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Embracing the idea that molecules can be programmed much like a computer, researchers can now perform remarkable feats on a very small scale. New Caltech faculty member Lulu Qian, assistant professor of bioengineering, performs research in the field of molecular programming because it allows her to design synthetic molecular systems with neural-network-like behaviors and tiny robots, both from the programmed interactions of DNA molecules. Originally from Nanjing, China, Qian received her bachelor's degree from Southeast University in 2002 and her PhD from Shanghai Jiao Tong University in 2007. After working as a postdoctoral scholar at Caltech in the laboratory of Shuki Bruck, Qian became a visiting fellow at Harvard University; she returned to Caltech and joined the faculty in July. Recently, Qian answered a few questions about her research, and how it feels to be back at Caltech.
What do you work on?
I work on rationally designing and creating molecular systems with programmable behaviors. I am interested in programming biological molecules—like DNA and RNA—to recognize molecular events from the biochemical environment, process information, make decisions, take actions, and to learn and evolve. Molecular programming is not just about using computer programs to aid the design and analysis of molecular systems; it is more about adapting the principles of computer science to create biochemical systems that can carry out instructions to perform tasks at the molecular level. For example, I develop simple and standard molecular components that can be used to perform a variety of tasks and systematic ways to configure the behavior of interacting molecules to carry out one computational or mechanical task or another. These custom-designed molecules can be ordered from a commercial supplier and mixed in a test tube to generate a "molecular program."
Using this approach, I have designed DNA circuits that can solve basic logic problems, and I have constructed a DNA neural network that can perform simple associative memory functions—much like a network of neurons in the brain, though in a rudimentary way. In my future research, I would like to improve the speed, robustness, and complexity of these implementations and to explore the possibility of creating molecular systems with learning capabilities, while also beginning new work in the field of molecular robots—tiny, nanoscale machines made of DNA that can perform a designed task such as sorting cargo or solving a maze.
What do you find most exciting about your research?
I am driven by curiosity—outside of the lab, I like Legos and puzzles—and I view life as a program, one that is much more sophisticated than any other program that we know of so far. The sequence of nucleotides that make up DNA—As, Ts, Cs, and Gs—encodes the program within a genome, orchestrating molecules to sense, to compute, to respond, and to grow. Because of their different lengths and sequences, one genome produces a bacterium while another produces a plant, or an insect, or a mammal. The genetic program describes how to make molecules, and molecules are machines that can achieve complex tasks to regulate the behaviors of individual cells. To better appreciate the molecular programs that nature creates, I want to understand what possible behaviors a network of interacting molecules can exhibit and how we can rationally design such behaviors.
But, I am also driven by my engineering nature. I want to design and build molecular systems with increasing complexity and sophistication. For example, you could imagine using such molecular machines to make a nanoscale factory that manufactures novel chemicals in a test tube. These chemicals could become new materials or new drugs. You could also imagine embedding such molecular machines into individual cells so that you could collect information from the molecular environment and regulate the cell's behavior. Such regulation could lead to responsive biosynthesis—the production of proteins or other molecules in response to a stimulus—or localized diagnostics followed by therapeutics.
How did you get into your field?
I started programming computers when I was 13 years old, and I have loved it ever since then. My dad was a philosopher, and because of his influence, I got curious about fundamental questions such as who I am and why I think the way that I do. At first, I tried to look for these answers in molecular biology, but as a programmer, biology was difficult for me to understand. Unlike in programming, you cannot just define a few logical principles to understand the behavior of an entire biological system or organism. At the time, biology was not as fun for me—or as logical—as computer programming.
But just before I went to graduate school, I discovered the first publication in DNA computing by Len Adleman at the University of Southern California. He used DNA molecules as a computing substrate to solve a hard math problem. The moment that I finished reading this paper, I felt completely excited. It was the first time that I saw a strong relationship between molecules that are traditionally only used in biology—like DNA and RNA—and computer programming. That was when I started working in my field.
Why are you excited to be at Caltech?
After working at other institutions, Caltech has been a very special place for me. I like that Caltech is small and is an environment in which we're encouraged to pursue fundamental research and appreciate the beauty of science. I am most excited about doing great science here. There are very talented students—I am looking for the most fun and creative minds to join my lab—and I have visionary colleagues. We have an excellent molecular programming community at Caltech, including Erik Winfree in computer science, Shuki Bruck in electrical engineering, Richard Murray in control and dynamical systems, Niles Pierce and Paul Rothemund in bioengineering, and now myself. And we now have this new division, Biology and Biological Engineering, which I believe will bring fundamental engineering to biological sciences and create interdisciplinary research activities.
- See more at: http://www.caltech.edu/content/programming-dna-molecular-robots-interview-lulu-qian#sthash.NSli3vtS.dpuf"
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CAMBRIDGE, Mass., July 10, 2014--(PR Newswire)--
To Get More Information: http://www.bigmarketresearch.com/synthetic-biology-market Synthetic biology is a novel field that finds its origin at the intersection of biology and engineering. It involves designing and construction of biological systems or devices that can be applied in varied domains to get specified results.
byCitorik RJ, Mimee M, Lu TK"Since their discovery, bacteriophages have contributed enormously to our understanding of molecular biology as model systems. Furthermore, bacteriophages have provided many tools that have advanced the fields of genetic engineering and synthetic biology. Here, we discuss bacteriophage-based technologies and their application to the study of infectious diseases. New strategies for engineering genomes have the potential to accelerate the design of novel phages as therapies, diagnostics, and tools. Though almost a century has elapsed since their discovery, bacteriophages continue to have a major impact on modern biological sciences, especially with the growth of multidrug-resistant bacteria and interest in the micro biome.". http://bit.ly/1tgAMyt
by Minsu Kim "This conceptual food by Royal College of Art graduate Minsu Kim would wriggle around on the plate and in your mouth (+ movie).
byRobinson CJ, Vincent HA, Wu MC, Lowe PT, Dunstan MS, Leys D, Micklefield J."Ligand-dependent control of gene expression is essential for gene functional analysis, target validation, protein production and metabolic engineering. However, the expression tools currently available are difficult to transfer between species and exhibit limited mechanistic diversity. Here we demonstrate how the modular architecture of purine riboswitches can be exploited to develop orthogonal and chimeric switches that are transferable across diverse bacterial species, modulating either transcription or translation, to provide tuneable activation or repression of target gene expres-sion, in response to synthetic non-natural effector molecules. Our novel riboswitch-ligand pairings are shown to regulate physiologically important genes required for bacterial motility in Escherichia coli and cell morphology in Bacillus subtilis. These findings are relevant for future gene function studies and antimicrobial target validation, whilst providing new modular and orthogonal regulatory components for deployment in synthetic biology regimes." http://bit.ly/1sXYZtg
byTechonomy "Techonomy’s offices on Manhattan’s West 22d Street have been buzzing ever since our half-day Techonomy Bio conference on June 17. We got an overwhelmingly positive reception for a meeting that brought leading researchers and experts in the life sciences together with IT and Internet thinkers and business generalists.
byHolm S."Theorists analyzing the concept of disease on the basis of the notion of dysfunction consider disease to be dysfunction requiring. More specifically, dysfunction-requiring theories of disease claim that for an individual to be diseased certain biological facts about it must be the case. Disease is not wholly a matter of evaluative attitudes. In this paper, I consider the dysfunction-requiring component of Wakefield's hybrid account of disease in light of the artifactual organisms envisioned by current research in synthetic biology. In particular, I argue that the possibility of artifactual organisms and the case of oncomice and other bred or genetically modified strains of organism constitute a significant objection to Wakefield's etiological account of the dysfunction requirement. I then develop a new alternative understanding of the dysfunction requirement that builds on the organizational theory of function. I conclude that my suggestion is superior to Wakefield's theory because it (a) can accommodate both artifactual and naturally evolved organisms, (b) avoids the possibility of there being a conflict between what an organismic part is supposed to do and the health of the organism, and (c) provides a nonarbitrary and practical way of determining whether dysfunction occurs." http://bit.ly/1pFgFse
Researchers detail the binding domain of BurrH, a DNA-binding protein. They also reprogrammed the domain, called BuD, showing its potential as a gene-editing tool.
Advances in synthetic biology have made it possible to convert biomass to chemicals, fuels and materials, and produce new therapeutic drugs
Synthetic biology is attracting attention from both scientists and regulators. But there is little agreement on what it is. Can we find a road out of synthetic biology’s definitional quagmire?
Life is a programming language, and molecular biologist Andrew Hessel thinks that it will be increasingly available to anyone interested in designing with the building blocks of life.
The Living's (Buildings that grow? @autodesk acquires The Living & bets on synthetic biology. #synthbio #theliving http://t.co/KmuQCZyZJK)
Synthetic Biology: Volume 1 (Specialist Periodical Reports) [Maxim Ryadnov, Luc Brunsveld, Hiroaki Suga, Eric Kool, Birger Lindberg Moller, Alexander Kros, Cristiano Chiarabelli, Stephen Hart, Maarten Merkx, Oliver Rackham, S Tekeuchi, Paul Dalby, Jeroen Cornelissen] on Amazon.com. *FREE* shipping on qualifying offers. Synthetic biology is a new area of biological research that combines science and engineering in order to design and build novel biological functions and systems. The definition of synthetic biology has been generally accepted as the engineering of biology: the synthesis of complex
byHaiyao Huang and Douglas Densmore "One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications. Major challenges in these efforts include increasing the scalability and robustness of engineered biological systems and streamlining and automating the synthetic biology workflow of specification-design-assembly-verification. We present here a summary of the advances in microfluidic technology, particularly microfluidic large scale integration, that can be used to address the challenges facing each step of the synthetic biology workflow. Microfluidic technologies allow precise control over the flow of biological content within microscale devices, and thus may provide more reliable and scalable construction of synthetic biological systems. The integration of microfluidics and synthetic biology has the capability to produce rapid prototyping platforms for characterization of genetic devices, testing of biotheraputetics, and development of biosensors."http://rsc.li/1xhURTw
The latest generation of DNA sequencers allows all the genes of a plant, as well as any pathogens present, to be charted literally within a few days. “This provides unprecedented opportunities for the diagnosis of plant diseases, as well as, for example, identifying and tracking new disease outbreaks,” says Dr Theo van der Lee, senior scientist at the Department of Bio-Interactions and Plant Health at Plant Research International. “We can now detect pathogens directly from infected plant material, usually without having to guess in advance which bacterium, fungus or virus is the culprit.”
An awesome new #synbio community page by PLOS http://bit.ly/1lzSlzL
Synthetic Biology Market - Global Industry Analysis, Size, Share, Growth, Trends and Forecast,2013 - 2019
With advances in biological and genomic sciences accelerating at an ever-increasing pace, what does the future hold? If biological progress is indeed advancing more rapidly than Moore’s Law, as many assert, what are the economic and societal implications? In this video from our June 17 Techonomy Bio conference, Alex Lash, biotech editor at Xconomy, interviews Drew Endy, bioengineer at Stanford, about biological processes.