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by Michel M. Maharbiz "The ability to synthesize biological constructs on the scale of the organisms we observe unaided is probably one of the more outlandish, yet recurring, dreams humans have had since they began to modify genes. This review brings together recent developments in synthetic biology, cell and developmental biology, computation, and technological development to provide context and direction for the engineering of rudimentary, autonomous multicellular ensembles." 
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The Nobel Prize in Physiology or Medicine 2012
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Environmental problems, such as depleting natural resources, highlight the need to establish a renewable chemical industry.
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Gerd Moe-Behrens
October 7, 2012 3:53 PM
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by
Anne Trafton
"New sensor can detect four different molecules, could be used to program cells to precisely monitor their environments.
Using genes as interchangeable parts, synthetic biologists design cellular circuits that can perform new functions, such as sensing environmental conditions. However, the complexity that can be achieved in such circuits has been limited by a critical bottleneck: the difficulty in assembling genetic components that don’t interfere with each other.
Unlike electronic circuits on a silicon chip, biological circuits inside a cell cannot be physically isolated from one another. “The cell is sort of a burrito. It has everything mixed together,” says Christopher Voigt, an associate professor of biological engineering at MIT.
Because all the cellular machinery for reading genes and synthesizing proteins is jumbled together, researchers have to be careful that proteins that control one part of their synthetic circuit don’t hinder other parts of the circuit...."
http://bit.ly/UM7UaV
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Gerd Moe-Behrens
October 6, 2012 6:24 PM
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*MIT media lab is one of the very cool places....*
In respect to #syntheticbiology the molecular machine group is of special interest. "The Molecular Machines group is focused on pioneering the field of Avogadro scale engineering, which seeks to understand and approach the fundamental limit of engineered complexity deliverable per unit cost. The group has a particular focus on applications within synthetic biology, novel computing machines, and nanostructured devices for energy production." Projects: GeneFab (rapid fabrication of large DNA molecules, with composition specified directly by the user), NanoFab (fabrication of nanowires based nanostructures and logic devices) and synthetic photosynthesis. see: http://bit.ly/SnguQK
But there is much more. It is really a pleasure to surf their sites. I am really enthusiastic about their work.
+Joichi Ito is a really interesting person to follow, with great ideas how work will be in the digital age.
Have a look at his You Tube Channel: http://www.youtube.com/user/joiito?feature=results_main
*Innovation in Open Networks*
http://bit.ly/WAqBBa
see also Wired special edition http://www.wired.co.uk/magazine
I like also the work by Neri Oxman
*3D PRINTING IS THE FUTURE OF MANUFACTURING AND NERI OXMAN SHOWS HOW BEAUTIFUL IT CAN BE*
http://bit.ly/OKr8AU
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Gerd Moe-Behrens
October 6, 2012 4:28 PM
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by
Kim T, Moore D, Fussenegger M.
"Although magnetic fields and paramagnetic inorganic materials were abundant on planet earth during the entire evolution of living species the interaction of organisms with these physical forces remains a little-understood phenomenon. Interestingly, rather than being genetically encoded, organisms seem to accumulate and take advantage of inorganic nanoparticles to sense or react to magnetic fields. Using a synthetic biology-inspired approach we have genetically programmed mammalian cells to show superparamagnetic behavior. The combination of ectopic production of the human ferritin heavy chain 1 (hFTH1), engineering the cells for expression of an iron importer, the divalent metal ion transferase 1 (DMT1) and the design of an iron-loading culture medium to maximize cellular iron uptake enabled efficient iron mineralization in intracellular ferritin particles and conferred superparamagnetic behavior to the entire cell. When captured by a magnetic field the superparamagnetic cells reached attraction velocities of up to 30μm/s and could be efficiently separated from complex cell mixtures using standard magnetic cell separation equipment. Technology that enables magnetic separation of genetically programmed superparamagnetic cells in the absence of inorganic particles could foster novel opportunities in diagnostics and cell-based therapies."
http://bit.ly/QMETxx
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Gerd Moe-Behrens
October 5, 2012 7:12 PM
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Keystone Symposium: Precision Genome Engineering and Synthetic Biology March 17—22, 2013 http://bit.ly/QQmYTz
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Gerd Moe-Behrens
October 5, 2012 6:19 PM
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By Liat Clark
"When Lepht Anonym hit the world stage in 2011 to describe how she cut open her flesh with vodka-sterilised vegetable peelers to stick bits of metal under her skin, there were probably a fair few intakes of breath. There was also a huge sigh of relief from a rapidly growing minority. Her words sowed a seed in the minds of people who had long-harboured thoughts of being superhuman, of fulfilling a childhood fantasy and becoming a cyborg. That seed said it was ok to experiment and suggested, instead of waiting for the impossible to happen, why not pick up your (sterilised) tools and make something possible happen today.
"I heard about finger magnets in April and by May I had an implant," Tim Cannon, co-founder of the Pittsburgh-based DIY bodyhacking group Grindhouse Wetware tells Wired.co.uk. "As soon as I heard that you could get this extra sense, I was blown away. Now I can feel electromagnetic fields."
Grinders, DIY biohackers or garage body mods; however Cannon and his team of body augmentation enthusiasts refer to themselves, one thing is clear -- the principles of their practice lie in transhumanism. They are under no illusion that what they are doing is groundbreaking stuff -- Kevin Warwick of Reading University implanted a RFID transmitter under his skin in 1998 and the practice of slicing up your own flesh has apparently become so commonplace that one tattoo artist recently stuck four magnets under his skin to hold his iPod nano in place. Cannon and his team, however, are adamant that while the mainstream transhumanist theorists continue to talk big, they are altering and enhancing their bodies now...."
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Gerd Moe-Behrens
October 5, 2012 5:21 PM
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by
Andy Coghlan
".....NASA has already begun research to realise this dream, says Lynn Rothschild at the Ames Research Center in Moffett Field, California. Rothschild is leader of NASA's new Synthetic Biology Initiative, which aims to build designer microbes for future crewed space missions. She shared her vision at last week's BioDesign Forum in Cambridge, UK.
Synthetic biology lies at the crossroads of biology and engineering. Its practitioners have built a biological toolkit consisting of chunks of genes, called biobricks, each of which performs a specific function - making a bacterium generate natural antifreeze molecules, for example. Biobricks can be inserted into other microbes to give them that function.
Using the approach, a microbe with the potential to survive on an alien world can become one that could sustain human life there...."
http://bit.ly/QBjqFW
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Gerd Moe-Behrens
October 3, 2012 5:01 PM
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A technique that uses acoustic waves to sort cells on a chip may create miniature medical analytic devices that could make Star Trek's tricorder seem a bit bulky in comparison, according to experts.
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Gerd Moe-Behrens
October 3, 2012 4:04 PM
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By Alan Boyle
"In the future, genetically modified organisms could be making our medicines, our fuel, our housewares, our houses — and they could even help us remake ourselves. All that may sound like science-fiction, but the future is already arriving, in the form of the bioplastic bottle you may be holding in your hand. Harvard geneticist George Church lays it all out in a new book, "Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves," written with Ed Regis. "We are already remaking ourselves and our world, retracing the steps of the original synthesis — redesigning, recoding and reinventing nature itself in the process," they write.
Even the book has been reinvented through DNA: "Regenesis" is one of those rare books that's been the focus of a research paper in the journal Science. All of its 53,426 words, along with 11 images and one Javascript app, were encoded into chunks of DNA, and then read back, just to prove it could be done. But DNA as a next-generation information storage medium is just one of the applications addressed in "Regenesis" — and that's not really all that far out.
If you want to talk about far-out, how about regenerating extinct species, ranging from woolly mammoths to Neanderthals? How about synthetic methods for photosynthesis, the process that turns carbon dioxide, water and sunlight into oxygen and fuel? How about tweaking the human genome to make ourselves immune to multiple viruses? Heck, why not make ourselves virtually immortal?......"
http://nbcnews.to/QQmq3j
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Gerd Moe-Behrens
October 9, 2012 3:36 PM
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by
Wilson ML, Cai Y, Hanlon R, Taylor S, Chevreux B, Setubal JC, Tyler BM,
+Jean Peccoud
"Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org."
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Gerd Moe-Behrens
October 8, 2012 3:31 PM
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by
BY JOHN WILBANKS
"THE SCIENTIFIC PAPER HAS LONG BEEN THE UNIT OF SCIENTIFIC KNOWLEDGE. NOW, WITH PRINT MEDIA LAPSING INTO OBSOLESCENCE, THE INTERNET IS POISED TO TRANSFORM SCIENCE PUBLISHING AND SCIENCE ITSELF.
The scientific publishing industry as we know it today represents a structure of the past. It is profoundly tied to the medium of print, which is itself an artifact of a technical revolution hundreds of years old. Moreover, its routines and structures are rooted in paper as a communications and archiving technology, and its business models are based on the costs of physical distribution and review by a select few.
Of course, paper-based systems aren’t very adaptable to the world of the internet. The outdated—but wildly profitable—business models based on the print medium have led to skyrocketing costs for scholarly journals over the past 30 years, costs that greatly outpace increases in cost of living. This is at odds with the rapidly decreasing costs of digital publication and distribution. Even worse, the paper-based status quo relies on strictly enforced barriers to public access that prevent the rapid dissemination of vital knowledge....."
http://bit.ly/RakhfO
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Gerd Moe-Behrens
October 8, 2012 3:17 PM
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*An adaptor from translational to transcriptional control enables predictable assembly of complex regulation*by
Chang C Liu, Lei Qi, Julius B Lucks, Thomas H Segall-Shapiro, Denise Wang, Vivek K Mutalik & Adam P Arkin"Bacterial regulators of transcriptional elongation are versatile units for building custom genetic switches, as they control the expression of both coding and noncoding RNAs, act on multigene operons and can be predictably tethered into higher-order regulatory functions (a property called composability). Yet the less versatile bacterial regulators of translational initiation are substantially easier to engineer. To bypass this tradeoff, we have developed an adaptor that converts regulators of translational initiation into regulators of transcriptional elongation in Escherichia coli. We applied this adaptor to the construction of several transcriptional attenuators and activators, including a small molecule–triggered attenuator and a group of five mutually orthogonal riboregulators that we assembled into NOR gates of two, three or four RNA inputs. Continued application of our adaptor should produce large collections of transcriptional regulators whose inherent composability can facilitate the predictable engineering of complex synthetic circuits."
http://bit.ly/R7I4QXComment:
*A welcome predictability*
Synthetic biology is the latest and most advanced phase of genetic engineering, holding great promise for helping to solve some of the world's most intractable problems, including the sustainable production of energy fuels and critical medical drugs, and the safe removal of toxic and radioactive waste from the environment. However, for synthetic biology to reach its promise, the design and construction of biological systems must be as predictable as the assembly of computer hardware.An important step towards attaining a higher degree of predictability in synthetic biology has been taken by a group of researchers with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab) under the leadership of computational biologist Adam Arkin. Arkin and his team have developed an "adaptor" that makes the genetic engineering of microbial components substantially easier and more predictable by converting regulators of translation into regulators of transcription in Escherichia coli. Transcription and translation make up the two-step process by which the coded instructions of genes are used to synthesize proteins.
"Application of our adaptor should produce large collections of transcriptional regulators whose inherent composability can facilitate the predictable engineering of complex biological circuits in microorganisms," Arkin says. "This in turn should allow for safer and more efficient constructions of increasingly complex functions in microorganisms."
....."
http://bit.ly/TmJpoG
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Gerd Moe-Behrens
October 7, 2012 4:12 PM
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by
Tae Seok Moon, Chunbo Lou, Alvin Tamsir, Brynne C. Stanton & Christopher A. Voigt
"Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics1. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits2, 3, 4, 5, 6, and they have been used in various cellular engineering applications, including the implementation of process control in metabolic networks and the coordination of spatial differentiation in artificial tissues. A key limitation is that the circuits are based on biochemical interactions occurring in the confined volume of the cell, so the size of programs has been limited to a few circuits1, 7. Here we apply part mining and directed evolution to build a set of transcriptional AND gates in Escherichia coli. Each AND gate integrates two promoter inputs and controls one promoter output. This allows the gates to be layered by having the output promoter of an upstream circuit serve as the input promoter for a downstream circuit. Each gate consists of a transcription factor that requires a second chaperone protein to activate the output promoter. Multiple activator–chaperone pairs are identified from type III secretion pathways in different strains of bacteria. Directed evolution is applied to increase the dynamic range and orthogonality of the circuits. These gates are connected in different permutations to form programs, the largest of which is a 4-input AND gate that consists of 3 circuits that integrate 4 inducible systems, thus requiring 11 regulatory proteins. Measuring the performance of individual gates is sufficient to capture the behaviour of the complete program. Errors in the output due to delays (faults), a common problem for layered circuits, are not observed. This work demonstrates the successful layering of orthogonal logic gates, a design strategy that could enable the construction of large, integrated circuits in single cells...."
http://bit.ly/Ta1AIK
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October 7, 2012 3:44 PM
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by
Richard Kitney, Paul Freemont
"Just over two years ago there was an article in Nature entitled “Five Hard Truths for Synthetic Biology”. Since then, the field has moved on considerably. A number of economic commentators have shown that synthetic biology very significant industrial potential. This paper addresses key issues in relation to the state of play regarding synthetic biology. It first considers the current background to synthetic biology, whether it is a legitimate field and how it relates to foundational biological sciences. The fact that synthetic biology is a translational field is discussed and placed in the context of the industrial translation process. An important aspect of synthetic biology is platform technology, this topic is also discussed in some detail. Finally, examples of application areas are described...."
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Gerd Moe-Behrens
October 6, 2012 5:19 PM
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*Crowdsourcing Discovery*
by Ethan Perlstein
"It is time to experiment with the way we experiment. Using the Internet, we will enable the public to fund and participate in an open model of basic scientific research.
The Web, itself the fruit of curiosity-driven basic research, has transformed every industry and creative endeavor it has touched, promoting collaboration, openness and efficiency. But scientists are stuck in a closed, pre-Internet mindset. We aim to change that.
Who are we, and what do we want to do? For 5 years, Ethan Perlstein's lab at Princeton University has been developing a new evolutionary approach to studying how drugs work. For nearly 2 decades, David Sulzer's lab at Columbia Med School has been a leader in the study of how drugs affect the brain.
Our labs will now join forces to tackle a longstanding puzzle in mental health research: how does the family of drugs called amphetamines, which includes methamphetamine ("crystal meth"), actually work? Millions of people take these drugs every day, but we don't fully understand what they do at the cellular level. How can we hope for new treatments to brain diseases or addiction without basic understanding?
Simple: we can't.
We will use powerful, proven techniques to determine precisely where these drugs go deep inside brain cells, because in order to figure out how drugs work you first have to locate where they accumulate. Decades ago a similar approach famously demonstrated where the psychedelic drug LSD works within the brain. Since this is uncharted territory, we don't know for sure where they will end up, which means that you get to experience the thrill of discovery as it occurs!
To make this open approach work we need your support, and we invite you to the kickoff party for the first fully crowdsourced basic research project. Come and meet the team to learn more about Crowdsourcing Discovery!"
http://bit.ly/R1UxWd
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Gerd Moe-Behrens
October 5, 2012 7:21 PM
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GenoREAD - Sequencing Verification Pipeline http://bit.ly/PG5nwA
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Gerd Moe-Behrens
October 5, 2012 6:42 PM
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A new exiting site by Nature
*SpotOn*
"SpotOn is a series of community events for the discussion of how science is carried out and communicated online.
Our flagship conference is the annual SpotOn London two day event, formerly called Science Online London, and now in its fifth year. We also host monthly SpotOn NYC events in NYC.
SpotOn discussions fall into three broad topic areas - policy, outreach and tools - and this site collates the conversations and other archive material around all of the events."
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Gerd Moe-Behrens
October 5, 2012 5:27 PM
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"George Church, the geneticist behind the Personal Genome Project, is envisioning a package deal: get your genome sequenced, and he and his collaborators will develop a line of induced pluripotent stem cells (IPS) from your tissue, so in the future, you’ll be able upgrade your system with organs and tissues bearing both your genes and special extras like genes from centenarians. It’s combining stem cells with gene therapy. In an interview with Church, David Ewing Duncan over at Technology Review asks him to elaborate. Why does he think this science fiction scenario is in our near future?
I don’t think people have fully appreciated how quickly adult stem cells and sequencing and synthetic biology have progressed. They have progressed by orders of magnitude since we got [induced pluripotent stem cells]…
Let’s use stem cells in bone marrow as an example. They are easy to use and to get to work when you implant them in bone marrow. You might one day have three choices. You can have bone marrow [1] from someone else that is matched to you, or [2] that is from you, or [3] bone marrow that is matched to you and comes to you, but is better than you. This better bone marrow might be [engineered to be] resistant to one virus, or to all viruses. It could have a bunch of alleles that you picked out of super centenarians, alleles that you have reason to believe are at least harmless and possibly helpful…And you will be able to do that for almost every stem cell population. Some of them are a little bit harder to replace, though.
IPS cells have already been used to grow an entire mouse from nearly scratch, he points out, and many crucial experiments have already been performed in rodents, so for human testing, “we’re talking about years, not decades,” he says. “It’s shorter than the Human Genome Project [which took 13 years], not less expensive, but definitely shorter.”...."
http://bit.ly/T6b0oG
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Gerd Moe-Behrens
October 5, 2012 7:15 AM
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"When you grow up you tend to get told the world is the way it is and your life is just to live your life inside the world. Try not to bash into the walls too much. Try to have a nice family life, have fun, save a little money.
That’s a very limited life. Life can be much broader once you discover one simple fact, and that is - everything around you that you call life, was made up by people that were no smarter than you. And you can change it, you can influence it, you can build your own things that other people can use.
The minute that you understand that you can poke life and actually something will, you know if you push in, something will pop out the other side, that you can change it, you can mold it. That’s maybe the most important thing. It’s to shake off this erroneous notion that life is there and you’re just gonna live in it, versus embrace it, change it, improve it, make your mark upon it.
I think that’s very important and however you learn that, once you learn it, you’ll want to change life and make it better, cause it’s kind of messed up, in a lot of ways. Once you learn that, you’ll never be the same again.Think different"
Steve Jobs
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Gerd Moe-Behrens
from GenoCon 2
October 4, 2012 6:08 PM
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OOoh - DIY bioinformatics - this looks like a great teaching and learning resource!
"Mission statement: We hope that Rosalind will inspire a new generation of bioinformatics students by attracting biologists who want to develop vital programming skills at their own pace in a unique environment as well as programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology."
A Gentle Introduction to Python could be useful...!
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Gerd Moe-Behrens
October 3, 2012 4:31 PM
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"This app is designed for synthetic biology researchers.
Synthetic biology researchers need to view informations for DNA parts called Biobricks.We put all the information of Biobricks into this app.
In this app, synthetic biology researchers and students can learn about the properties of the DNA parts.They can search parts they want or view them by category. This app can be really helpful for someone work on synthetic biology."
