SynBioFromLeukipp...
Follow
Find
83.5K views | +20 today
SynBioFromLeukipposInstitute
Your new post is loading...
Your new post is loading...
Scooped by Socrates Logos
Scoop.it!

Comprehensive Environmental Assessment and Its Application to Synthetic Biology Applications

Comprehensive Environmental Assessment and Its Application to Synthetic Biology Applications | SynBioFromLeukipposInstitute | Scoop.it

A workshop was held to test a Comprehensive Environmental Assessment framework for its ability to identify important research questions to support future ecological risk assessments of synthetic biology applications, using a case study of cyanobacteria engineered to produce industrial products. It brought together engineers and ecologists in a one-day workshop to systematically consider: 1)possible pathways of entry of these cyanobacteria into the environment, 2) what organisms or entities might be exposed, and 3) potential environmental impacts from such exposure. Anticipated products from the workshop include:

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Research on Aging: Consumer Genomics/What Do People Do With Their Genomes?

(Visit: http://www.uctv.tv/) Consumer genomics is certainly a hot topic, but what does it mean for the end user -- you? Genetic testing holds much promise for understanding a person's risk for certain diseases. Does this mean we should all get a DNA test? What are the benefits and limitations of genetic screenings? What if your genome scan shows you a have a gene variation related to a common disease? Is it possible to lower the risk of getting sick by simple lifestyle changes? Join Dr. Cinnamon Bloss with the Scripps Translational Science Institute as she makes sense of it all. Series: "Stein Institute for Research on Aging" [4/2012] [Health and Medicine] [Show ID: 23249]

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

End-to-end assembly of gold nanorods via oligopeptide linking and surfactant control

by

Jain T, Roodbeen R, Reeler NE, Vosch T, Jensen KJ, Bjørnholm T, Nørgaard K.

"We report two novel approaches for fabricating self-assembled chains of end-to-end linked Au nanorods separated by a nanogap. In one approach, bi-functional cysteine end-capped oligopeptides of different lengths are used as the linking agent. The widths of the produced nanogaps scale with the length and tertiary structure of the peptide linker. Functionalized oligopeptides containing an acetylene group are also employed as a linker, and the functional group is uniquely identified using surface-enhanced Raman spectroscopy. The development of an oligopeptide-linking platform is motivated by the ease of synthesis and high modularity of peptides; these features enable the possibility to integrate diverse functionality into molecular nanogap junctions - synthesized in water. The stepwise nanochain formation is followed via the evolution of the longitudinal plasmon absorption band in combination with transmission electron microscopy. The reaction rate and extent is tuned by controlling the concentration of the stabilizing CTAB surfactant in the solution. At very low surfactant concentrations, spontaneous end-to-end linking of the Au nanorods is observed even in the absence of linking peptide. The assembled AuNRs may act as next-generation electrodes in a platform for molecular electronics and synthetic biology."

 

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Pamela Silver: Synthesizing a new biology

Interview by Caitlin Sedwick

"Pamela Silver is a strong believer in the potential of synthetic biology and is a leader in this young and rapidly developing field (1, 2). Although she's now interested in designing novel biological systems, she began as a more conventional scientist, coming to the discipline after forging a successful career studying nuclear (3, 4) and RNA (5) biology. We called her at her office at Harvard's Department of Systems Biology to discuss how she arrived at this new frontier and what she sees coming up on her horizon......"

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Genome-scale genetic manipulation methods for exploring bacterial molecular biology - Molecular BioSystems (RSC Publishing)

Review by

Alla G Gagarinova and Andrew Emili

"Bacteria are diverse and abundant, playing key roles in human health and disease, the environment, and biotechnology. Despite progress in genome sequencing and bioengineering, much remains unknown about the functional organization of prokaryotes. For instance, roughly a third of the protein-coding genes of the best-studied model bacterium, Escherichia coli, currently lack experimental annotations. Systems-level experimental approaches for investigating the functional associations of bacterial genes and genetic structures are essential for defining the fundamental molecular biology of microbes, preventing the spread of antibacterial resistance in the clinic, and driving the development of future biotechnological applications. This review highlights recently introduced large-scale genetic manipulation and screening procedures for the systematic exploration of bacterial gene functions, molecular relationships, and the global organization of bacteria at the gene, pathway, and genome levels."

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Biosensing: When less is more in a nano pore - Nature Nanotechnology

by

Li-Qun Gu, Brandon Ritzo & Yong Wang

http://www.nature.com/nnano/journal/v7/n4/full/nnano.2012.48.html?WT.ec_id=NNANO-201204

"Chemically modifying solid-state nanopores with a single nitrilotriacetic acid receptor allows the reversible detection of single proteins."

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Synbio and design

Synbio and design | SynBioFromLeukipposInstitute | Scoop.it

Design Indaba drives a better world through creativity with conferences, expos, magazines and projects that improve the quality of living in Cape Town and the world.

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

ScienceDirect.com - Current Opinion in Biotechnology - A retrosynthetic biology approach to therapeutics: from conception to delivery

ScienceDirect.com - Current Opinion in Biotechnology - A retrosynthetic biology approach to therapeutics: from conception to delivery | SynBioFromLeukipposInstitute | Scoop.it

Rethrosynthetic Biology - What is that?

A retrosynthetic biology approach to therapeutics: from conception to delivery

by
Planson AG, Carbonell P, Grigoras I, Faulon JL.

"De novo biosynthetic pathways are designed, assembled and optimized to produce high-value compounds such as drugs and chemical building blocks from renewable resources. Microorganisms are used as synthetic platforms of systems biology where biochemical pathways are engineered into the host metabolic network. Retrosynthetic biology offers a creative pathway design concept that has gained interest because of its potential to identify novel metabolic ways for therapeutic production. Retrosynthetic biology uses the backward search of retrosynthetic analysis to devise and optimize tailor-made pathways. The retrosynthetic process can be seamlessly integrated into a complete circuitry system for therapeutic applications where production, sensing and delivery act as constitutive interconnecting parts. The aim of this review is to highlight recent efforts toward synthetic design for therapeutic development."
http://bit.ly/HUOnUT

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Artificial microbes: Balanced regulation of synthetic biology, Nature

by Joyce Tait & David Castle

http://bit.ly/HpoqtJ

"Contrary to the opinion of Genya Dana and colleagues (Nature 483, 29; 2012), the greater sophistication of modified microbes created by synthetic biology could make them less, not more, difficult to regulate, manage and monitor than their naturally occurring counterparts.

Several routes could lead to a hypothetical disaster scenario, in which artificially produced microorganisms spread unchecked in the environment (see go.nature.com/pncgxs). But we need to take into account that some of these paths would be favoured over others, and that ecological and other interactions might attenuate or amplify those different probabilities. Synthetic biology could then be used to engineer environmental safety into these organisms."

 

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Life Technologies launches new genome editing technology

Life Technologies launches new genome editing technology | SynBioFromLeukipposInstitute | Scoop.it

"Life Technologies Corp. has announced the launch of GeneArt Precision TALs, generally referred to as TAL effector proteins (TALE), which allow researchers the ability to edit genomes and control gene activity with unprecedented precision and reliability.

According to Daniel Schroen, Life Technologies’ director of market development, the new technology gives researchers to focus precisely on DNA and manipulate it in a new way. For example, the TAL effectors allow them to activate new genes or insert new genes to add functionality. Within the biorefining industry, he notes that the technology can be used in a variety of capacities, including the optimization of enzymes to break down biomass, or the design of more efficient algae strains....."

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

MIT Project Aims to Deliver Printable, Mass-Market Robots

MIT Project Aims to Deliver Printable, Mass-Market Robots | SynBioFromLeukipposInstitute | Scoop.it

"Printers can make mugs, chocolate and even blood vessels. Now, MIT scientists want to add robo-assistants to the list of printable goodies.

Today, MIT announced a new project, “An Expedition in Computing Printable Programmable Machines,” that aims to give everyone a chance to have his or her own robot.

Need help peering into that unreasonably hard-to-reach cabinet, or wiping down your grimy 15th-story windows? Walk on over to robo-Kinko’s to print, and within 24 hours you could have a fully programmed working origami bot doing your dirty work.

“No system exists today that will take, as specification, your functional needs and will produce a machine capable of fulfilling that need,” MIT robotics engineer and project manager Daniela Rus said.

Unfortunately, the very earliest you’d be able to get your hands on an almost-instant robot might be 2017. The MIT scientists, along with collaborators at Harvard University and the University of Pennsylvania, received a $10 million grant from the National Science Foundation for the 5-year project. Right now, it’s at very early stages of development.

So far, the team has prototyped two mechanical helpers: an insect-like robot and a gripper. The 6-legged tick-like printable robot could be used to check your basement for gas leaks or to play with your cat, Rus says. And the gripper claw, which picks up objects, might be helpful in manufacturing, or for people with disabilities, she says...."

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Advanced DNA assembly technologies i... [Expert Opin Drug Discov. 2012] - PubMed - NCBI

by
Tsvetanova B, Peng L, Liang X, Li K, Hammond L, Peterson TC, Katzen F.

"Recombinant DNA technologies have had a fundamental impact on drug discovery. The continuous emergence of unique gene assembly techniques resulted in the generation of a variety of therapeutic reagents such as vaccines, cancer treatment molecules and regenerative medicine precursors. With the advent of synthetic biology there is a growing need for precise and concerted assembly of multiple DNA fragments of various sizes, including chromosomes. In this article, we summarize the highlights of the recombinant DNA technology since its inception in the early 1970s, emphasizing on the most recent advances, and underscoring their principles, advantages and shortcomings. Current and prior cloning trends are discussed in the context of sequence requirements and scars left behind. Our opinion is that despite the remarkable progress that has enabled the generation and manipulation of very large DNA sequences, a better understanding of the cell's natural circuits is needed in order to fully exploit the current state-of-the-art gene assembly technologies."

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Biotechnology Advances - Prospects of nanoparticle-DNA binding and its implications in medical biotechnology

Biotechnology Advances - Prospects of nanoparticle-DNA binding and its implications in medical biotechnology | SynBioFromLeukipposInstitute | Scoop.it

by

Hongjie An, Bo Jin 

"Bio-nanotechnology is a new interdisciplinary R&D area that integrates engineering and physical science with biology through the development of multifunctional devices and systems, focusing biology inspired processes or their applications, in particular in medical biotechnology. DNA based nanotechnology, in many ways, has been one of the most intensively studied fields in recent years that involves the use and the creation of bio-inspired materials and their technologies for highly selective biosensing, nanoarchitecture engineering and nanoelectronics. Increasing researches have been offered to a fundamental understanding how the interactions between the nanoparticles and DNA molecules could alter DNA molecular structure and its biochemical activities. This minor review describes the mechanisms of the nanoparticle-DNA binding and molecular interactions. We present recent discoveries and research progresses how the nanoparticle-DNA binding could vary DNA molecular structure, DNA detection, and gene therapy. We report a few case studies associated with the application of the nanoparticle-DNA binding devices in medical detection and biotechnology. The potential impacts of the nanoparticles via DNA binding on toxicity of the microorganisms are briefly discussed. The nanoparticle-DNA interactions and their impact on molecular and microbial functionalities have only drown attention in recent a few years. The information presented in this review can provide useful references for further studies on biomedical science and technology."

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

what’s MyOpenArchive?

what’s MyOpenArchive? | SynBioFromLeukipposInstitute | Scoop.it

MyOpenArchive is an international Non-Profit Organization that advocates Open Access for never-before-published research papers on the web and provides Self-Archiving platform to enable better knowledge sharing in a way that’s easy to publish. One of our goals is to advocate “Open Access” mind as widely as possible.

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

SOBA: Data Visualization and Data Journalism in Science

SOBA: Data Visualization and Data Journalism in Science | SynBioFromLeukipposInstitute | Scoop.it

Inaugural ScienceOnline Bay Area (SOBA) Event: Data Visualization and Data Journalism in Science SOBA is a monthly discussion series on how science is carried out and communicated online.

Thursday, April 19, 2012 from 7:00 PM to 8:30 PM (PT)
San Francisco, CA

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Experiment and mathematical modeling of gene expression dynamics in a cell-free system

by Stögbauer T, Windhager L, Zimmer R, Rädler JO.

"Cell-free in vitro expression is increasingly important for high-throughput expression screening, high yield protein production and synthetic biology applications. Yet its potential for quantitative investigation of gene expression and regulatory circuits is limited by the availability of data on composition, kinetic rate constants and standardized computational tools for modeling. Here we report on calibration measurements and mathematical modeling of a reconstituted in vitro expression system. We measured a series of GFP expression and mRNA transcription time courses under various initial conditions and established the translation step as the bottle neck of in vitro protein synthesis. Cell-free translation was observed to expire after 3 h independent of initial template DNA concentration. We developed a minimalistic rate equation model and optimized its parameters by performing a concurrent fit to measured time courses. The model predicts the dependence of protein yield not only on template DNA concentration, but also on experimental timing and hence is a valuable tool to optimize yield strategies."

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

DNA2.0 Optimizing Gene Expression Webinar

Learn more at www.DNA20.com - Video
Gene synthesis allows researchers to tailor gene sequences for optimal utility for any application. However, the relationship between gene sequence and expression is complex and depends on a wide range of sequence variables. DNA2.0 uses a systematic engineering approach, GeneGPS™, to navigate these variables with a minimal number of test genes to optimize performance. Application of this approach with a variety of protein targets and expression hosts will be described.

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

PLoS Genetics: Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

PLoS Genetics: Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency | SynBioFromLeukipposInstitute | Scoop.it

by

Wenfeng Qian, Jian-Rong Yang, Nathaniel M. Pearson, Calum Maclean, Jianzhi Zhang

"Cellular efficiency in protein translation is an important fitness determinant in rapidly growing organisms. It is widely believed that synonymous codons are translated with unequal speeds and that translational efficiency is maximized by the exclusive use of rapidly translated codons. Here we estimate the in vivo translational speeds of all sense codons from the budding yeast Saccharomyces cerevisiae. Surprisingly, preferentially used codons are not translated faster than unpreferred ones. We hypothesize that this phenomenon is a result of codon usage in proportion to cognate tRNA concentrations, the optimal strategy in enhancing translational efficiency under tRNA shortage. Our predicted codon–tRNA balance is indeed observed from all model eukaryotes examined, and its impact on translational efficiency is further validated experimentally. Our study reveals a previously unsuspected mechanism by which unequal codon usage increases translational efficiency, demonstrates widespread natural selection for translational efficiency, and offers new strategies to improve synthetic biology."

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Brazil's iGEM Team!

Brazil's iGEM Team! | SynBioFromLeukipposInstitute | Scoop.it

Brazil, iGEM, team... What are you guys talking about!?

"iGEM competition is an acronym for "International Genetically Engineered Machine" competition. This event happens every year at MIT (Massachussets Institute of Technology). There, thousands of undergraduate and graduate students present very exciting projects developed during the year using genetic engineering methods in a new approach: Synthetic Biology."

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Lighting up plant cells to engineer biology

Lighting up plant cells to engineer biology | SynBioFromLeukipposInstitute | Scoop.it

Cambridge researchers have developed a new technique for measuring and mapping gene and cell activity through fluorescence in living plant tissue.

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

data.nature.com

"Welcome to data.nature.com – the NPG Linked Data Platform
The Linked Data Platform provides access to datasets from NPG published as linked data and made available through SPARQL services. The data are queryable interactively through a form interface and remotely through a service endpoint.

What is Available?
NPG is making available a number of datasets for public access as linked data. These include data about articles published by NPG from 1869 through to the present day. Additionally the datasets include NPG product and subject ontologies.

Data Organization
The datasets are organized by graphs with one graph maintained per object type. A directory graph maintains descriptions for each of the individual graphs with class and property counts, and vocabularies used. An NPG vocabulary is used for object type properties as well as to augment object descriptions:

npg:
http://ns.nature.com/terms/
Service Endpoints
A form interface using the /query endpoint is provided for interactive queries and contains both example and template query forms, while the /sparql endpoint is available for remote queries:

/query - form interface (non-streaming)
/sparql - endpoint (streaming)
Multiple result set formats are provided and HTTP content negotiation is supported. Documentation is available on the nature.com developers portal.

Service Features
The following service features are supported:

caching
streaming
content negotiation
built-in namespaces
Send any feedback or comments to developers@nature.com."

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Synthetic Biology Open Language (SBOL)

"Synthetic Biology Open Language (SBOL) is a software standard for the electronic exchange of specifications and descriptions of genetic parts, devices, modules, systems, and engineered genomes.

For a general introduction and the motivation for SBOL, readers can go to the Get Started Page
To learn more about SBOL, follow one of the links below."

 
more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Engineering Molecular Circuits Using Synthetic Biology in Mammalian Cells - review

Engineering Molecular Circuits Using Synthetic Biology in Mammalian Cells - review

by
Wieland M, Fussenegger M.
"Synthetic biology has made significant leaps over the past decade, and it now enables rational and predictable reprogramming of cells to conduct complex physiological activities. The bases for cellular reprogramming are mainly genetic control components affecting gene expression. A huge variety of these modules, ranging from engineered fusion proteins regulating transcription to artificial RNA devices affecting translation, is available, and they often feature a highly modular scaffold. First endeavors to combine these modules have led to autoregulated expression systems and genetic cascades. Analogous to the rational engineering of electronic circuits, the existing repertoire of artificial regulatory elements has further enabled the ambitious reprogramming of cells to perform Boolean calculations or to mimic the oscillation of circadian clocks. Cells harboring synthetic gene circuits are not limited to cell culture, as they have been successfully implanted in animals to obtain tailor-made therapeutics that have made it possible to restore urea or glucose homeostasis as well as to offer an innovative approach to artificial insemination. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering Volume 3 is June 07, 2012. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates."

 

more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Synthetic biology research at the heart of controversy over new national lab in Richmond

Synthetic biology research at the heart of controversy over new national lab in Richmond | SynBioFromLeukipposInstitute | Scoop.it

"In January, when the Lawrence Berkeley National Laboratory (LBNL) announced it had chosen Richmond, Calif. as the site for its new research facility, the city was all trumpets and fanfare, with welcome banners flying and “I [heart] LBNL” pins fastened to lapels. And why not? The lab’s second campus, scheduled to open in 2016, is expected to generate hundreds of jobs and millions of dollars in tax revenue for Richmond in the coming years. For a city plagued by unemployment, poverty and crime, this is thrilling news.

But amidst all the excitement, some questions remain unanswered, most notably: exactly what kind of research will take place at the lab? The new LBNL campus will join existing federal labs throughout the East Bay, including the Joint Bioenergy Institute (JBEI) and the Energy Biosciences Institute (EBI), and will focus on biosciences and biofuel production. But it will also house a once-obscure field of lab research that is fast becoming the latest green science craze: synthetic biology. And that has some people worried.

Dubbed “extreme genetic engineering” by critics like Jim Thomas of the Action Group on Erosion, Technology and Concentration, an international watchdog group that researches the effects of emerging technologies, synthetic biology is the design and construction of novel biological entities. This may lead to the production of new kinds of DNA, enzymes, cells and even artificial life forms. It promises to allow scientists to do things like create new, more efficient ways to generate biofuels from sugar......"

more...
No comment yet.