"Plants synthesize a huge variety of terpenoid natural products, including photosynthetic pigments, signaling molecules and defensive substances. These are often produced as complex mixtures, presumably shaped by selective pressure over evolutionary timescales, some of which have been found to have pharmaceutical and other industrial uses. Elucidation of the relevant biosynthetic pathways can provide increased access (e.g., via molecular breeding or metabolic engineering), and enable reverse genetic approaches towards understanding the physiological role of these natural products in plants as well. While such information can be obtained via a variety of approaches, this review describes the emerging use of synthetic biology to recombinantly reconstitute plant terpenoid biosynthetic pathways in heterologous host organisms as a functional discovery tool, with a particular focus on incorporation of the historically problematic cytochrome P450 mono-oxygenases. Also falling under the synthetic biology rubric and discussed here is the nascent application of genome-editing tools to probe physiological function."
Dissertation presented to obtain the Master Degree in Molecular, Genetics and Biomedicine
Apura, PatrÃcia de Faria Pais
Transcriptional and post-transcriptional control of gene expression dictate the levels of proteins in the cell. Therefore the modulation of gene expression can have important consequences for biotechnological and/or pharmaceutical purposes. Among the types of cellular RNAs, small RNAs (sRNAs) have been an emerging class of bacterial gene expression regulators, which mostly act by base-pairing with one or more mRNA target(s) affecting their translation and/or their stability. Here, we focus on the study of SraL sRNA, more specifically in the validation of putative targets for this sRNA obtained in a previous transcriptomic analysis. Until now SraL was only shown to regulate the mRNA levels of Trigger Factor, an important protein chaperone. The information here reported give strong evidence for SraL involvement in the cysteine biosynthetic pathway, which requires further investigation. Nevertheless, our results could not provide a validation of those putative targets previously obtained by transcriptomic analyses. Optimization of protein expression requires not only an increase of the stability of mRNA transcripts but also an optimal behavior of function-encoding DNA segments, which are often context-dependent. Building on the work of others, we have designed a set of combinatorial promoters and 5âUTRs and evaluated their effects/outcomes using Superfolder GFP as reporter. Our data shows a clear variability of protein levels within our set of constructs. The highest levels of protein were associated with the implementation of an insulation sequence flanking the promoter region and the introduction of 5â stabilizing structures at the mRNA level. Further investigation concerning the alteration of the rate of the mRNA decay by depletion of the function of participating nucleases, might constitute an advantageous approach. The knowledge collected will be extremely important to design robust modules which substantially increase protein production. This field is rapidly growing and much remains to be discovered about these important regulatory processes.
UVa researchers see promise in 'synthetic biology' Richmond Times-Dispatch CHARLOTTESVILLE — The phrase “synthetic biology” may sound like science fiction, but some biology students at the University of Virginia say this field will play an...
On Wednesday, April 27th it was time for the 5th edition of Do it Together Bio. The event was led by Laura Cinti and Howard Boland who are co-founders of the C-Lab collective and also winners of the latest Designers & Artists 4 Genomics Award.
"Isaac Yonemoto is a chemist, but he’s been writing software code since he was a kid. He calls himself a “semi-recreational” programmer, and now, he’s running an experiment that combines this sideline with his day job. In short, he’s using open source software techniques to kickstart the world of cancer research.
Patent-free and crowd-funded by the bitcoin digital currency, Yonemoto’s project seeks to resurrect work on a promising anti-cancer compound called 9-deoxysibiromycin, or 9-DS. Early tests indicated it could provide a treatment for melanoma, kidney cancer, and breast cancer, but then, for various reasons, research on the compound was abandoned. So Yonemoto stepped in and restarted the project online, as if it was an open source software project, raising money for additional research through an online fundraising campaign.
Although the stakes are different, Yonemoto compares his gambit to previous efforts to resurrect abandoned video games such as the classic versions of Command and Conquer—one of his favorites. “Here we have this abandonware compound,” he says, “and open-sourcing is a way of resurrecting abandonware.”
9-DS was developed by Barbara Gerratana, a professor with the University of Maryland, College Park. Back in the 1970s, Russian scientists thought that its parent compound might be useful as a cancer treatment, but they found that it stressed the heart and shelved their work. Decades later, Gerratana discovered that by loping off an oxygen molecule, she could not only avoid the coronary side-effects but also create a more effective drug.
The rub is that Gerratana took a job with the National Institute of Health and was unable to pursue the work. And because she had already published her research without patenting it, drug companies were unlikely to sponsor the work. The good news is that because it was never patented, it’s in the public domain. Anyone can work on it, kinda like open source software. Yonemoto, who had worked on the project under a grant, jumped in.
Last week, he launched a fund-raising campaign for the research, and so far, he has taken in $12,000 of the $50,000 he’ll need to test the compound on mice. About $2,000 of that comes from bitcoin donations. He calls the campaign Project Marilyn, and it’s just one fundraising up and running on his website Indysci.org, which you can think of as a kickstarter platform for open scientific research that will publish its data openly. “We’re going to push the data to a decentralized server—possibly GitHub,” he says, referring to the popular service for hosting open source software projects.
His fundraising technique that’s very much at odds with the way that most drugs are researched these days, but in a sense, it’s also a return to the roots of mid-century drug research, when the polio vaccine, for instance, was developed and distributed patent-free. “I’ve never been a big fan of patents and this seemed like good opportunity,” says Yonemoto, who unlike most chemists, constantly nods to things like bitcoin and free software pioneer Richard Stallman in the course of conversation.
What we’re seeing here is the result of a decade long cross pollination between the biology and computer science, kicked off by the computerized sequencing of the human genome. The computer science world’s open source ethos is starting to rub off, Yonemoto says. “Biology is becoming more like a computer science discipline,” he says.
The question is whether this will actually work. Yonemoto may be able to continue the research. But turning this into a mass produced drug would take some serious money—more than you can likely raise online. The hope is that his small project can attract more researchers—and larger investors—to the problem. “Biological processes are primarily stochastic, and computer processes are supposed to be deterministic,” he says. “But I think there is going to be a convergence to some degree.”"
"Pattern formation is essential in the development of animals and plants. The central problem in pattern formation is how can genetic information be translated in a reliable manner to give specific spatial patterns of cellular differentiation.
The French-flag model of stripe formation is a classic paradigm in developmental biology. Cell differentiation, represented by the different colours of the French flag, is caused by a gradient of a signalling molecule (morphogen); i.e. at high, middle or low concentrations of the morphogen a "blue", "white" or "red" gene stripe is activated, respectively. How cellular gene regulatory networks (GRNs) respond to the morphogen, in a concentration-dependent manner, is a pivotal question in developmental biology. Synthetic biology is a promising new tool to study the function and properties of gene regulatory networks (GRNs) by building them from first principles. This study developed synthetic biology methods to build some of the fundamental mechanisms behind stripe formation.
In previous studies, gene circuits with predefined behaviors have been successfully built and modeled, but mostly on a case-by-case basis. In this study published in Nature Communications, researchers from the EMBL/CRG Systems Biology Research Unit at the CRG, went beyond individual networks and explored both computational and synthetic mechanisms for a complete set of 3-node stripe-forming networks in Escherichia coli. The approach combined experimental synthetic biology led by Mark Isalan, now Reader in Gene Network Engineering at the Department of Life Sciences of Imperial College London with computational modelling led by James Sharpe, ICREA Research Professor and head of the Multicellular Systems Biology lab at the CRG."
In October 2013, Greg Gage and Tim Marzullo unveiled a cyborg cockroach that could be controlled from a smartphone through electrodes attached to its antennae and a wireless unit on its back. Imagine in the coming years what would happen if we are able to go much smaller and nanoscale computing devices could be integrated with individual bacteria. And what if these hybrid devices could be designed to control colonies of bacteria? Of course a big problem could be powering such devices, but bacteria based batteries are already a reality.
So should we allow this living technology to develop and be autonomous? If it was possible, then the extension of "the internet of things" to "the internet of biology" e.g., bacteria, molds, plants and crops should also be possible -- in fact all living things could be networked and online. An online connection could enable living systems to be controlled by software allowing bioware "apps" to add functionality beyond that allowed by biology.
What if the bacteria connected online could be turned into sophisticated swarms with collective intelligence spread over many miles, vastly exceeding the primitive-by-comparison biological sensing? What if the synthesis of bacteria and silicon-powered intelligence gave rise to a new symbiotic life form? I would imagine that these swarms could be used to remove pollutants, sent out to sense the environment, even monitor the emergence of new viruses in the wild. Perhaps even more exciting could be the direct control of the machinery within the cells. Enter the realm of cybernetic synthetic biology.
What exactly is cybernetic synthetic biology? From my point of view I see this as the integration of biological organisms with small silicon-based computing devices and I've been pondering this concept -- as well as the consequences -- for around 12 months. In my own scientific work I am interested in understanding the chemical origin of life, creating new life forms, and investigating new ways of controlling chemistry and biochemistry. The taming of existing life forms using silicon seems extremely attractive, albeit a few decades off (although some would argue that silicon, such as in the form of smart phones, is already controlling us through social media and messaging).
Although the internet of biology seems rather outlandish, I really think it might be very interesting to anticipate what the consequences of such a technology could be. Could a responsible approach explaining the potential wins, wonders, and pitfalls be used to educate the public and policy makers? This would also give scientists and technology developers time to think about the implementation as well as debate possible safety measures.
We are now entering a time of research developments, technological innovation and policy development where it is not only possible to peer review scientific ideas, but also to discuss possible consequences before the work is done. Could such a discussion not only focus on the merits of the science in question, feasibility and value for money, but also the impact of success on society as a whole? This approach is not without risks. Preventing science that generates anxiety could inhibit chance discoveries that is the very essence of blue-sky thinking. Of course we need to responsibly discuss the risks, as well as address the fears say of unleashing the god-particle equivalent of black hole that swallows the Earth, or perhaps a bioweapon that can be remotely programmed by their masters to lie silent and then unleash all manner of terror.
However, I feel that this is unlikely, and scientists have a duty to push the boundaries -- and in this case redefine how the fusion of technology and living systems will shape the future. A serious debate is needed. A future where biology and computers are integrated poses significant questions, especially if native living things are replaced by a new technology. It may be that the future for human kind will be as hybrid biological-robots. I guess we'd better start discussing this now.
"Synthetic biology has developed numerous parts for building synthetic gene circuits. However, few parts have been described for prokaryotes to integrate two signals at a promoter in an AND fashion, i.e. the promoter is only activated in the presence of both signals. Here we present a new part for this function: a split intein T7 RNA polymerase. We divide T7 RNA polymerase into two expression domains and fuse each to a split intein. Only when both domains are expressed does the split intein mediate protein trans-splicing, yielding a full-length T7 RNA polymerase that can transcribe genes via a T7 promoter. We demonstrate an AND gate with the new part: the signal-to-background ratio is very high, resulting in an almost digital signal. This has utility for more complex circuits and so we construct a band-pass filter in Escherichia coli. The split intein approach should be widely applicable for engineering artificial gene circuit parts"
"The CRISPR-Cas9 system is revolutionizing genomic engineering and equipping scientists with the ability to precisely modify the DNA of essentially any organism. Just how powerful is this technique? The ability for precision genome engineering comes with the potential to enhance food production, medicinal discoveries, and energy solutions, to name a few. In this booklet, we invite you to explore a selection of Science articles that highlight how this technique has grown into "
"BackgroundOne of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of regulatory regions, and have been designed to meet a single design criterion.ResultsIn this contribution we introduce a multiobjective formulation for the design of biocircuits. We set up the basis for an advanced optimization tool for the modular and systematic design of biocircuits capable of handling high levels of complexity and multiple design criteria. Our methodology combines the efficiency of global Mixed Integer Nonlinear Programming solvers with multiobjective optimization techniques. Through a number of examples we show the capability of the method to generate non intuitive designs with a desired functionality setting up a priori the desired level of complexity.ConclusionsThe methodology presented here can be used for biocircuit design and also to explore and identify different design principles for synthetic gene circuits. The presence of more than one competing objective provides a realistic design setting where every solution represents an optimal trade-off between different criteria."
How do you transform mushrooms into furniture, or re-wire algae to conduct electricity? Biohacking, the practice of rewiring the biology of living organisms for practical uses, is evolving from a fringe science to a more legitimate academic discipline. But just as the movement is gathering converts, it’s also attracting controversy. Special correspondent Spencer Michels reports. Continue reading →