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A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity

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Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A. Doudna, Emmanuelle Charpentier

"Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing."
http://bit.ly/NKtTxD

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ACS Synthetic Biology: Volume 1, Issue 8 (ACS Publications)

ACS Synthetic Biology: Volume 1, Issue 8 (ACS Publications) | SynBioFromLeukipposInstitute | Scoop.it

Bio-Design Automation: Nobody Said It Would Be Easy

Ensemble Bayesian Analysis of Bistability in a Synthetic Transcriptional Switch

An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications

Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks

Computational Modeling of Synthetic Microbial Biofilms

Hierarchical Modeling for Synthetic Biology

Specification and Simulation of Synthetic Multicelled Behaviors

A Data-Driven Framework for Identifying Nonlinear Dynamic Models of Genetic Parts

http://bit.ly/RoryO1

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A tunable zinc finger-based framework for Boolean logic computation in mammalian cells

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Jason J. Lohmueller, Thomas Z. Armel and Pamela A. Silver

"The ability to perform molecular-level computation in mammalian cells has the potential to enable a new wave of sophisticated cell-based therapies and diagnostics. To this end, we developed a Boolean logic framework utilizing artificial Cys2– His2 zinc finger transcription factors (ZF-TFs) as computing elements. Artificial ZFs can be designed to specifically bind different DNA se- quences and thus comprise a diverse set of com- ponents ideal for the construction of scalable networks. We generate ZF-TF activators and repres- sors and demonstrate a novel, general method to tune ZF-TF response by fusing ZF-TFs to leucine zipper homodimerization domains. We describe 15 transcriptional activators that display 2- to 463-fold induction and 15 transcriptional repressors that show 1.3- to 16-fold repression. Using these ZF-TFs, we compute OR, NOR, AND and NAND logic, employing hybrid promoters and split intein- mediated protein splicing to integrate signals. The split intein strategy is able to fully reconstitute the ZF-TFs, maintaining them as a uniform set of computing elements. Together, these components comprise a robust platform for building mammalian synthetic gene circuits capable of precisely modulating cellular behavior."

a free PDF can be found here: http://1.usa.gov/N69CWP

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Dissecting neural function using targeted genome engineering technologies

 http://1.usa.gov/Nv9VdM

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Light- induced electron transfer and ATP synthesis in a carotene synthesizing insect : Scientific Reports : Nature Publishing Group

Light- induced electron transfer and ATP synthesis in a carotene synthesizing insect : Scientific Reports : Nature Publishing Group | SynBioFromLeukipposInstitute | Scoop.it
A singular adaptive phenotype of a parthenogenetic insect species (Acyrthosiphon pisum) was selected in cold conditions and is characterized by a remarkable apparition of a greenish colour.

-first eveidence for photosynthesis in insects

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Exploiting diversity and synthetic biology for the production of algal biofuels : Nature : Nature Publishing Group

Exploiting diversity and synthetic biology for the production of algal biofuels : Nature : Nature Publishing Group | SynBioFromLeukipposInstitute | Scoop.it

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D. Ryan Georgianna & Stephen P. Mayfield

"Modern life is intimately linked to the availability of fossil fuels, which continue to meet the world's growing energy needs even though their use drives climate change, exhausts finite reserves and contributes to global political strife. Biofuels made from renewable resources could be a more sustainable alternative, particularly if sourced from organisms, such as algae, that can be farmed without using valuable arable land. Strain development and process engineering are needed to make algal biofuels practical and economically viable."
http://bit.ly/OnayAf

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Want to Get 70 Billion Copies of Your Book In Print? Print It In DNA | The Loom | Discover Magazine

Want to Get 70 Billion Copies of Your Book In Print? Print It In DNA | The Loom | Discover Magazine | SynBioFromLeukipposInstitute | Scoop.it

"I have been meaning to read a book coming out soon called Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. It’s written by Harvard biologist George Church and science writer Ed Regis. Church is doing stunning work on a number of fronts, from creating synthetic microbes to sequencing human genomes, so I definitely am interested in what he has to say. I don’t know how many other people will be, so I have no idea how well the book will do. But in a tour de force of biochemical publishing, he has created 70 billion copies. Instead of paper and ink, or pdf’s and pixels, he’s used DNA.

Much as pdf’s are built on a digital system of 1s and 0s, DNA is a string of nucleotides, which can be one of four different types. Church and his colleagues turned his whole book–including illustrations–into a 5.27 MB file–which they then translated into a sequence of DNA. They stored the DNA on a chip and then sequenced it to read the text. The book is broken up into little chunks of DNA, each of which has a portion of the book itself as well as an address to indicate where it should go. They recovered the book with only 10 wrong bits out of 5.27 million. Using standard DNA-copying methods, they duplicated the DNA into 70 billion copies.
Scientists have stored little pieces of information in DNA before, but Church’s book is about 1,000 times bigger. I doubt anyone would buy a DNA edition of Regenesis on Amazon, since they’d need some expensive equipment and a lot of time to translate it into a format our brains can comprehend. But the costs are crashing, and DNA is a far more stable medium than that hard drive on your desk that you’re waiting to die. In fact, Regenesis could endure for centuries in its genetic form. Perhaps librarians of the future will need to get a degree in biology…"

http://bit.ly/P1j75q

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Scientists develop 'bionic eye' which could restore sight to the blind - Telegraph

Scientists develop 'bionic eye' which could restore sight to the blind - Telegraph | SynBioFromLeukipposInstitute | Scoop.it
A radical new approach to “bionic eye” implants holds out the hope of restoring near-normal sight to the blind, scientists claim.
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The bacteria-eating virus that could one day power your mobile phone

The bacteria-eating virus that could one day power your mobile phone | SynBioFromLeukipposInstitute | Scoop.it
Bioengineers at the University of South California, Berkeley have discovered that a virus can convert movement into electricity that could be used to power portable electronics as you walk down the street.
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Metabolic Engineering and Synthetic Biology for the Production of Isoquinoline Alkaloids

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Yit-Lai Chow and Fumihiko Sato

"Plant alkaloids constitute a vast range of compounds with potent bioactivities and are a source of numerous drugs and drug precursors currently used as pharmaceutics. However, the low yield of natural alkaloids in plant tissues limits large-scale drug development. Among the many classes of alkaloids, isoquinoline alkaloids have been intensively studied at the molecular level and efforts to improve their quality and yield are being actively pursued. This chapter describes the major tools used to produce secondary metabolites: (1) synthetic chemistry, (2) metabolic engineering of plants, and (3) synthetic biological approaches. While each of these methods has its advantages and limitations, immense effort in various disciplines as well as combinatorial approaches in metabolic engineering will likely realize an efficient and robust system for the mass production of alkaloids in the foreseeable future."
http://bit.ly/NnSR9x

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Futurity.org – Biofilms can’t stick to new medical material

Futurity.org – Biofilms can’t stick to new medical material | SynBioFromLeukipposInstitute | Scoop.it
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NIH backs Rice University study of delay in gene transcription networks

NIH backs Rice University study of delay in gene transcription networks | SynBioFromLeukipposInstitute | Scoop.it
A Rice University researcher and his colleagues have received a National Institutes of Health grant to see how delays in gene transcription – life's most basic messaging system – affect cellular processes.
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33rd Square | New Technique In Synthetic Biology Uses Materials Within The Cell

33rd Square | New Technique In Synthetic Biology Uses Materials Within The Cell | SynBioFromLeukipposInstitute | Scoop.it

comment on: A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions http://bit.ly/MBzzZD

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Free Open Course: 7.342 Systems and Synthetic Biology: How the Cell Solves Problems (MIT)

Free Open Course: 7.342 Systems and Synthetic Biology: How the Cell Solves Problems (MIT) | SynBioFromLeukipposInstitute | Scoop.it
MIT
Free open course:

7.342 *Systems and Synthetic Biology*: How the Cell Solves Problems (MIT)
A millennial challenge in biology is to decipher how vast arrays of molecular interactions inside the cell work in concert to produce a cellular function. Systems biology, a new interdisciplinary field of science, brings together biologists and physicists to tackle this grand challenge through quantitative experiments and models. In this course, we will discuss the unifying principles that all organisms use to perform cellular functions. We will also discuss key challenges faced by a cell in both single and multi-cellular organisms. Finally, we will discuss how researchers in the field of synthetic biology are using the new knowledge gained from studying naturally-occurring biological systems to create artificial gene networks capable of performing new functions. 7.342 Systems and Synthetic Biology: How the Cell Solves Problems (MIT) course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. Many instructors of the Advanced Undergraduate Seminars are postdoctoral scientists with a strong interest in teaching.
Source: Massachusetts Institute of Technology
Language: English
Author: Youk, Hyun
Lisence Terms: Content within individual OCW courses is (c) by the individual authors unless otherwise noted. MIT OpenCourseWare materials are licensed by the Massachusetts Institute of Technology under a Creative Commons License (Attribution-NonCommercial-ShareAlike). For further information see http://ocw.mit.edu/terms/index.htm
Tags: systems biology, synthetic biology, cell, cellular functions, biological systems, artificial gene networks, molecular interactions, molecular biology, genes, RNA, proteins, macromolecules, intracellular biochemical interactions, extracellular molecules, gene expression, stochastic gene expression,
Course Publishing Date: Mar 30, 2011

http://bit.ly/MCPKJq

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Book converted to DNA then 'read' to show off bio-digital storage

Book converted to DNA then 'read' to show off bio-digital storage | SynBioFromLeukipposInstitute | Scoop.it
Bioengineers have turned a book into DNA. The researchers also have shown they can decode the DNA to re-create the book, which includes 53,4...
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Microbial engineering for the production of advanced biofuels : Nature : Nature Publishing Group

Microbial engineering for the production of advanced biofuels : Nature : Nature Publishing Group | SynBioFromLeukipposInstitute | Scoop.it

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Pamela P. Peralta-Yahya, Fuzhong Zhang, Stephen B. del Cardayre & Jay D. Keasling

"Advanced biofuels produced by microorganisms have similar properties to petroleum-based fuels, and can 'drop in' to the existing transportation infrastructure. However, producing these biofuels in yields high enough to be useful requires the engineering of the microorganism's metabolism. Such engineering is not based on just one specific feedstock or host organism. Data-driven and synthetic-biology approaches can be used to optimize both the host and pathways to maximize fuel production. Despite some success, challenges still need to be met to move advanced biofuels towards commercialization, and to compete with more conventional fuels."
http://bit.ly/Onmkxx

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Doing Biotech in My Bedroom - Technology Review

Doing Biotech in My Bedroom - Technology Review | SynBioFromLeukipposInstitute | Scoop.it

A new generation of biologists embraces the do-it-yourself ethic of computer programming.

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Network-Scale Engineering: Systems Approaches to Synthetic Biology

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Patrick M. Boyle

"The field of Synthetic Biology seeks to develop engineering principles for biological systems. Modular biological parts are repurposed and recombined to develop new synthetic biological devices with novel functions. The proper functioning of these devices is dependent on the cellular context provided by the host organism, and the interaction of these devices with host systems. The field of Systems Biology seeks to measure and model the properties of biological phenomena at the network scale. We present the application of systems biology approaches to synthetic biology, with particular emphasis on understanding and remodeling metabolic networks. Chapter 2 demonstrates the use of a Flux Balance Analysis model of the Saccharomyces cerevisiae metabolic network to identify and construct strains of S. cerevisiae that produced increased amounts of formic acid. Chapter 3 describes the development of synthetic metabolic pathways in Escherichia coli for the production of hydrogen, and a directed evolution strategy for hydrogenase enzyme improvement. Chapter 4 introduces the use of metabolomic profiling to investigate the role of circadian regulation in the metabolic network of the photoautotrophic cyanobacterium Synechococcus elongatus PCC 7942. Together, this work demonstrates the utility of network-scale approaches to understanding biological systems, and presents novel strategies for engineering metabolism."

http://hvrd.me/PuJFjx

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Next-Generation Digital Information Storage in DNA

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George M. Church, Yuan Gao, Sriram Kosuri

"Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. Here, we develop a strategy to encode arbitrary digital information in DNA, write a 5.27-megabit book using DNA microchips, and read the book using next-generation DNA sequencing."

http://bit.ly/RkS1vQ

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PLOS ONE Launches Synthetic Biology Collection | EveryONE

PLOS ONE Launches Synthetic Biology Collection | EveryONE | SynBioFromLeukipposInstitute | Scoop.it

By Rachel Bernstein

"Today PLOS ONE is happy to announce the launch of the Synthetic Biology Collection, including over 50 papers published in the last six years that illustrate the many facets of this dynamically evolving research area.

Synthetic biology is an innovative emerging field that exists at the intersection of many traditional disciplines, including biology, chemistry, and engineering, with aims to create biological systems that can be programmed to do useful things like produce drugs or biofuels, among other applications. Despite its potential, the heavily interdisciplinary nature of the research can make it difficult to publish in traditional discipline-specific journals.

However, PLOS ONE’s broad scope allows for the publication of work crossing many traditional research boundaries, making it an ideal venue for many different types of synthetic biology research. For example, the papers in the collection cover topics including DNA synthesis and assembly, standardized biological “parts” akin to interchangeable mechanical parts, protein engineering, and complex network and pathway analysis and modeling, as described in the Collection Overview written by collection editors Jean Peccoud of Virginia Tech and Mark Isalan of the Centre for Genomic Regulation.

The Collection has roots in PLOS ONE’s very first issue, which included two publications from the field. Since then, the number of synthetic biology articles published in the journal has grown steadily. The collection launched today highlights selected synthetic biology articles published in PLOS ONE since 2006, and it is intended to be a growing resource that will be updated regularly with new papers as the field continues to grow and develop.

Collection Citation: Synthetic Biology (2012) PLOS Collections: http://www.ploscollections.org/syntheticbiology"

http://bit.ly/Pq90rg

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The Donald Danforth Plant Science Center

The Donald Danforth Plant Science Center | SynBioFromLeukipposInstitute | Scoop.it

Synthetic and systems level explorations in biology: Symposium Donald Danforth Plant Science Center Sep 26- 28 http://bit.ly/OYQxS2

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Foundation technologies in synthetic biology: tools for use in understanding plant immunity

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Combinatorial biosynthesis of cyclic lipopeptide antibiotics: a model for synthetic biology to accelerate the evolution of secondary metabolite biosynthetic pathways - ACS Synthetic Biology (ACS Pu...

Combinatorial biosynthesis of cyclic lipopeptide antibiotics: a model for synthetic biology to accelerate the evolution of secondary metabolite biosynthetic pathways - ACS Synthetic Biology (ACS Pu... | SynBioFromLeukipposInstitute | Scoop.it

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Richard H. Baltz

"Nonribosomal peptide synthetases (NRPSs) are giant multienzymes that carryout sequencial assembly line couplings of amino acids to generate linear or cyclic peptides. NRPSs are composed of repeating enzyme domains with modular organization to activate and couple specific amino acids in a particular order. From a synthetic biology perspective, they can be considered as peptide assembly machines composed of devices to couple fatty acids to L-amino acids, L-amino acids to L-amino acids, and D-amino acids to L-amino acids. The coupling devices are composed of specific parts that contain two or more enzyme domains that can be exchanged combinatorially to generate novel peptide assembly machines to produce novel peptides. The potent lipopeptide antibiotics daptomycin and A54145E have identical cyclic depsipeptide ring structures and stereochemistry, but have divergent amino acid sequences. As their biosynthetic gene clusters are derived from an ancient ancestral lipopetide pathway, these lipopeptides provided an attractive model to develop combinatorial biosynthesis to generate antibiotics superior to daptomycin. These studies on combinatorial biosynthesis have helped generate guidelines for the successful assembly of NRPS parts and devices that can be used to generate novel lipopeptide structures, and have established a basis for future synthetic biology studies to further develop combinatorial biosynthesis as a robust approach to natural product drug discovery."

http://bit.ly/Pns4GI

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Science Weekly Extra: Craig Venter on the science of synthetic biology

Science Weekly Extra: Craig Venter on the science of synthetic biology | SynBioFromLeukipposInstitute | Scoop.it

Podcast:Craig Venter argues that a series of talks in Dublin in 1943 marked the birth of synthetic biology http://bit.ly/PVItQT

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Expanding the genetic code of Drosophila melanogaste

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Ambra Bianco, Fiona M Townsley, Sebastian Greiss, Kathrin Lang & Jason W Chin

"Genetic code expansion for unnatural amino acid mutagenesis has, until recently, been limited to cell culture. We demonstrate the site-specific incorporation of unnatural amino acids into proteins in Drosophila melanogaster at different developmental stages, in specific tissues and in a subset of cells within a tissue. This approach provides a foundation for probing and controlling processes in this established metazoan model organism with a new level of molecular precision."
http://bit.ly/Of4g8D

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