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."
The clothing industry employs 25 million people globally contributing to many livelihoods and the prosperity of communities, to women’s independence, and the establishment of significant infrastructures in poorer countries. Yet the fashion industry is also a significant contributor to the degradation of natural systems, with the associated environmental footprint of clothing high in comparison with other products. Routledge Handbook of Sustainability and Fashion recognizes the complexity of aligning fashion with sustainability. It explores fashion and sustainability at the levels of products, processes, and paradigms and takes a truly multi-disciplinary approach to critically question and suggest creative responses to issues of:• Fashion in a post-growth society • Fashion, diversity and equity • Fashion, fluidity and balance across natural, social and economic systems This handbook is a unique resource for a wide range of scholars and students in the social sciences, arts and humanities interested in sustainability and fashion.
"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 →
"In yeast cell-surface displays, functional proteins, such as cellulases, are genetically fused to an anchor protein and expressed on the cell surface. Saccharomyces cerevisiae, which is often utilized as a cell factory for the production of fuels, chemicals and proteins, is the most commonly used yeast for cell-surface display. To construct yeast cells with a desired function, such as the ability to utilize cellulose as a substrate for bioethanol production, cell-surface display techniques for the efficient expression of enzymes on the cell membrane need to be combined with metabolic engineering approaches for manipulating target pathways within cells. In this minireview, we summarize the recent progress of biorefinery fields in the development and application of yeast cell-surface displays from a synthetic biology perspective and discuss approaches for further enhancing cell-surface display efficiency."
The phrase “synthetic biology” may sound like science fiction, but a small group of biology students at the University of Virginia say this field will play an important role in our lives over the next few years.