engineering, you would have been advised to enroll in a class called "Introduction to Design." Students in this class were provided components such as wooden spools and metal rods, and were told to build a useful device from these parts.

A teaching assistant from that era noted that students taking that class spent little time engineering their machines because it took them so long to decide what to build. When that teaching assistant, Woodie Flowers, became an MIT professor and took over teaching that class, he made two big changes that had a major impact on the students. The first was to assign all the teams a common task, challenging them, for example, to "design a machine that puts a round peg into a square hole" or to "build a mechanical device that can roll down a 30° incline plane in 3 minutes." With an explicit design challenge to meet, students no longer spent so much time wondering what to build and, instead, could concentrate on designing and engineering specific types of machines. The second change was to make each of these engineering assignments competitive. Student teams engaged in sportslike battles to determine which team's machine could perform with the greatest accuracy, consistency, and precision. Not surprisingly, MIT students enjoyed measuring their success against others.

A generation later, other disciplines are embracing the notion of teaching through kit-based design competitions. A prime example is the annual FIRST Robotics Competition, which was founded by Flowers of MIT and inventor Dean Kamen, president of DEKA Research & Development Corporation in Manchester, N.H. Last year, for example, more than 350 high school teams from five countries worked with kits having the same parts, each group striving to build the "best" robots within six weeks. Their efforts are judged regionally, with the local winners advancing to the finals, where the teams match their robots against one another in a competitive atmosphere that rivals what happens at the Super Bowl or World Cup. This design competition engenders not only palpable enthusiasm but lasting learning among the students who participate. Moreover, the event continues to grow, attracting more teams and younger students...."

 

ASCB Annual Meeting Highlights:
Pamela A. Silver, Karmella Haynes, and Ron Weiss
Synthetic meets cell biology
Mol. Biol. Cell 2012 23:6 967

 

"Synthetic Biology for Human Health: Ethical and Policy Issues Bioethics Special Issue

Guest Editors: Nikola Biller-Andorno, Ruud ter Meulen, Ainsley J Newson
CLOSING DATE FOR SUBMISSIONS: 1st October, 2012

The Editors of Bioethics are pleased to announce a special issue in 2013 on the ethical and policy issues in synthetic biology for human health. Synthetic biology is an emerging field with important potential applications for human health, such as innovative drugs, new vaccines, tissue regeneration, or even synthetic cells. Synthetic biology aims to be able to design, engineer and build biological systems that do not occur in nature as well as re-engineer systems that already exist. This raises fundamental ethical questions about the moral status of life, the conceptualization of risks and benefits as well as possible implications for future people. Questions also arise about how we should approach these ethical issues and the moral grounding which ought to guide policy and regulatory issues in this area.
We invite submissions on all aspects of this topic. Questions include but are not limited to:

Is there anything inherently morally objectionable in creating or (re-)designing life?
What are appropriate methodological paradigms for ethical debates over synthetic biology for human health?
What questions does synthetic biology for human health pose with regards to justice
When should we consider the risks that may arise in the development of synthetic biology applications for human health as morally justifiable to take
How should we interpret contested concepts important to normative thinking about synthetic biology and human health? (e.g. life, risk, public interest, health and dignity).
What should be the moral grounds for any specific regulation of synthetic biology research and applications to human health?"