SynBioFromLeukipposInstitute

by
Yaochuan Mei et al

"Trialkylgermyl functionalization allows development of high-performance soluble small-molecule organic semiconductors with mobilities greater than 5 cm2 V−1 s−1. Spray-deposited organic thin-film transistors show a record mobility of 2.2 cm2 V−1 s−1 and demonstrate the potential for incorporation in large-area, low-cost electronic applications."
http://bit.ly/ZnPBPH

comment:
High performance semiconductor spray paint could be a game changer for organic electronics http://bit.ly/ZQ2nmu

by C. J. Paddon et al

"In 2010 there were more than 200 million cases of malaria, and at least 655,000 deaths1. The World Health Organization has recommended artemisinin-based combination therapies (ACTs) for the treatment of uncomplicated malaria caused by the parasite Plasmodium falciparum. Artemisinin is a sesquiterpene endoperoxide with potent antimalarial properties, produced by the plant Artemisia annua. However, the supply of plant-derived artemisinin is unstable, resulting in shortages and price fluctuations, complicating production planning by ACT manufacturers2. A stable source of affordable artemisinin is required. Here we use synthetic biology to develop strains of Saccharomyces cerevisiae (baker’s yeast) for high-yielding biological production of artemisinic acid, a precursor of artemisinin. Previous attempts to produce commercially relevant concentrations of artemisinic acid were unsuccessful, allowing production of only 1.6 grams per litre of artemisinic acid3. Here we demonstrate the complete biosynthetic pathway, including the discovery of a plant dehydrogenase and a second cytochrome that provide an efficient biosynthetic route to artemisinic acid, with fermentation titres of 25 grams per litre of artemisinic acid. Furthermore, we have developed a practical, efficient and scalable chemical process for the conversion of artemisinic acid to artemisinin using a chemical source of singlet oxygen, thus avoiding the need for specialized photochemical equipment. The strains and processes described here form the basis of a viable industrial process for the production of semi-synthetic artemisinin to stabilize the supply of artemisinin for derivatization into active pharmaceutical ingredients (for example, artesunate) for incorporation into ACTs. Because all intellectual property rights have been provided free of charge, this technology has the potential to increase provision of first-line antimalarial treatments to the developing world at a reduced average annual price."

http://bit.ly/17kZm2M

by
Knuuttila T, Loettgers A.

"Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their construction is typically combined with experiments on model organisms as well as mathematical modeling and simulation. What is especially interesting about this combinational modeling practice is that, apart from greater integration between these different epistemic activities, it has also led to the questioning of some central assumptions and notions on which synthetic biology is based. As a result synthetic biology is in the process of becoming more "biology inspired."

http://bit.ly/ZGVEOP

by
Christina Agapakis

"Synthetic biology is often referred to as “the field of the future,” the foundation of a fuels, materials, medicines, as well as the way we produce knowledge of biological systems. But while the self-consciously revolutionary language of synthetic biology declares a change of the industrial status quo, the metaphors we rely on are explicit references to the successful revolutions of past industrial technologies. The term synthetic biology echoes the successes of synthetic chemistry, while the guiding concept of standardization in genetic components is modeled on 19th century standardization of interchangeable parts. Industrial metaphors mix further as we climb the abstraction hierarchy; genetic parts are assembled to fit into a cellular chassis, creating logic gates and circuits that can compute biological information, leading to the control of cellular factories, rapidly designed, built, and commercialized on an “Ikea”-like scale.

These metaphors help us to understand how an industrial revolution might emerge from a biology lab, showing a possible path from ideas to industry. Like the “horseless carriage,” perhaps the analogies of living cells to computers give us a sense of familiarity with a technology whose potential we have not yet fully grasped. Industrial metaphors have long played a role in how we understand biology and the human body, from Fritz Kahn’s 1927 paintings of “Man as Industrial Palace to analogies between brains and computers. By referencing the products and methods of previous industrial revolutions, synthetic biology aims not only to aid understanding but also to demonstrate the future potential of the field. These metaphors draw the projected lines of Moore’s exponential increase as strands of DNA, imagining analogous and expanding industries based on carbon and sunlight rather than silicon and fossil fuels...."

http://bit.ly/127iAGK

 

*Synthetic Biology: Tools and Applications*
Book  edited by Huimin Zhao

 

"......  from the content:


Protein Engineering as an Enabling Tool for Synthetic BiologyPC Cirino, S Qian - Synthetic Biology: Tools and Applications, 2013Proteins are essential ingredients in any natural or synthetic biological system, and the extent to which properties of one or more proteins can be modified in direct and desired ways often dictates success in synthetic biology and metabolically engineered systems. ... Synthetic Biology: Tools and ApplicationsH Zhao - 2013Synthetic Biology provides a framework to examine key enabling components in the emerging area of synthetic biology. Chapters contributed by leaders in the field address tools and methodologies developed for engineering biological systems at many levels, ... Design and Application of Synthetic Biology DevicesBC Heng, M Fussenegger - Synthetic Biology: Tools and Applications, 2013Synthetic biology is the rational and systematic design/construction of biological systems with desired functionalityl—4 This is achieved through applying engineering and computational principles within the field of molecular biology. 1_4 As such, synthetic ... Transforming Synthetic Biology with Cell-Free SystemsA Ranjil, JC Wu, BC Bundy, MC Jewett - Synthetic Biology: Tools and Applications, 2013Synthetic biology is a new approach for engineering biology by design. At its heart, this emerging discipline seeks to make biology easier to engineer and to harness biology to serve society. Already, this new paradigm for engineering biology is enabling a deeper ... Pathway Engineering as an Enabling Synthetic Biology ToolDT Eriksen, S Li, H Zhao - Synthetic Biology: Tools and Applications, 2013Pathway engineering has proven indispensable in the design of microbes for production of value-added products such as drugs, biofuels, and specialty chemicals. 1—4 Typically, a heterologous metabolic pathway producing the value-added compound is introduced into ..."

http://bit.ly/11lOU7J ;

by
Timothy R. Sampson,Sunil D. Saroj,Anna C. Llewellyn,Yih-Ling Tzeng& David S. Weiss

"CRISPR/Cas (clustered regularly interspaced palindromic repeats/CRISPR-associated) systems are a bacterial defence against invading foreign nucleic acids derived from bacteriophages or exogenous plasmids1, 2, 3, 4. These systems use an array of small CRISPR RNAs (crRNAs) consisting of repetitive sequences flanking unique spacers to recognize their targets, and conserved Cas proteins to mediate target degradation5, 6, 7, 8. Recent studies have suggested that these systems may have broader functions in bacterial physiology, and it is unknown if they regulate expression of endogenous genes9, 10. Here we demonstrate that the Cas protein Cas9 of Francisella novicida uses a unique, small, CRISPR/Cas-associated RNA (scaRNA) to repress an endogenous transcript encoding a bacterial lipoprotein. As bacterial lipoproteins trigger a proinflammatory innate immune response aimed at combating pathogens11, 12, CRISPR/Cas-mediated repression of bacterial lipoprotein expression is critical for F. novicida to dampen this host response and promote virulence. Because Cas9 proteins are highly enriched in pathogenic and commensal bacteria, our work indicates that CRISPR/Cas-mediated gene regulation may broadly contribute to the regulation of endogenous bacterial genes, particularly during the interaction of such bacteria with eukaryotic hosts."

http://bit.ly/ZApkKe

An interview with the synthetic biologist Christina Agapakis

byALEXIS C. MADRIGAL

"As tools for engineering life’s building blocks have proliferated in recent years, our definition of human life has become more expansive. For example, we are learning that the vast ecosystems of microbes inside our bodies are as integral to our health as our own tissues, affecting everything from our immune systems to our brain chemistry. Meanwhile, the field of biology itself keeps expanding—see, for example, synthetic biology, the new subfield that uses the combined insights of molecular biology, engineering, and chemistry to construct biological parts and processes. The synthetic biologist Christina Agapakis, a postdoctoral researcher at UCLA, works at the intersection of these developments. She is also part of a cohort of scientists rethinking the role of biology in our culture. Alexis Madrigal: People have big expectations for biology in the 21st century. Many say that biotech will be as big as information technology was in recent decades. Is that true? Christina Agapakis: People want synthetic biology and biotechnology to be the next industrial revolution. Looking back, people have tended over time to imagine bodies functioning in ways that were analogous to the dominant technological paradigm of their day, whether that was steam engines or computers. I hope that soon biology will be the technology we judge things by. Maybe we’re going to see industry and computational stuff start to look more like biology, rather than biology looking more like industry and computation. AM: Some synthetic biologists have pushed to bring an engineering mind-set to biology. People talk about creating standard DNA “parts,” called BioBricks. What are those? CA: The idea behind BioBrick parts is that you can have a collection of pieces of DNA that have specific useful functions—off-the-shelf DNA parts. You are able to say, “Okay, I need a part that is fluorescent,” or “I need a part that will activate in response to this chemical.” Then you can mix and match: you put them both in a bacterium, and then you have fluorescence in response to some chemical—so we can have this kind of RadioShack. AM: You’ve looked at how communities of bacteria work together in the human body and elsewhere. To what extent could we actively engineer our own microbial ecosystem in the future? CA: We can influence it—we can change the diversity in our gut, and that can influence health. There’s the fecal-transplant example: Sometimes even antibiotics can’t clear up serious digestive infections, and you can’t repopulate the gut with enough good bacteria to get rid of the bad ones. But if you transplant the microbial community from a healthy gut into the person who has this infection, the healthy bacteria will push out the infectious bacteria. The challenge is, you can’t say “You need this many of this and this many of this, and it’s going to stay like that forever.” It’s more a matter of setting the right initial conditions...."

http://bit.ly/Y7tCO1

via +Eugenio Battaglia 

An Introduction to Social Media for Scientists

by
Holly M. Bik, Miriam C. Goldstein

"In many ways, the fast-paced evolution of the internet parallels the move toward “big data” in science. In less than a decade, online tools have exploded in popularity and witnessed rapid expansion (Figure 1), with an increasing number of scientists now looking to take advantage of these web-based resources (see Box 1 and Table 1 for an overview and comparison of existing tools). Social media portals in particular undergo regular reinvention and transformation, with different tools becoming popular for different populations [1]. Although a number of guides exist online, many researchers still feel overwhelmed and hesitant toward the virtual world, lacking sufficient information and guidance through formal scientific channels such as peer-reviewed journals. To better familiarize researchers with existing internet resources, here we discuss prospective benefits that can stem from online science conversations, explain how scientists can efficiently and effectively harness online resources, and provide an overview of popular online tools."


http://bit.ly/11QMkFk

BY DANIELA HERNANDEZ

"Drew Endy wants to build a programming language for the body.

Endy is the co-director of the International Open Facility Advancing Biotechnology — BIOFAB, for short — where he’s part of a team that’s developing a language that will use genetic data to actually program biological cells. That may seem like the stuff of science fiction, but the project is already underway, and the team intends to open source the language, so that other scientists can use it and modify it and perfect it.

The effort is part of a sweeping movement to grab hold of our genetic data and directly improve the way our bodies behave — a process known as bioengineering. With the Supreme Court exploring whether genes can be patented, the bioengineering world is at crossroads, but scientists like Endy continue to push this technology forward.

Genes contain information that defines the way our cells function, and some parts of the genome express themselves in much the same way across different types of cells and organisms. This would allow Endy and his team to build a language scientists could use to carefully engineer gene expression – what they call “the layer between the genome and all the dynamic processes of life.”...."

http://bit.ly/11wYtiC

by
Shiksha Mantri,K. Tanuj Sapra,Stephen Cheley,Thomas H. Sharp& Hagan Bayley

"The bottom-up construction of artificial tissues is an underexplored area of synthetic biology. An important challenge is communication between constituent compartments of the engineered tissue, and between the engineered tissue and additional compartments, including extracellular fluids, further engineered tissue and living cells. Here we present a dimeric transmembrane pore that can span two adjacent lipid bilayers, and thereby allow aqueous compartments to communicate. Two heptameric staphylococcal α-hemolysin pores were covalently linked in an aligned cap-to-cap orientation. The structure of the dimer, (α7)2, was confirmed by biochemical analysis, transmission electron microscopy and single-channel electrical recording. We show that one of two β-barrels of (α7)2 can insert into the lipid bilayer of a small unilamellar vesicle, while the other spans a planar lipid bilayer. The (α7)2 pores spanning two bilayers were also observed by transmission electron microscopy."

http://bit.ly/13l2Hg1

 edited by Huimin Zhao

 

*Computational Protein Design for Synthetic Biology*

byF Richter, D Baker 

"The objective of (computational) protein design and engineering is to create proteins with functions that are not available in natural proteomes. In many synthetic biology applications, just like in natural organisms, proteins are the workhorses that carry out the actual desired ..."

http://bit.ly/ZuSNbw

by
Alexander M. Jones, Guido Grossmann, Jonas ÅH Danielson, Davide Sosso, Li-Qing Chen, Cheng-Hsun Ho, Wolf B Frommer 

"Revolutionary new technologies, namely in the areas of DNA sequencing and molecular imaging, continue to impact new discoveries in plant science and beyond. For decades we have been able to determine properties of enzymes, receptors and transporters in vitro or in heterologous systems, and more recently been able to analyze their regulation at the transcriptional level, to use GFP reporters for obtaining insights into cellular and subcellular localization, and tp measure ion and metabolite levels with unprecedented precision using mass spectrometry. However, we lack key information on the location and dynamics of the substrates of enzymes, receptors and transporters, and on the regulation of these proteins in their cellular environment. Such information can now be obtained by transitioning from in vitro to in vivo biochemistry using biosensors. Genetically encoded fluorescent protein-based sensors for ion and metabolite dynamics provide highly resolved spatial and temporal information, and are complemented by sensors for pH, redox, voltage, and tension. They serve as powerful tools for identifying missing processes (e.g., glucose transport across ER membranes), components (e.g., SWEET sugar transporters for cellular sugar efflux), and signaling networks (e.g., from systematic screening of mutants that affect sugar transport or cytosolic and vacuolar pH). Combined with the knowledge of properties of enzymes and transporters and their interactions with the regulatory machinery, biosensors promise to be key diagnostic tools for systems and synthetic biology."

http://bit.ly/15ndp9Y

by abudgett

"Arizona State University is beginning to establish its place on the map in the burgeoning field of synthetic biology.

 Notable strides in research are being made by faculty members and students in the School of Biological and Health Systems Engineering, one of ASU’s Ira A. Fulton Schools of Engineering. Assistant professor Karmella Haynes was recently the featured speaker on the subject of advances in synthetic biology for the Arizona Science Center’s New Frontiers in Medical Science lecture series. Some of the data Haynes presented in her talk was derived from research being conducted by bioengineering senior Caroline Hom. The research involving identification and production of reagents that activate genes in different types of cancer cells earned Hom an opportunity to give a talk about her work at the recent annual conference of the Institute of Biological Engineering (IBE) – a rare achievement for an undergraduate...."

Foto: ioengineering doctoral student Behzad Damadzedah (left) works in the lab with assistant professor  +Karmella Haynes  . They and others at ASU are seeking ways that synthetic biology research can contribute to new or better treatments for various diseases. Damazedah recently reported on his research at the annual Synthetic Biology Engineering Research Center retreat. 

http://bit.ly/XF2eo5