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The Magic of Microbes: ONR Engineers Innovative Research in Synthetic Biology

The Magic of Microbes: ONR Engineers Innovative Research in Synthetic Biology
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RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology

Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational “switches” that can turn gene expression “on” or “off” depending on the intracellular environment. This “synthetic RNA and RNP world” will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems.
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Can The Cooper Hewitt Design Triennial Save Us From The Next Global Die-Off?

Can The Cooper Hewitt Design Triennial Save Us From The Next Global Die-Off? | SynBioFromLeukipposInstitute | Scoop.it
The Sixth Extinction is bringing death and destruction to ecosystems ranging from Brazilian rainforest to Siberian tundra. In terms of environmental devastation, it may be as catastrophic as the five previous global die-offs. The difference is that this one’s our fault. So what are we going to do about it?

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A British designer named Alexandra Daisy Ginsberg has a solution: Use the cutting-edge field of synthetic biology to create new organisms capable of absorbing toxins and treating diseases, compensating for species that are already gone and providing support for those that remain. Beginning this Friday, a selection of her bespoke organisms will be featured at the Cooper Hewitt Design Triennial alongside an attractive selection of furniture, jewelry and wallpaper. It’s a jarring juxtaposition – and a welcome endorsement of the burgeoning field of speculative design.
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Synthetic biology breakthrough creates biosensors on demand

Synthetic biology breakthrough creates biosensors on demand | SynBioFromLeukipposInstitute | Scoop.it

Biosensors are powerful tools in synthetic biology for engineering metabolic pathways or controlling synthetic and native genetic circuits in bacteria.

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Synthetic Biology,Tools and Applications

The book is great, you're interested! get and read his book here: http://bit.ly/1PP0rbh

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High molecular weight DNA assembly in vivo for synthetic biology applications.

DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.
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The US intelligence chief added gene editing to a list of threats that includes North Korea's nukes and Syria's chemical weapons

The United States' top intelligence official just added gene editing technology to a list of threats that includes North Korea's nukes and Syria's chemical weapons, MIT's Technology Review reported.

Director of National Intelligence James Clapper testified before the Senate Armed Services Committee on Tuesday about 2016's US Intelligence Community's Worldwide Threat Assessment.

Genome editing is a technology used to cut and paste DNA inside living cells.

In recent years, a technique known as CRISPR has been widely adopted because it is far easier and more precise than previous methods.

It has been touted for its potential to cure or eradicate diseases and modify crops, but critics worry it could lead to the creation of designer babies or rogue organisms.
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Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion

Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion | SynBioFromLeukipposInstitute | Scoop.it
Cells routinely compartmentalize enzymes for enhanced efficiency of their metabolic pathways. Here we report a general approach to construct DNA nanocaged enzymes for enhancing catalytic activity and stability. Nanocaged enzymes are realized by self-assembly into DNA nanocages with well-controlled stoichiometry and architecture that enabled a systematic study of the impact of both encapsulation and proximal polyanionic surfaces on a set of common metabolic enzymes. Activity assays at both bulk and single-molecule levels demonstrate increased substrate turnover numbers for DNA nanocage-encapsulated enzymes. Unexpectedly, we observe a significant inverse correlation between the size of a protein and its activity enhancement. This effect is consistent with a model wherein distal polyanionic surfaces of the nanocage enhance the stability of active enzyme conformations through the action of a strongly bound hydration layer. We further show that DNA nanocages protect encapsulated enzymes against proteases, demonstrating their practical utility in functional biomaterials and biotechnology.
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Genetically encoded sensors enable real-time observation of metabolite production.

Engineering cells to produce valuable metabolic products is hindered by the slow and laborious methods available for evaluating product concentration. Consequently, many designs go unevaluated, and the dynamics of product formation over time go unobserved. In this work, we develop a framework for observing product formation in real time without the need for sample preparation or laborious analytical methods. We use genetically encoded biosensors derived from small-molecule responsive transcription factors to provide a fluorescent readout that is proportional to the intracellular concentration of a target metabolite. Combining an appropriate biosensor with cells designed to produce a metabolic product allows us to track product formation by observing fluorescence. With individual cells exhibiting fluorescent intensities proportional to the amount of metabolite they produce, high-throughput methods can be used to rank the quality of genetic variants or production conditions. We observe production of several renewable plastic precursors with fluorescent readouts and demonstrate that higher fluorescence is indeed an indicator of higher product titer. Using fluorescence as a guide, we identify process parameters that produce 3-hydroxypropionate at 4.2 g/L, 23-fold higher than previously reported. We also report, to our knowledge, the first engineered route from glucose to acrylate, a plastic precursor with global sales of $14 billion. Finally, we monitor the production of glucarate, a replacement for environmentally damaging detergents, and muconate, a renewable precursor to polyethylene terephthalate and nylon with combined markets of $51 billion, in real time, demonstrating that our method is applicable to a wide range of molecules.
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Biosensors on demand

Biosensors are powerful tools in synthetic biology for engineering metabolic pathways or controlling synthetic and native genetic circuits in bacteria. Scientists have had difficulty developing a method to engineer “designer” biosensor proteins that can precisely sense and report the presence of specific molecules, which has so far limited the number and variety of biosensor designs able to precisely regulate cell metabolism, cell biology, and synthetic gene circuits.
But new research published in Nature Methods ("Engineering an allosteric transcription factor to respond to new ligands") by a team at Harvard’s Wyss Institute for Biologically Inspired Engineering and Harvard Medical School (HMS) has leveraged combination of computational protein design, in vitro synthesis and in vivo testing to establish a first-of-its-kind strategy for identifying custom-tailored biosensors.
"Our original motivation for developing customizable biosensors was to get a life or death feedback loop for metabolic engineering," said George Church, Ph.D., Wyss Institute Core Faculty member, Professor of Genetics at HMS, Professor of Health Sciences and Technology at Harvard and the Massachusetts Institute of Technology (MIT), and the senior author on the study. "This would essentially give us 'Darwinian evolution on steroids', where colonies of bacteria genetically programmed to output a desirable commodity molecule would rapidly become more efficient from generation to generation as only the best metabolic producers will be 'self-identified' for survival."
"This advance represents a powerful new way for us to access the chemical diversity of the biosphere by mining for new pathways to make useful molecules," said Srivatsan Raman, Ph.D., formerly a Postdoctoral Fellow at the Wyss Institute and HMS and currently Assistant Professor of Biochemistry at University of Wisconsin-Madison, who is the corresponding author on the study.
To develop the method, researchers chose as their test case a natural regulatory protein from E. coli called LacI. LacI is an allosteric transcription factor (aTF), which becomes active in response to sensing "inducer" metabolites or molecules in the bacterium’s environment, thereby triggering expression of a downstream gene. Using LacI, the team set out to develop a framework for re-engineering new biosensor variants that would respond to four inducer molecules (lactitol, sucralose, gentiobiose, and fucose) that cannot be metabolized by natural E. coli. Sucralose, for example, is a completely synthetic sugar molecule sold commercially as Splenda®.
To synthesize and identify the custom-made LacI variants for sensing these four new inducers, the team designed a novel workflow incorporating a combinatorial synthesis strategy that relies on computational protein design and the Wyss Institute’s custom DNA synthesis resources to build a variant library of potential new biosensor designs comprising hundreds of thousands of mutated LacI proteins.
Then, to identify the variants with the most specific responses to the four target molecules of interest, the team engineered groups of E. coli bacteria to express green fluorescent protein (GFP) when the desired molecule was detected, thereby making the bacteria fluoresce. Performing high-throughput in vivo screening of the sensor library in the engineered E. coli, the team identified the most effective variants by their high fluorescence, then filtered them out and genetically sequenced them to reveal the DNA profiles and design maps for transforming aTFs into custom-tailored sensors with high specificity.
The results are striking in that an optimized engineered aTF sensor can be identified for sensing any arbitrary molecule using this approach, opening new doors in synthetic biology by putting allosteric proteins in the control of genetic engineers.
"The LacI protein we chose to re-design into a custom biosensor is only one of thousands of different allosteric transcription factors that exist in nature," said Noah Taylor, a graduate researcher at the Wyss Institute who recently finished his Ph.D. in Biological and Biomedical Sciences at HMS, and the first author on the study. "The ability to engineer LacI using nothing more than sequence and structure information suggests we could find tens, hundreds, or even thousands of other biosensors that respond to different molecules."
Biosensors built using this approach provide feedback on how much of a certain metabolite is present inside a cell. Metabolically engineered bacteria can be outfitted with these custom aTFs, enabling them to monitor their own bioproduction of a desired chemical, pharmaceutical or biofuel. This allows sophisticated designs in which the lack of sufficient product could result in the death of an individual cell, eliminating it from the culture. In this way, powerful evolutionary methods can be harnessed for metabolic engineering.
Sensitive detection of metabolites within cells also presents a new paradigm for the way scientists can interrogate single cells. Until now, it has been very challenging to study the metabolic state of a single individual cell. But designer biosensors could be utilized as custom responders to metabolites of interest, giving insight into the metabolic states of live cells in close to real time.
"We are now utilizing the method to find biosensors for a variety of high-value targets, particularly those that can aid in protecting the environment," said Alexander Garruss, co-author on the study, who is a graduate researcher at the Wyss Institute and a Ph.D. candidate in Bioinformatics and Integrative Genomics at HMS.
Beyond measuring metabolites within cells, the combinatorial synthesis approach paves a path forward toward designing countless new and highly specific biological sensors for novel applications such as environmental monitoring, medical diagnostics, bioremediation, and precision gene therapies.
"The team’s ability to engineer custom biosensors for virtually any molecule is another triumph showing the power of synthetic biology, and its ability to generate valuable new tools to advance medicine and protect our environment," said Wyss Institute Founding Director Donald Ingber, M.D., who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and the Vascular Biology Program at Boston Children’s Hospital and Professor of Bioengineering at the Harvard John A. Paulson School of Engineering and Applied Sciences.
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The art is alive at UC Irvine exhibit

The art is alive at UC Irvine exhibit | SynBioFromLeukipposInstitute | Scoop.it
The new exhibit at UC Irvine's Beall Center for Art + Technology is a place where art has come to life — literally.

The show, "Wetware: Art Agency Animation," opened Saturday, featuring nine artists who created works of synthetic biology art — pieces made out of biological or electronics materials.

Amino acids, contained bacteria, enzymes, microbial fuel cells, cell phone motors and other components were integrated into more than a dozen artworks.

"Nearly all the artwork here is alive," said Jens Hauser, one of the exhibit's curators. "It is artwork being an organism. It is not art for the market, but for the market of ideas. The food for thought."

Three of the nine artists developed their pieces for "Wetware" during a three-week UCI residency in October and November.

British artist Anna Dumitriu and a duo from Amsterdam, Evelina Domnitch and Dmitry Gelfand, were chosen from a pool of about 40 applicants when the university put out a call in July.

Originally, the residency program was meant for one artist. But when "Wetware's" curators, Hauser and David Familian, received the applications and project proposals during the summer, they were so impressed by the talent that they decided to feature more works.

During the three artists' stay in Irvine, they were paired with UCI researchers to develop their scientific art.

"This was the first time that our lab has worked with artists," said Elliot Hui, a UCI associate professor who worked with Domnitch and Gelfand in the Hui Lab for biological microtechnology. "Art can definitely help communicate scientific concepts, but in a more beautiful and relatable way."

The Hui Lab helped generate a liquid solution that would glow for Domnitch and Gelfand's piece, titled "Luminiferous Drift." The artwork was inspired by images of a swirling, hexagon-shaped jet stream above Saturn's north pole.

On the exhibit's opening day Saturday, Gelfand presented the duo's work to guests, using a syringe to pour drops of the solution into bath water in a spinning, cylindrical container. The solution — which includes materials such as horseradish enzyme, luminol, sodium hydroxide and hydrogen peroxide — glowed on contact with the water.

As it spun in the bath, the solution formed a hexagonal shape meant to visualize the same movements above Saturn.

"The rotating bath and a disc at the bottom are both spinning at different speeds, allowing it to create that hexagonal shape," Gelfand said. "We very much wanted our piece to be a guided, sensory experience."

Before the duo leaves Irvine next week, the artists plan to build a system that will automatically drip the solution into the bath, Gelfand said.

Dumitriu collaborated with UCI's Liu Laboratory for Synthetic Evolution for her artwork, which includes framed sheets of black velvet with yeast imprinted in the fibers and a necklace with beads arranged in the shape of an engineered antibody from the Liu Lab.

Lab members often described the antibody's components as being similar to beads. The metaphor inspired the idea for Dumitriu's 452-bead necklace, which also contains the 21 types of amino acids needed to make the actual engineered antibody, Dumitriu said. Within each bead is one amino acid, and the beads are arranged in the precise order as in the antibody.

"I wanted to use these objects to take people through a journey," Dumitriu said. "A lot of people are nervous to look at art because they think they don't know how to understand it. But I think the real key is to take time and ask what it is making you feel. That's how you understand art."

The exhibit also showcases the works of artists from Austria, Mexico and the United States.
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Towards the first data acquisition standard in Synthetic Biology.

This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is a based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine. A data model is described which has been specifically developed for synthetic biology. The model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data. DICOM-SB also includes services orientated towards the automatic exchange of data and information between modalities and repositories. DICOM-SB has been developed in the context of systematic design in synthetic biology - which is based on the engineering principles of modularity, standardization and characterization. The systematic design approach utilizes the design, build, test and learn design cycle paradigm. DICOM-SB has been designed to be compatible with and complementary to other standards in synthetic biology, including SBOL. In this regard, the software provides effective interoperability. The new standard has been tested by experiments and data exchange between Nanyang Technological University in Singapore and Imperial College London.
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Optogenetic control of nuclear protein export

Optogenetic control of nuclear protein export | SynBioFromLeukipposInstitute | Scoop.it
Active nucleocytoplasmic transport is a key mechanism underlying protein regulation in eukaryotes. While nuclear protein import can be controlled in space and time with a portfolio of optogenetic tools, protein export has not been tackled so far. Here we present a light-inducible nuclear export system (LEXY) based on a single, genetically encoded tag, which enables precise spatiotemporal control over the export of tagged proteins. A constitutively nuclear, chromatin-anchored LEXY variant expands the method towards light inhibition of endogenous protein export by sequestering cellular CRM1 receptors. We showcase the utility of LEXY for cell biology applications by regulating a synthetic repressor as well as human p53 transcriptional activity with light. LEXY is a powerful addition to the optogenetic toolbox, allowing various novel applications in synthetic and cell biology.
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New 'nanoneedles' puncture cell membrane to release payload on command.

New 'nanoneedles' puncture cell membrane to release payload on command. | SynBioFromLeukipposInstitute | Scoop.it

Synthetic biology uses natural molecules and assembles them into a system that acts unnaturally.  The ability to control the transfer of molecules through cellular membranes is an important function in synthetic biology.  However, building...

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Artist Makes 3-D Portraits From DNA Found on Gum, Cigarette Butts, and Fingernails

Artist Makes 3-D Portraits From DNA Found on Gum, Cigarette Butts, and Fingernails | SynBioFromLeukipposInstitute | Scoop.it
"It all started with wondering what I could learn about someone from a little piece ... they left behind," says artist Heather Dewey-Hagborg. Using discarded items like cigarette butts, chewing gum, and fingernails, she extracted traces of DNA to create masks based on the owner's genetic profile. While difficult to determine how closely these portraits match the original holder, they do put a human face on larger questions surrounding genetic surveillance. Filmmakers Veena Rao and Emily Sheskin present Dewey-Hagborg's "Stranger Visions" series and her counter-surveillance product Invisible, a set of sprays she claims erases the majority of one's DNA footprint.

The Short Film Showcase spotlights exceptional short videos created by filmmakers from around the web and selected by National Geographic editors. We look for work that affirms National Geographic's belief in the power of science, exploration, and storytelling to change the world. The filmmakers created the content presented, and the opinions expressed are their own, not those of the National Geographic Society.

Know of a great short film that should be part of our Showcase? Email SFS@ngs.org to submit a video for consideration.
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The Art Of Synthetic Bio

The Art Of Synthetic Bio | SynBioFromLeukipposInstitute | Scoop.it
Artists are now interested in synthetic biology to use cellular images to depict the inner workings of living organisms. They are also raising questions about what synthetic biologists should do or should not do.

Bio-art is a new discipline of the art of depicting varying manifestations of what is really possible with synthetic biology, a brand new field of modern biology. Synthetic biology started in the early 2000s when Craig Venter and his colleagues showed for the first time that they could assemble a new, though primitive bacterial cell by using cellular spare parts. The idea of synthetic biology as the name itself suggests is the ability to create a new organism either similar or identical to one that exists, or even a hitherto non-existent organism with unique properties.

This is asking to alter life not just at the genetic level, but at the cellular and organismic levels. Synthetic biology has also created new ways of creating modern medicines and machines, and even the very make-up of life as we know it. As much as this prospect excites a scientist, it also throws open limitless opportunities to do what was something not even imaginable all these years. It also raises the spectre of humans playing God and disturbing nature in possibly many irreversible ways. Such changes or modifications are bound to have discernible timely and spatial impacts on our world.

This worries a whole lot of people. For example, the latest technique of gene editing, scientists themselves have declared at a meeting of the US National Academy of Sciences in December 2015, should not be used on human embryos as some Chinese scientists had attempted earlier in the year.

It should be remembered that it was a group of scientists gathered at the Asilomar Conference Center in California in 1975 who imposed a voluntary code of conduct in dealing with the gene splicing technology or rDNA technology that resulted in the world famous National Institute of Health (NIH) rDNA voluntary guidelines that are followed throughout the world. This is the most responsible way of dealing with the organisms created by those technologies. Once non-scientists got involved, the rDNA technology came under the grips of people who were politically motivated, and the whole field became politicized beyond repair.
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A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation

A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation | SynBioFromLeukipposInstitute | Scoop.it
The ability to precisely modify genomes and regulate specific genes will greatly accelerate several medical and engineering applications. The CRISPR/Cas9 (Type II) system binds and cuts DNA using guide RNAs, though the variables that control its on-target and off-target activity remain poorly characterized. Here, we develop and parameterize a system-wide biophysical model of Cas9-based genome editing and gene regulation to predict how changing guide RNA sequences, DNA superhelical densities, Cas9 and crRNA expression levels, organisms and growth conditions, and experimental conditions collectively control the dynamics of dCas9-based binding and Cas9-based cleavage at all DNA sites with both canonical and non-canonical PAMs. We combine statistical thermodynamics and kinetics to model Cas9:crRNA complex formation, diffusion, site selection, reversible R-loop formation, and cleavage, using large amounts of structural, biochemical, expression, and next-generation sequencing data to determine kinetic parameters and develop free energy models. Our results identify DNA supercoiling as a novel mechanism controlling Cas9 binding. Using the model, we predict Cas9 off-target binding frequencies across the lambdaphage and human genomes, and explain why Cas9’s off-target activity can be so high. With this improved understanding, we propose several rules for designing experiments for minimizing off-target activity. We also discuss the implications for engineering dCas9-based genetic circuits.
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Toward total synthesis of cell function: Reconstituting cell dynamics with synthetic biology.

Biological phenomena, such as cellular differentiation and phagocytosis, are fundamental processes that enable cells to fulfill important physiological roles in multicellular organisms. In the field of synthetic biology, the study of these behaviors relies on the use of a broad range of molecular tools that enable the real-time manipulation and measurement of key components in the underlying signaling pathways. This Review will focus on a subset of synthetic biology tools known as bottom-up techniques, which use technologies such as optogenetics and chemically induced dimerization to reconstitute cellular behavior in cells. These techniques have been crucial not only in revealing causal relationships within signaling networks but also in identifying the minimal signaling components that are necessary for a given cellular function. We discuss studies that used these systems in a broad range of cellular and molecular phenomena, including the time-dependent modulation of protein activity in cellular proliferation and differentiation, the reconstitution of phagocytosis, the reconstitution of chemotaxis, and the regulation of actin reorganization. Finally, we discuss the potential contribution of synthetic biology to medicine.
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The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production | SynBioFromLeukipposInstitute | Scoop.it
Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work. In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http://www.secondarymetabolites.org) is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.
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Yeast converts sugar to make renewable nylon - Futurity

Yeast converts sugar to make renewable nylon - Futurity | SynBioFromLeukipposInstitute | Scoop.it
A new hybrid way to convert sugar into nylon works at room temperature and uses inexpensive materials.

The technique combines a genetically engineered strain of yeast with a lead catalyst.

Previous attempts to combine biocatalysis and chemical catalysis to produce biorenewable chemicals have resulted in low conversion rates. That’s usually because the biological processes leave residual impurities that harm the effectiveness of chemical catalysts.

Zengyi Shao and Jean-Philippe Tessonnier, assistant professors of chemical and biological engineering at Iowa State University, are lead authors of a paper in the journal Angewandte Chemie International Edition that describes the successful hybrid conversion process.

Shao says it “opens the door to the production of a broad range of compounds not accessible from the petrochemical industry.”

Moving forward, the engineers will work to scale up their technology by developing a continuous conversion process, says Tessonnier.
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Chemical cages: New technique advances synthetic biology

Chemical cages: New technique advances synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
Living systems rely on a dizzying variety of chemical reactions essential to development and survival. Most of these involve a specialized class of protein molecules--the enzymes.
In a new study, Hao Yan, director of the Center for Molecular Design and Biomimetics at Arizona State University's Biodesign Institute presents a clever means of localizing and confining enzymes and the substrate molecules they bind with, speeding up reactions essential for life processes.
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Engineering an allosteric transcription factor to respond to new ligands

Engineering an allosteric transcription factor to respond to new ligands | SynBioFromLeukipposInstitute | Scoop.it
Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. Bacterial allosteric transcription factors (aTFs) are a major class of regulatory proteins, but few aTFs have been redesigned to respond to new effectors beyond natural aTF-inducer pairs. Altering inducer specificity in these proteins is difficult because substitutions that affect inducer binding may also disrupt allostery. We engineered an aTF, the Escherichia coli lac repressor, LacI, to respond to one of four new inducer molecules: fucose, gentiobiose, lactitol and sucralose. Using computational protein design, single-residue saturation mutagenesis or random mutagenesis, along with multiplex assembly, we identified new variants comparable in specificity and induction to wild-type LacI with its inducer, isopropyl β-D-1-thiogalactopyranoside (IPTG). The ability to create designer aTFs will enable applications including dynamic control of cell metabolism, cell biology and synthetic gene circuits.
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Meet the Radical Scientists Who Want to Grow Our Seafood In a Lab

Meet the Radical Scientists Who Want to Grow Our Seafood In a Lab | SynBioFromLeukipposInstitute | Scoop.it
In thirty years, meat that was grown in a laboratory might be a perfectly ordinary sight at your local grocery store. The technology to produce it exists, and it’s getting cheaper every day.

But while epicureans are already lining up to order the first stem cell burgers and meatless meatballs, another major protein source has yet to be added to this future food menu: seafood.

Fish, shellfish, and crustaceans are dietary staples for billions of people, and unsustainable fishing practices are decimating stocks worldwide. Some say fish farms are the answer, but these come with a host of environmental problems. That’s why a handful of scientists, entrepreneurs, artists and designers recently have begun to ponder a more radical solution: replacing nets with petri dishes.

“I think once people are more aware of the seafood supply chain, they’ll be looking for alternatives,” Dominique Barnes, co-founder of New Wave Foods told Gizmodo. “If you’re going to eat seafood, why not eat something that tastes just as good, with the same nutritional benefit, texture and flavor?”

Barnes’ company, a startup at the San Fransisco tech incubator IndieBio, made headlines last fall for its ambitious plan to create synthetic shrimp that’s indistinguishable from the real thing. The two-woman team is close to bringing its first “seafood” to market—and their success could pave the way for other entrepreneurs searching for a foothold in this emerging industry. But there are still a host of technical challenges to be overcome, and some experts question whether lab-grown seafood will ever be anything more than a technological novelty.

If you’ve heard anything about lab-grown meat, it’s probably thanks to a certain stem cell burger which created an international sensation in 2013. But efforts to grow meat in vitro can be traced back over a decade earlier—and one of the very first attempts involved fish.

In 2002, Morris Benjaminson, a professor emeritus at Touru University, received a small grant from NASA to explore the possibility of lab-grown meat, with the idea that future astronauts might use the technology to enjoy steak nights in space. In a rather grisly experiment, Benjaminson and his colleagues excised chunks of goldfish muscle from live fish and dunked them in vats of fetal bovine serum, a nutrient-rich cocktail brewed from the blood of unborn calves. After about a week, the severed fish chunks had grown in size by 14 percent and resembled small filets.
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TECNOx: A Latin American Syn Bio (and more) student competition | PLOS Synthetic Biology Community

TECNOx: A Latin American Syn Bio (and more) student competition | PLOS Synthetic Biology Community | SynBioFromLeukipposInstitute | Scoop.it
TECNOx: A Latin American Syn Bio (and more) student competition
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Integrative Systems and Synthetic Biology of Cell-Matrix Adhesion Sites.

The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.
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