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[185 Pages Report] Synthetic Biology Market report categories the global market by Technology (Nanotechnology, Gene Synthesis, Bioinformatics, Cloning & Sequencing), Application (Pharmaceuticals, Biomaterials, Biofuels, Bioremediation), Tool(Oligos,...
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CBE Life Sci Educ. 2014 Summer;13(2):285-296.
Gerd Moe-Behrens's insight:
by A. Malcolm Campbell,* Todd Eckdahl,† Brian Cronk,‡ Corinne Andresen,† Paul Frederick,† Samantha Huckuntod,† Claire Shinneman,† Annie Wacker,* and Jason Yuan† "The Vision and Change report recommended genuine research experiences for undergraduate biology students. Authentic research improves science education, increases the number of scientifically literate citizens, and encourages students to pursue research. Synthetic biology is well suited for undergraduate research and is a growing area of science. We developed a laboratory module called pClone that empowers students to use advances in molecular cloning methods to discover new promoters for use by synthetic biologists. Our educational goals are consistent with Vision and Change and emphasize core concepts and competencies. pClone is a family of three plasmids that students use to clone a new transcriptional promoter or mutate a canonical promoter and measure promoter activity in Escherichia coli. We also developed the Registry of Functional Promoters, an open-access database of student promoter research results. Using pre- and posttests, we measured significant learning gains among students using pClone in introductory biology and genetics classes. Student posttest scores were significantly better than scores of students who did not use pClone. pClone is an easy and affordable mechanism for large-enrollment labs to meet the high standards of Vision and Change." free PDF
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Get Your Free Trial Here: https://www.labster.com/courses/LabsterX/SyntheticBiology/2015/about ABOUT THE VIRTUAL LAB SIMULATION In the Synthetic ...
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What sorts of breakthroughs are possible by modifying an organism’s genome – something researchers are now able to do ever more cheaply and efficiently?
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Biocomputers can potentially be used to control development, cell differentiation and re-programming, as all these processes depend on gene regulatory networks. Another application area is tissue engineering and tissue regeneration. Metabolic engineering has the potential to produce from simple, inexpensive starting materials a large number of chemicals that are currently derived from nonrenewable resources or limited natural resources. The metabolic flux can potentially be controlled by a biocomputer. Interesting might also be to control the immune system by a biocomputer, e.g. in transplantation medicine. An important application area is the control of malign growth. Some interesting experiments with logic based biological devices have been executed to detect cancer cells (e.g. small-cell lung cancer, prostate cancer, HeLa cells), and to induce selective apoptosis of these cells. Furthermore, biocomputers can be used to engineer context-dependent programmable drugs. A biocomputer with a context-sensing mechanism, which can simultaneously sense different types of molecules, has been engineered. In the future it might be used to detect a broad range of molecular disease symptoms, and react with the release of a drug molecule suitable for the treatment of the specific condition. In line with this concept a programmable NOR-based device has been developed capable of differentiating between prokaryotic cell strains based on their unique expression profile. http://bit.ly/YI13bF
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Gerd Moe-Behrens's insight:
Biological systems need to be monitored in respect to disease diagnostic, to drug screening, to understand experimental systems, and to observe the environment. In line with this, a biocomputer has been utilized to detect multiple disease indicators, such as mRNA of disease-related genes associated with small-cell lung cancer and prostate cancer. Moreover, they can be used in experimental models, such as conditional transgenes or inducible expression systems. Environmental monitoring is another interesting application. A cell based biosensor using logic gates has been used to detect arsenic, mercury and copper ion levels. http://bit.ly/YI13bF
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BACKGROUND:
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From
biorxiv
Gene regulation in biological systems is impacted by the cellular and genetic context-dependent effects of the biological parts which comprise the circuit. Here, we have sought to elucidate the limitations of engineering biology from an architectural point of view, with the aim of compiling a set of engineering solutions for overcoming failure modes during the development of complex, synthetic genetic circuits. Using a synthetic biology approach that is supported by computational modelling and rigorous characterisation, AND, OR and NOT biological logic gates were layered in both parallel and serial arrangements to generate a repertoire of Boolean operations that include NIMPLY, XOR, half adder and half subtractor logics in single cell. Subsequent evaluation of these near-digital biological systems revealed critical design pitfalls that triggered genetic context dependent effects, including 5′ UTR interference and uncontrolled switch-on behaviour of σ54 promoter. Importantly, this work provides a representative case study to the debugging of genetic context dependent effects through principles elucidated herein, thereby providing a rational design framework to program single prokaryotic cell with diversified digital operations.
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Gerd Moe-Behrens's insight:
Shown is a simplified diagram of a modular memory device, which is a transcriptionally controlled network composed of two transcription factor encoding genes, a sensor gene and a positive (+) auto feedback gene (P-GAL = GAL 1/10 promoter, P-CYC = CYC 1 promoter, DNA BD = sequence encoding a DNA binding domain of the respective transcription factor). The network can be in three states, off, on and memory. The system is in of state, if it has never been exposed to a signal (here galactose). It is on, if galactose is present. In this case the signal induces the synthesis of a transcription factor, the sensor. This triggers the expression of another transcription factor able to bind to its own promoter. The system is in memory state, if the signal is removed. The auto feedback activator is able to initiate its own expression even if the inducing signal is lacking, which means that the system has stored information.
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Gerd Moe-Behrens's insight:
by
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Gerd Moe-Behrens's insight:
A final state machine, as shown here, is a theoretical model which can help to understand what is going on in the central processing unit. Simplified: Symbols a and b are written on a tape, which is read by the machine letter by letter from left to right. In this example the tape ends with the final letter b. Each letter provides the instruction to the machine into which state (S1, or S0) it should move; here a means move to state state 0 (S0) and b codes the instruction move to state 1 (S1). The final state of the machine in this example is thus S1. http://bit.ly/YI13bF
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Alexandra Daisy Ginsberg explores how synthetic biology and design can be utilised to do useful things, engineering a better future. Daisy is an artist, designer and writer investigating the dynamic that exists between synthetic biology and design.
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The iGEM Team BIOSINT México, considered that when people talk about ethics, specifically, the members of all the teams, lack of an ethical code to serve as a guide for considering the ethical aspects of the projects.
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In this review, we address recent advances in the field of synthetic biology and describe how those tools have been applied to produce a wide variety of chemicals in microorganisms. Here we classify the expansion of the synthetic biology toolbox into three different categories based on their primary function in strain engineering-for design, for construction, and for optimization. Next, focusing on recent years, we look at how chemicals have been produced using these new synthetic biology tools. Advances in producing fuels are briefly described, followed by a more thorough treatment of commodity chemicals, specialty chemicals, pharmaceuticals, and nutraceuticals. Throughout this review, an emphasis is placed on how synthetic biology tools are applied to strain engineering. Finally, we discuss organism and host strain diversity and provide a future outlook in the field. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering Volume 6 is July 16, 2015. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
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Researchers at the University of California, Berkeley, have developed an easy way to put bacteria under a molecular lock and key in order to contain its
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Introducting Synthetic Biology - By IGem Team Tu Munich 2011 | science buddie | cool science projectfun physics experiments, physical experiments, chemistry experiments for class 12, college chemistry experiments, halloween chemistry experiments, chemistry ...
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Science Documentary: Personalized Medicine, Synthetic Biology a documentary on genetic design Within our DNA lies the instructions for our cells. These cellular ...
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Fact: Scientists have found a rare species of bacteria that ‘breathes’ uranium and thrives in abandoned uranium ore processing sites.
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Synthetic Biology Startup Zymergen Emerges From Stealth With $44 Million - http://t.co/QFluBy5U28 http://t.co/uqlqu9waaE
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A rewritable recombinase addressable data module, able to store data within a DNA sequence (simplified): Serine integrase and excisionase are used to invert and restore specific DNA sequences. The system has two potential inputs; a set and a reset transcription signal. This set signal drives expression of integrase which inverts a DNA element, functioning as a genetic data register. Flipping the register converts the flanking sites (triangle). The system is now in state 1 (S1). Alternatively a reset signal drives integrase and excisionase expression and restores register orientation and the flanking sites. The system is in its other state (S0). The register comprises a promoter, which is driving state dependent, strand-specific transcription of either red or green fluorescent protein, the two possible outputs of the system. http://bit.ly/YI13bF
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Gerd Moe-Behrens's insight:
by Stephanie Garlock Anna H. Chen, a graduate of HMS’s systems biology department, led the new research while a doctoral student in the lab of Adams professor of biochemistry and systems biology Pamela Silver. The team, which published its work in the journal Science Advances on Friday, June 12, began by examining the mechanism behind the circadian rhythm in the cyanobacterium Synechococcus elongatus. These photosynthesizing bacteria use three key proteins to regulate their cycles of day and night. Past research had already established that, even when simply combined in a test tube, the three will bind and unbind in a regular, circadian rhythm. Chen used these proteins to build an “oscillator”—a biological function that turns off and on in a regular pattern—and transplanted it into the gut bacterium Escherichia coli. For synthetic biologists, the process used to identify and deploy these proteins is, by now, a relatively well-understood one. The “real genius” of Chen’s experiment, Silver reflected, was therefore in its specific implementation: building a system that would put these tools together in the right way, and provide a mechanism to prove that it had worked. The team created a fluorescent protein marker that would operate “downstream” of the oscillator. Over a three-day period, they observed it turn on and off on a regular, 24-hour cycle, proving that the rhythm had taken hold in the normally non-circadian E. coli, The result was the first transplantable, 24-hour circadian clock. While other researchers have been able to produce either a time delay or a rhythm on a shorter time-scale, the Silver lab is the first to create a system using a 24-hour cycle, which allows it to “interface with virtually all of life,” Silver said. The experiment, Chen explained, provided a proof of principle. Now, scientists can swap out the pulsing fluorescent marker protein for any one of a variety of other functions, which could then be similarly tied to a daylong cycle. “This back and forth is not just a random back and forth,” Chen added. “That 24-hour timing is really important to humans, because we live on the day-night cycle. We live on this Earth.” This new clock is one of a number of biological building blocks that researchers in Silver’s lab have begun producing over the last few years (see, “Synthetic Biology’s New Menagerie,” September-October 2014, page 42). The burgeoning field of synthetic biology, in which her lab has played a leading role, is specifically oriented toward creating real-world uses for these newly engineered pieces of biology, and the authors note several potential applications for a transplantable circadian clock....."
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Gerd Moe-Behrens's insight:
Molecular implementation of a final state machine. The upper part of the figure contains the definitions for this machine: The symbols a, b, and t (terminator) are implemented as a sequence of six specific nucleotides. The state (S1 or S0) of the machine is defined by a 5′ overhang (generated during the computing process, see below) consisting of 4 specific nucleotides (inside the frames). The terminator defines the final symbol read. The machine consists of an input molecule, a transition molecule, an output detector and two enzymes Fokl and ligase. The input molecule consist of a Fokl recognition site (F), a spacer x (a certain defined number of nucleotides), a nucleotide sequence defining a and b, a sequence with the remaining symbols (rem = n numbers of a and b in a defined order) and the terminator sequence (t). Fokl is a restriction endonuclease which can bind to F. It cleaves the DNA (without further sequence specificity) on the sense strand 9 nucleotides downstream and the anti-sense strand 13 nucleotides upstream of the nearest nucleotide of the recognition site. Thus the space x defines where Fokl is cutting. The cleavage of the input molecule results in the first intermediate state (S0), an 5′ overhang, reading a. Ligase ligate this product with the transition molecule. This transition molecule determinates the transition between the states, in this example: if a is read, move from S0 to S0. Other transition molecules can be generated defining all the other possible transition rules. These molecules are designed such that the 4 bases long 3' overhang reads the symbol, the spacer x defines the cutting point of Fokl 1 and the state the machine will transit to (here S0). The input molecule and the transition molecule get ligated. A new digestion with Fokl leaves an 5' overhang representing S0 and a reading b. This cycle continues until all remaining symbols (rem) are read and state transitions are executed. The last digestion leaves a 5' overhang with a terminator sequence defining the final state, in general either S0 or S1 (in this example S0). The molecule in its final state, gets ligated to an output detector, engineered to recognize either state 0 or 1. This forms an output-reporting molecule, which can be detected by gel electrophoresis.
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