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Creation and Synthetic Biology: Book Review

Creation and Synthetic Biology: Book Review | SynBioFromLeukipposInstitute | Scoop.it
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By Christina Agapakis 


"What is the origin of life on Earth? What is the future of life in the age of synthetic biology? These are two of the biggest questions of contemporary biology, and the questions that drive Adam Rutherford’s new book, Creation: How Science is Reinventing Life Itself, a compelling and accessible two-part look through the history and future of living cells. Through chapters that span the early history of microscopy to recent debates on the regulation of biotechnology and genomics, Rutherford tells the complicated story of the science of life as it might have been and as it might be. These two difficult questions, of origins and offspring, have been tightly linked in the life sciences for over a century. In the work of engineer-biologists like Jacques Loeb–who at the beginning of the 20th century sought to create “artificial life” through manipulation of sea urchin eggs–engineering was a tool for experimentation to better understand biology. For Loeb, engineering could be used to examine the validity of biological theory: “the proof of the explicability of any single life phenomenon is furnished as soon at it is successfully controlled unequivocally through physical or chemical means or is repeated in all details with nonliving materials.” Echoes of this sentiment are found everywhere in synthetic biology today, where Richard Feynman’s much more quotable remark is frequently invoked: “What I cannot create, I do not understand.”..."

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New class of synthetic molecules mimics antibodies

New class of synthetic molecules mimics antibodies | SynBioFromLeukipposInstitute | Scoop.it
A Yale University lab has crafted the first synthetic molecules that have both the targeting and response functions of antibodies.
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▶ Synthetic Aesthetics: New Frontiers in Contemporary Design

Paola Antonelli, Director of R&D and Senior Curator, Department of Architecture and Design, MoMA, introduces the symposium Synthetic Aesthetics: New Frontiers in Contemporary Design, an investigation of the intersections between synthetic biology and design.

The symposium features guest speakers David Benjamin, Daisy Ginsberg, Dan Grushkin, and William Shih.
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George Church on the Future of Human Genomics and Synthetic Biology - YouTube

http://research.ncsu.edu/ges In his talk “The Future of Human Genomics and Synthetic Biology,” Church discussed the exponentially fast pace of emerging genet...
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The automated lab

The automated lab | SynBioFromLeukipposInstitute | Scoop.it
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by
Erika Check Hayden

"Start-up firms say robotics and software that autonomously record every detail of an experiment can transform the efficiency and reliability of research.
Max Hodak has spent much of his academic career fixing the ways that scientists collect data. As a biomedical engineering student at Duke University in Durham, North Carolina, it frustrated him that his laboratory recorded its experiments in paper notebooks, leaving researchers to scour through the pages to find relevant data. So in 2008, he indexed all the notebook data on a computer and wrote a program to allow users to query it. “People were saying, 'Why are you wasting your time? That's not going to lead to publication,'” he recalls. But a year-and-a-half later, he returned to the lab from a stint in Silicon Valley to find that many of those earlier sceptics were now using his system. To Hodak, it was a sign that he should pursue his quest for efficiency in the lab. “I was always more interested in finding ways to do analysis more efficiently than in doing the actual analysis,” he says......"


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An open source future for synthetic biology

An open source future for synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
If the controversy over genetically modified organisms (GMOs) tells us something indisputable, it is this: GMO food products from corporations like Monsanto are suspected to endanger health. On the other hand, an individual’s right to genetically modify and even synthesize entire organisms as part of his dietary or medical regimen could someday be a human right.
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The limits of synthetic biology

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Zakeri B, Carr PA

"The pioneering works of Watson, Crick, Wilkins, and Franklin [1,2] on the structure of DNA have captivated our imaginations for over half a century and continue to shape our future endeavors. The genetic code, a mystery for many years, was soon thereafter decoded by organic chemists employing organic synthesis of polynucleotides [3]. Ever since, the construction of DNA has been central to our ability to probe the molecular nature of life. Synthetic biologists now push the limits of what can be engineered using DNA – from scratch if needed: complex genetic circuits, large metabolic pathways, and even whole genomes."

 http://bit.ly/1zWIsVE

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Core Concept: Synthetic biology—change, accelerated

Core Concept: Synthetic biology—change, accelerated | SynBioFromLeukipposInstitute | Scoop.it
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by
Danielle Venton

"Dr. Jay Keasling has biologically done what no one has been able to do chemically: cheaply and quickly synthesize an effective malaria medication (1).

Many of the 400 million individuals infected with malaria each year suffer because of a lack of effective, affordable therapies, especially after the malaria-causing Plasmodium parasite became resistant to often-used chloroquine-based drugs.
Artemisinin-based drugs are now faster acting and more effective. However, so far, the chemical has been laboriously sourced from the plant Artemisia annua, a type of wormwood. It appeared to be too expensive for large-scale use; that is, until Keasling recruited the tools of synthetic biology to coax yeast cells into making …"


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Nature makes all articles free to view

Nature makes all articles free to view | SynBioFromLeukipposInstitute | Scoop.it
Publisher permits subscribers and media to share read-only versions of its papers.
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New device could make large biological circuits practical

New device could make large biological circuits practical | SynBioFromLeukipposInstitute | Scoop.it
Innovation from MIT could allow many biological components to be connected to produce predictable effects.
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by
David L. Chandler 

"Researchers have made great progress in recent years in the design and creation of biological circuits — systems that, like electronic circuits, can take a number of different inputs and deliver a particular kind of output. But while individual components of such biological circuits can have precise and predictable responses, those outcomes become less predictable as more such elements are combined.

A team of researchers at MIT has now come up with a way of greatly reducing that unpredictability, introducing a device that could ultimately allow such circuits to behave nearly as predictably as their electronic counterparts. The findings are published this week in the journal Nature Biotechnology, in a paper by associate professor of mechanical engineering Domitilla Del Vecchio and professor of biological engineering Ron Weiss.
The lead author of the paper is Deepak Mishra, an MIT graduate student in biological engineering. Other authors include recent master’s students Phillip Rivera in mechanical engineering and Allen Lin in electrical engineering and computer science.
There are many potential uses for such synthetic biological circuits, Del Vecchio and Weiss explain. “One specific one we’re working on is biosensing — cells that can detect specific molecules in the environment and produce a specific output in response,” Del Vecchio says. One example: cells that could detect markers that indicate the presence of cancer cells, and then trigger the release of molecules targeted to kill those cells.
It is important for such circuits to be able to discriminate accurately between cancerous and noncancerous cells, so they don’t unleash their killing power in the wrong places, Weiss says. To do that, robust information-processing circuits created from biological elements within a cell become “highly critical,” Weiss says.
To date, that kind of robust predictability has not been feasible, in part because of feedback effects when multiple stages of biological circuitry are introduced. The problem arises because unlike in electronic circuits, where one component is physically connected to the next by wires that ensure information is always flowing in a particular direction, biological circuits are made up of components that are all floating around together in the complex fluid environment of a cell’s interior.
Information flow is driven by the chemical interactions of the individual components, which ideally should affect only other specific components. But in practice, attempts to create such biological linkages have often produced results that differed from expectations.
“If you put the circuit together and you expect answer ‘X,’ and instead you get answer ‘Y,’ that could be highly problematical,” Del Vecchio says.
The device the team produced to address that problem is called a load driver, and its effect is similar to that of load drivers used in electronic circuits: It provides a kind of buffer between the signal and the output, preventing the effects of the signaling from backing up through the system and causing delays in outputs.
While this is relatively early-stage research that could take years to reach commercial application, the concept could have a wide variety of applications, the researchers say. For example, it could lead to synthetic biological circuits that constantly measure glucose levels in the blood of diabetic patients, automatically triggering the release of insulin when it is needed.
The addition of this load driver to the arsenal of components available to those designing biological circuits, Del Vecchio says, “could escalate the complexity of circuits you could design,” opening up new possible applications while ensuring that their operation is “robust and predictable.”
James Collins, a professor of biomedical engineering at Boston University who was not associated with this research, says, “Efforts in synthetic biology to create complex gene circuits are often hindered by unanticipated or uncharacterized interactions between submodules of the circuits. These interactions alter the input-output characteristics of the submodules, leading to undesirable circuit behavior.”..."



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Neri Oxman creates 3D-printed structures for interplanetary voyages

Neri Oxman creates 3D-printed structures for interplanetary voyages | SynBioFromLeukipposInstitute | Scoop.it
Neri Oxman's team at MIT Media Lab has created 3D-printed "skins" designed to facilitate synthetic biological processes for travelling to other planets.
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Edinburgh wins gold in iGEM 2014

Edinburgh wins gold in iGEM 2014 | SynBioFromLeukipposInstitute | Scoop.it
Each year, it begins with 30 or so Edinburgh University applicants. Everyone is highly qualified; their interest in the subject has propelled them to the top of their respective classes for the bet...
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Congratulations!

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Programmable RNA recognition and cleavage by CRISPR/Cas9

Programmable RNA recognition and cleavage by CRISPR/Cas9 | SynBioFromLeukipposInstitute | Scoop.it
stimulate
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by
Mitchell R. O’Connell, Benjamin L. Oakes, Samuel H. Sternberg, Alexandra East-Seletsky, Matias Kaplan & Jennifer A. Doudna

"The CRISPR-associated protein Cas9 is an RNA-guided DNA endonuclease that uses RNA–DNA complementarity to identify target sites for sequence-specific double-stranded DNA (dsDNA) cleavage1, 2, 3, 4, 5. In its native context, Cas9 acts on DNA substrates exclusively because both binding and catalysis require recognition of a short DNA sequence, known as the protospacer adjacent motif (PAM), next to and on the strand opposite the twenty-nucleotide target site in dsDNA4, 5, 6, 7. Cas9 has proven to be a versatile tool for genome engineering and gene regulation in a large range of prokaryotic and eukaryotic cell types, and in whole organisms8, but it has been thought to be incapable of targeting RNA5. Here we show that Cas9 binds with high affinity to single-stranded RNA (ssRNA) targets matching the Cas9-associated guide RNA sequence when the PAM is presented in trans as a separate DNA oligonucleotide. Furthermore, PAM-presenting oligonucleotides (PAMmers) stimulate site-specific endonucleolytic cleavage of ssRNA targets, similar to PAM-mediated stimulation of Cas9-catalysed DNA cleavage7. Using specially designed PAMmers, Cas9 can be specifically directed to bind or cut RNA targets while avoiding corresponding DNA sequences, and we demonstrate that this strategy enables the isolation of a specific endogenous messenger RNA from cells. These results reveal a fundamental connection between PAM binding and substrate selection by Cas9, and highlight the utility of Cas9 for programmable transcript recognition without the need for tags."

http://bit.ly/13kZBNX

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Frontiers | Developments in the Tools and Methodologies of Synthetic Biology

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by
Kelwick R, MacDonald JT, Webb AJ, Freemont P.

"Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a "body of knowledge" from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community."

http://bit.ly/1zHrWLy

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MoMA | Designing Life: Synthetic Biology and Design

MoMA | Designing Life: Synthetic Biology and Design | SynBioFromLeukipposInstitute | Scoop.it
MoMA | Designing Life: Synthetic Biology and Design
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Synthetic biology on a piece of paper: Brighter future for disease diagnostics? - Genetic Literacy Project

Synthetic biology on a piece of paper: Brighter future for disease diagnostics? - Genetic Literacy Project | SynBioFromLeukipposInstitute | Scoop.it
A new technology that allows synthetic gene circuits to be printed on paper could allow us to cheaply and accurately detect diseases.
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Synthetic biology: Toehold gene switches make big footprints

Synthetic biology: Toehold gene switches make big footprints | SynBioFromLeukipposInstitute | Scoop.it
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by
Simon Ausländer & Martin Fussenegger

"The development of RNA-based devices called toehold switches that regulate translation might usher in an era in which protein production can be linked to almost any RNA input and provide precise, low-cost diagnostics."


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A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis | SynBioFromLeukipposInstitute | Scoop.it
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by
Medema MH, Cimermancic P, Sali A, Takano E, Fischbach MA

"Bacterial secondary metabolites are widely used as antibiotics, anticancer drugs, insecticides and food additives. Attempts to engineer their biosynthetic gene clusters (BGCs) to produce unnatural metabolites with improved properties are often frustrated by the unpredictability and complexity of the enzymes that synthesize these molecules, suggesting that genetic changes within BGCs are limited by specific constraints. Here, by performing a systematic computational analysis of BGC evolution, we derive evidence for three findings that shed light on the ways in which, despite these constraints, nature successfully invents new molecules: 1) BGCs for complex molecules often evolve through the successive merger of smaller sub-clusters, which function as independent evolutionary entities. 2) An important subset of polyketide synthases and nonribosomal peptide synthetases evolve by concerted evolution, which generates sets of sequence-homogenized domains that may hold promise for engineering efforts since they exhibit a high degree of functional interoperability, 3) Individual BGC families evolve in distinct ways, suggesting that design strategies should take into account family-specific functional constraints. These findings suggest novel strategies for using synthetic biology to rationally engineer biosynthetic pathways."


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ProQuest Document View - Application of synthetic biology and optogenetics to controlling gene expression

ProQuest Document View - Application of synthetic biology and optogenetics to controlling gene expression | SynBioFromLeukipposInstitute | Scoop.it
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Dissertation
by
Cao, Jicong

(congratulations!)

"Considerable work has focused on the control of gene expression, motivated by both a fundamental interest in biological research as well as by applications ranging from gene therapy to metabolic engineering.

Synthetic biology provides the platform and tools to design artificial regulators to control mRNA translation. In this work, we report a genetically encoded system to regulate mRNA translation using the Pumilio and FBF (PUF) domains in mammalian cells. PUF domain serves as a designable scaffold to recognize specific RNA elements, and the specificity can be altered easily to target any 8-nt RNA. In this system, the gene expression could be varied by over 17-fold when using PUF-based activators and repressors. The specificity of the method was established by using wild-type and mutant PUF domains.
Optogenetics is a technology that allows control of cellular events using visible light as the signal/inducer. We designed an optogenetic system that employs the light-sensitive dimerizing partners from Arabidopsis thaliana , Cryptochrome 2 (CRY2) and Cryptochrome-interacting basic-helix-loop-helix 1 (CIB1), to reconstitute an RNA binding peptide and a translation initiation protein, thereby activating target mRNA translation downstream of the binding sites. Moreover, the combination of the two technologies allows us to construct to a light-inducible gene expression system using PUF domains, which can be used to regulate cellular RNA functions in a light-sensitive manner.
Additionally, we found that PUF domains could also be used to repress mRNA translation in E. coli. Such a system adds an important tool of RNA/protein interaction into the repertoire of tools for genetic circuit construction in E. coli."



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Natural photoreceptors and their application to synthetic biology

Natural photoreceptors and their application to synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
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by
Schmidt D, Cho YK

"The ability to perturb living systems is essential to understand how cells sense, integrate, and exchange information, to comprehend how pathologic changes in these processes relate to disease, and to provide insights into therapeutic points of intervention. Several molecular technologies based on natural photoreceptor systems have been pioneered that allow distinct cellular signaling pathways to be modulated with light in a temporally and spatially precise manner. In this review, we describe and discuss the underlying design principles of natural photoreceptors that have emerged as fundamental for the rational design and implementation of synthetic light-controlled signaling systems. Furthermore, we examine the unique challenges that synthetic protein technologies face when applied to the study of neural dynamics at the cellular and network level."


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Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology

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Cafferty BJ, Hud NV

"For more than half a century chemists have searched for a plausible prebiotic synthesis of RNA. The initial advances of the 1960s and 1970s were followed by decades of measured progress and a growing pessimism about overcoming remaining challenges. Fortunately, the past few years have provided a number of important advances, including new abiotic routes for the synthesis of nucleobases, nucleosides, and nucleotides. Recent discoveries also provide additional support for the hypothesis that RNA is the product of evolution, being preceded by ancestral genetic polymers, or pre-RNAs, that are synthesized more easily than RNA. In some cases, parallel searches for plausible prebiotic routes to RNA and pre-RNAs have provided more than one experimentally verified synthesis of RNA substructures and possible predecessors. Just as the synthesis of a contemporary biological molecule cannot be understood without knowledge of cellular metabolism, it is likely that an integrated approach that takes into account both plausible prebiotic reactions and plausible prebiotic environments will ultimately provide the most satisfactory and unifying chemical scenarios for the origin of nucleic acids. In this context, recent advances towards the abiotic synthesis of RNA and candidates for pre-RNAs are beginning to suggest that some molecules (e.g., urea) were multi-faceted contributors to the origin of nucleic acids, and the origin of life."

 http://1.usa.gov/1yPK30W

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Research and Markets: Global Synthetic Biology Market 2014-2018: Market to Reach $5.6 Billion in 2018, Growing at a CAGR of 24% | Business Wire

Research and Markets: Global Synthetic Biology Market 2014-2018: Market to Reach $5.6 Billion in 2018, Growing at a CAGR of 24% | Business Wire | SynBioFromLeukipposInstitute | Scoop.it
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Connecting The Microcosmos and The Macro World

Connecting The Microcosmos and The Macro World | SynBioFromLeukipposInstitute | Scoop.it
By Glen Martin Good luck trying to jam Christina Agapakis into any kind of vocational box. Her CV cites disparate accomplishments as a scientist, writer, and artist — and teacher.
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World’s First Artificial Enzymes Created Using Synthetic Biology

World’s First Artificial Enzymes Created Using Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
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"A team of researchers have created the world’s first enzymes made from artificial genetic material.
 
The synthetic enzymes, which are made from molecules that do not occur anywhere in nature, are capable of triggering chemical reactions in the lab.
 
The research is published in the journal Nature and promises to offer new insights into the origins of life, as well as providing a potential starting point for an entirely new generation of drugs and diagnostics. In addition, the authors speculate that the study increases the range of planets that could potentially host life.
 
All life on Earth depends on the chemical transformations that enable cellular function and the performance of basic tasks, from digesting food to making DNA. These are powered by naturally-occurring enzymes which operate as catalysts, kick-starting the process and enabling such reactions to happen at the necessary rate.
 
For the first time, however, the research shows that these natural biomolecules may not be the only option, and that artificial enzymes could also be used to power the reactions that enable life to occur.
 
The findings build on previous work in which the scientists, from the MRC Laboratory of Molecular Biology in Cambridge and the University of Cambridge, created synthetic molecules called “XNAs”. These are entirely artificial genetic systems that can store and pass on genetic information in a manner similar to DNA.
 
Using these XNAs as building blocks, the new research involved the creation of so-called “XNAzymes.” Like naturally occurring enzymes, these are capable of powering simple biochemical reactions.
 
Dr. Alex Taylor, a Post-doctoral Researcher at St John’s College, University of Cambridge, who is based at the MRC Laboratory and was the study’s lead author, said: “The chemical building blocks that we used in this study are not naturally occurring on Earth, and must be synthesized in the lab. This research shows us that our assumptions about what is required for biological processes– the ‘secret of life’– may need some further revision. The results imply that our chemistry, of DNA, RNA and proteins, may not be special and that there may be a vast range of alternative chemistries that could make life possible.”..."


  http://bit.ly/1vivCBR

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