SynBioFromLeukipp...
Follow
Find
82.5K views | +45 today
SynBioFromLeukipposInstitute
Your new post is loading...
Your new post is loading...
Scooped by Socrates Logos
Scoop.it!

A reconfigurable NAND/NOR genetic logic gate

by

Goni-Moreno A, Amos M.

"Engineering genetic Boolean logic circuits is a major research theme of synthetic biology. By altering or introducing connections between genetic components, novel regulatory networks are built in order to mimic the behaviour of electronic devices such as logic gates. While electronics is a highly standardized science, genetic logic is still in its infancy, with few agreed standards. In this paper we focus on the interpretation of logical values in terms of molecular concentrations.
RESULTS:
We describe the results of computational investigations of a novel circuit that is able to trigger specific differential responses depending on the input standard used. The circuit can therefore be dynamically reconfigured (without modification) to serve as both a NAND/NOR logic gate. This multi-functional behaviour is achieved by a) varying the meanings of inputs, and b) using branch predictions (as in computer science) to display a constrained output. A thorough computational study is performed, which provides valuable insights for the future laboratory validation. The simulations focus on both single-cell and population behaviours. The latter give particular insights into the spatial behaviour of our engineered cells on a surface with a non-homogeneous distribution of inputs.
CONCLUSIONS:
We present a dynamically-reconfigurable NAND/NORgenetic logic circuit that can be switched between modes of operation via a simple shift in input signal concentration. The circuit addresses important issues in genetic logic that will have significance for more complex synthetic biology applications....."
http://bit.ly/PthS0J

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

The Conversation:Part 4: Synthetic Biology | The Tomorrow Project

The Conversation:Part 4: Synthetic Biology | The Tomorrow Project | SynBioFromLeukipposInstitute | Scoop.it

Video:

 

Designer, researchers and scientists Alexandra Daisy Ginsberg, Christina Agapakis and Patrick Boyle in conversation with Intel Futurist Brian David Johnson.

http://bit.ly/UjTq1w

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

A dictionary based informational genome analysis

by

Castellini A, Franco G, Manca V.

"In the post-genomic era several methods of computational genomics are emerging to understand how thewhole information is structured within genomes. Literature of last five years accounts for severalalignment-free methods, arisen as alternative metrics for dissimilarity of biological sequences. Among theothers, recent approaches are based on empirical frequencies of DNA k-mers in whole genomes.
RESULTS:
Any set of words (factors) occurring in a genome provides a genomic dictionary. About sixty genomes wereanalyzed by means of informational indexes based on genomic dictionaries, where a systemic view replaces alocal sequence analysis. A software prototype applying a methodology here outlined carried out somecomputations on genomic data. We computed informational indexes, built the genomic dictionaries withdifferent sizes, along with frequency distributions. The software performed three main tasks: computation ofinformational indexes, storage of these in a database, index analysis and visualization. The validation wasdone by investigating genomes of various organisms. A systematic analysis of genomic repeats of severallengths, which is of vivid interest in biology (for example to compute excessively represented functionalsequences, such as promoters), was discussed, and suggested a method to define synthetic genetic networks.
CONCLUSIONS:
We introduced a methodology based on dictionaries, and an efficient motif-finding software application forcomparative genomics. This approach could be extended along many investigation lines, namely exported inother contexts of computational genomics, as a basis for discrimination of genomic pathologies...."

http://1.usa.gov/S5IuCQ

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

Feds Charge Activist with 13 Felonies for Rogue Downloading of Academic Articles | Threat Level | Wired.com

Feds Charge Activist with 13 Felonies for Rogue Downloading of Academic Articles | Threat Level | Wired.com | SynBioFromLeukipposInstitute | Scoop.it
Federal prosectors are adding additional counts against well-known coder and activist Aaron Swartz, who was charged last year in connection to breaching hacking laws for downloading millions of academic articles from a subscription database at the...
more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Is International Governance on the Horizon for Synthetic Biology?

Is International Governance on the Horizon for Synthetic Biology? | SynBioFromLeukipposInstitute | Scoop.it

 http://bit.ly/PxD1X4

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

Great Expectations | MIT OpenCourseWare

Great Expectations | MIT OpenCourseWare | SynBioFromLeukipposInstitute | Scoop.it

 

"We are thrilled to release the first episode of our newest open educational offering, ChemLab Boot Camp! It's a video series that chronicles the experiences of 14 real MIT freshmen as they get their first taste of working in MIT chemistry labs.

Each year, groups of MIT freshmen are introduced to MIT's laboratory environment through a four-week January course called 5.301 Chemistry Laboratory Techniques. In January 2012, a film crew followed these students as they competed to complete experiments. The stakes in the class are high—students who pass the class are guaranteed a job in an MIT research lab.

In January 2012, a film crew followed 14 students as they struggled to complete experiments required in the class. The stakes are high—students who pass the class are guaranteed a job in an MIT research lab."

http://bit.ly/NACFAM

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

A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals

A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals | SynBioFromLeukipposInstitute | Scoop.it

by

Baojun Wanga, Mauricio Barahonaa, Martin Buck

"Cells perceive a wide variety of cellular and environmentalsignals, which are often processed combinatorially to generate particular phenotypic responses. Here, we employ both single and mixed cell type populations, pre-programmed with engineeredmodularcell signalling and sensing circuits, as processing units to detect and integratemultipleenvironmentalsignals. Based on an engineeredmodulargenetic AND logic gate, we report the construction of a set of scalable synthetic microbe-based biosensors comprising exchangeable sensory, signal processing and actuation modules. These cellular biosensors were engineered using distinct signalling sensory modules to precisely identify various chemical signals, and combinations thereof, with a quantitative fluorescent output. The geneticlogic gate used can function as a biological filter and an amplifier to enhance the sensing selectivity and sensitivity of cell-based biosensors. In particular, an Escherichia coli consortium-basedbiosensor has been constructed that can detect and integrate three environmentalsignals (arsenic, mercury and copper ion levels) via either its native two-component signal transduction pathways or synthetic signalling sensors derived from other bacteria in combination with acell-cell communication module. We demonstrate how amodularcell-basedbiosensor can be engineered predictably using exchangeable synthetic gene circuit modules to sense and integratemultiple-input signals. This study illustrates some of the key practical design principles required for the future application of these biosensors in broad environmental and healthcare areas."
http://bit.ly/PEyd0A

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

RNA processing enables predictable programming of gene expression

by

Lei Qi, Rachel E Haurwitz, Wenjun Shao, Jennifer A Doudna & Adam P Arkin

"Complex interactions among genetic components often result in variable systemic performance in designed multigene systems1, 2. Using the bacterial clustered regularly interspaced short palindromic repeat (CRISPR) pathway3, 4 we develop a synthetic RNA-processing platform, and show that efficient and specific cleavage of precursor mRNA enables reliable and predictable regulation of multigene operons. Physical separation of linked genetic elements by CRISPR-mediated cleavage is an effective strategy to achieve assembly of promoters, ribosome binding sites, cis-regulatory elements, and riboregulators into single- and multigene operons with predictable functions in bacteria. We also demonstrate that CRISPR-based RNA cleavage is effective for regulation in bacteria, archaea and eukaryotes. Programmable RNA processing using CRISPR offers a general approach for creating context-free genetic elements and can be readily used in the bottom-up construction of increasingly complex biological systems in a plug-and-play manner."
http://bit.ly/S3acWm

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

Crick-HEI Systems and Synthetic Biology Workshop

Crick-HEI Systems and Synthetic Biology Workshop | SynBioFromLeukipposInstitute | Scoop.it

The workshop aims to bring together systems and synthetic biology researchers from across the Crick partner institutes to encourage collaboration.
Location: Lecture Theatre 311, Huxley Building, Imperial College London, South Kensington Campus. Sep 19

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

Synthetic Genomics Inc. Purchases Patent Portfolio from Febit Holding GmbH - The Sacramento Bee

Synthetic Genomics Inc. Purchases Patent Portfolio from Febit Holding GmbH - The Sacramento Bee | SynBioFromLeukipposInstitute | Scoop.it
/PRNewswire/ -- Synthetic Genomics Inc. (SGI), a privately held company developing and commercializing genomic-driven solutions to solve a range of global challenges, today announced they have purchased from Febit Holding GmbH the worldwide rights...
more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Enter the Third Dimension

Enter the Third Dimension | SynBioFromLeukipposInstitute | Scoop.it

Cell culture goes 3-D with devices that better mimic in vivo conditions

by
Amber Dance

"Many drugs have looked like blockbusters in the cell-culture dish—easily infiltrating target cells and carrying out their tasks—only to flop in animals or people. The problem is simple: unlike those culture dishes, “we’re not flat,” says Shuichi Takayama of the University of Michigan in Ann Arbor.

One issue with traditional 2-D culture is that cells in a single layer attached to glass or plastic have unfettered access to the media above them. They grow unusually quickly, as they imbibe a steady stream of nutrients. When drugs are added, the cells absorb them just as easily. But when those same drugs come up against the complex vasculature and cellular barriers in a living organism, they may fail to even reach their targets.

In addition, 2-D culture requires cells to interface with an unnatural material. “The interactions [cells] have with the plastic or glass, it’s not the same as the cell-cell interactions they have in vivo,” says Glauco Souza of Nano3D Biosciences, Inc., in Houston. Even when researchers layer a culture dish with proteins such as those found in the extracellular matrix, “that’s a very artificial substrate.”

After more than a century of mostly flat cultures, cells in the laboratory can now experience 3-D environments. “This area has really heated up because people have realized the benefits of 3-D,” says Jeffrey Morgan of Brown University in Providence, Rhode Island. “There is a lot of innovation going on.”

Adding the third dimension makes a world of difference. It changes cells’ gene expression, their protein production, and their very shapes. It can influence how cells differentiate, proliferate, interact, and survive in culture. For example, liver tissue grown in 2-D cannot metabolize drugs.

And in a recent study, John March of Cornell University in Ithaca, New York, discovered that a 3-D ..."
http://bit.ly/NAmrI8

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

Turning a new phage

by

Lauren Gravitz

"The idea of using bacteria-fighting viruses as a weapon against hard-to-treat infections is making a surprising comeback, but with a twist on how it has been attempted for nearly a century. Researchers and companies are now tweaking and deconstructing these bacteria killers in an effort to develop a new arsenal against antibiotic-resistant superbugs—one with more potency and a better likelihood of regulatory approval....."

http://bit.ly/QgJ5Co

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

GenoCon2 | Open Design Geno-Construction

GenoCon2 | Open Design Geno-Construction | SynBioFromLeukipposInstitute | Scoop.it

GenoCon is an open rational design platform for genome construction utilizing Open Data Innovation for #SynBio http://bit.ly/UfTijI

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

Biohackers And DIY Cyborgs Clone Silicon Valley Innovation

Biohackers And DIY Cyborgs Clone Silicon Valley Innovation | SynBioFromLeukipposInstitute | Scoop.it
In basements, garages, startup spaces, and university laboratories, DIY researchers, scientists, programmers, and neurologists are collaborating on brain interfaces that can control video games with human thoughts.
more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Application of synthetic biology in cyanobacteria and algae

by

Bo Wang, Jiangxin Wang, Weiwen Zhang and Deirdre R. Meldrum

"Cyanobacteria and algae are becoming increasingly attractive cell factories for producing renewable biofuels and chemicals due to their ability to capture solar energy and CO2 and their relatively simple genetic background for genetic manipulation. Increasing research efforts from the synthetic biology approach have been made in recent years to modify cyanobacteria and algae for various biotechnological applications. In this article, we critically review recent progresses in developing genetic tools for characterizing or manipulating cyanobacteria and algae, the applications of genetically modified strains for synthesizing renewable products such as biofuels and chemicals. In addition, the emergent challenges in the development and application of synthetic biology for cyanobacteria and algae are also discussed...."

http://bit.ly/QmsFsh

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

The 1st public biobrick: exploring public access to the tools of synthetic biology | The 4th Domain

The 1st public biobrick: exploring public access to the tools of synthetic biology | The 4th Domain | SynBioFromLeukipposInstitute | Scoop.it

 London Sep 24 http://bit.ly/OFv5GK

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

MULTIDISCIPLINARY APPROACH BETWEEN EXPERIMENTAL BIOLOGY, THEORETICAL MODELLING AND SYNTHETIC BIOLOGY

 http://bit.ly/Uai6he

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

Printing Evolves: An Inkjet for Living Tissue

Printing Evolves: An Inkjet for Living Tissue | SynBioFromLeukipposInstitute | Scoop.it
Biomedical engineers are working on ways to print living human tissue, in the hope of one day producing personalized body parts and implants on demand.
more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

Synthetic two-way communication between mammalian cells

by

Bacchus W, Lang M, El-Baba MD, Weber W, Stelling J, Fussenegger M.

"The design of synthetic biology-inspired control devices enabling entire mammalian cells to receive, process and transfer metabolic information and so communicate with each other via synthetic multichannel networks may provide new insight into the organization of multicellular organisms and future clinical interventions. Here we describe communication networks that orchestrate behavior in individual mammalian cells in response to cell-to-cell metabolic signals. We engineered sender, processor and receiver cells that interact with each other in ways that resemble natural intercellular communication networks such as multistep information processing cascades, feed-forward-based signaling loops, and two-way communication. The engineered two-way communication devices mimicking natural control systems in the development of vertebrate extremities and vasculature was used to program temporal permeability in vascular endothelial cell layers. These synthetic multicellular communication systems may inspire future therapies or tissue engineering strategies."
http://1.usa.gov/T00Sns

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

Engineering plant metabolism into microbes: from systems biology to synthetic biology

Engineering plant metabolism into microbes: from systems biology to synthetic biology | SynBioFromLeukipposInstitute | Scoop.it

by

Peng, Namita Bhan, Mattheos AG Koffas

"Plant metabolism represents an enormous repository of compounds that are of pharmaceutical and biotechnological importance. Engineering plant metabolism into microbes will provide sustainable solutions to produce pharmaceutical and fuel molecules that could one day replace substantial portions of the current fossil-fuel based economy. Metabolic engineering entails targeted manipulation of biosynthetic pathways to maximize yields of desired products. Recent advances in Systems Biology and the emergence of Synthetic Biology have accelerated our ability to design, construct and optimize cell factories for metabolic engineering applications. Progress in predicting and modeling genome-scale metabolic networks, versatile gene assembly platforms and delicate synthetic pathway optimization strategies has provided us exciting opportunities to exploit the full potential of cell metabolism. In this review, we will discuss how systems and synthetic biology tools can be integrated to create tailor-made cell factories for efficient production of natural products and fuel molecules in microorganisms."

http://bit.ly/UkRfO3

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

"This paper describes an approach to synthetic biology that does not require genetic engineering"

Found on Twitter

@balapagos: http://t.co/FSGhzVVN(preview) ;

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

DNA Laser Printing (TM)

DNA Laser Printing (TM) | SynBioFromLeukipposInstitute | Scoop.it
Cambrian Genomics makes the first hardware/systems for laser printing DNA.
"DNA Laser Printer" is a trademark of Cambrian Genomics Inc.

Researchers in academia & industry order or clone >$1b/year of DNA.
more...
No comment yet.
Scooped by Socrates Logos
Scoop.it!

SynBio for Drug Discovery

SynBio for Drug Discovery | SynBioFromLeukipposInstitute | Scoop.it

Engineering mammalian cells for therapeutic applications, Fussenegger, Basel , Sept 25 http://bit.ly/OTZwVf

more...
No comment yet.