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2013 Genome Symposium | Department of Biology | New York University

2013 Genome Symposium | Department of Biology | New York University | SynBioFromLeukipposInstitute | Scoop.it
Register now for the 12 Annual Genomics Symposium entitled "Synthetic Biology & Microbial Ecology". The symposium takes place on June 7th. Reserve your spot now!
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The Seventh International Meeting on Synthetic Biology - SB7.0

The Seventh International Meeting on Synthetic Biology - SB7.0 | SynBioFromLeukipposInstitute | Scoop.it
The goal of SB7.0 is to unite the international synthetic biology communities to take a fresh look at the key topics and challenges that our field face.
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Interactive and scalable biology cloud experimentation for scientific inquiry and education 

Interactive and scalable biology cloud experimentation for scientific inquiry and education  | SynBioFromLeukipposInstitute | Scoop.it
A real-time interactive, fully automated, low-cost and scalable biology cloud experimentation platform could provide access to scientific experimentation for learners and researchers alike.
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A New Era of Genome Integration – Simply Cut and Paste!

Genome integration is a powerful tool in both basic and applied biological research. However, traditional genome integration, which is typically mediated by homologous recombination, has been constrained by low efficiencies and limited host range. In recent years, the emergence of homing endonucleases and programmable nucleases has greatly enhanced integration efficiencies and allowed alternative integration mechanisms such as non-homologous end joining and microhomology-mediated end joining, enabling integration in hosts deficient in homologous recombination. In this review, we will highlight recent advances and breakthroughs in genome integration methods made possible by programmable nucleases, and their new applications in synthetic biology and metabolic engineering.
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Analytic framework for a stochastic binary biological switch

We propose and solve analytically a stochastic model for the dynamics of a binary biological switch, defined as a DNA unit with two mutually exclusive configurations, each one triggering the expression of a different gene. Such a device has the potential to be used as a memory unit for biological computing systems designed to operate in noisy environments. We discuss a recent implementation of this switch in living cells, the recombinase addressable data (RAD) module. In order to understand the behavior of a RAD module we compute the exact time-dependent joint distribution of the two expressed genes starting in one state and evolving to another asymptotic state. We consider two operating regimes of the RAD module, a fast and a slow stochastic switching regime. The fast regime is aggregative and produces unimodal distributions, whereas the slow regime is separative and produces bimodal distributions. Both regimes can serve to prepare pure memory states when all cells are expressing the same gene. The slow regime can also separate mixed states by producing two subpopulations, each one expressing a different gene. Compared to the genetic toggle switch based on positive feedback, the RAD module ensures more rapid memory operations for the same quality of the separation between binary states. Our model provides a simplified phenomenological framework for studying RAD memory devices and our analytic solution can be further used to clarify theoretical concepts in biocomputation and for optimal design in synthetic biology.
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New device could lead to tiny 'DNA photocopiers'

New device could lead to tiny 'DNA photocopiers' | SynBioFromLeukipposInstitute | Scoop.it
A new way to control a powerful but finicky process called the polymerase chain reaction raises the possibility of a “DNA photocopier” small enough to hold in your hand. Such a device could identify the bacteria or virus causing an infection even before the symptoms appear.

Kary Mullis developed PCR in 1983 and received the Nobel Prize for his invention. A key advance in the field of molecular biology, it can make billions of identical copies of small segments of DNA for use in molecular and genetic analyses.

Vanderbilt University biomedical engineers Nicholas Adams and Frederick Haselton came up with an out-of-the-box idea, which they call adaptive PCR. It uses left-handed DNA (L-DNA) to monitor and control the molecular reactions that take place in the PCR process.

Left-handed DNA is the mirror image of the DNA found in all living things. It has the same physical properties as regular, right-handed DNA but it does not participate in most biological reactions. As a result, when fluorescently tagged L-DNA is added to a PCR sample, it behaves in an identical way to the regular DNA and provides a fluorescent light signal that reports information about the molecular reactions taking place and can be used to control them.

In order to test their idea, Adams and Haselton recruited William Gabella, research assistant professor of physics, to create a working prototype of an adaptive PCR machine and then they tested it extensively with the assistance of biomedical engineering undergraduate Austin Hardcastle.
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SBOLme: a repository of SBOL parts for metabolic engineering

The Synthetic Biology Open Language (SBOL) is a community-driven open language to promote standardization in synthetic biology. To support the use of SBOL in metabolic engineering, we developed SBOLme, the first open-access repository of SBOL 2.0-compliant biochemical parts for a wide range of metabolic engineering applications. The URL of our repository is http://www.cbrc.kaust.edu.sa/sbolme.
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Engineered Probiotics as Living Medicine

Engineered Probiotics as Living Medicine | SynBioFromLeukipposInstitute | Scoop.it
Modern medicine has found many ways to use a pill of chemicals to improve human health for people around the world. Drugs are taken for infections, cancer treatment, metabolic disorders, and every other ailment. Despite the impact of chemical medicines, there are many problems that need a smarter solution with more targeted benefits. One smarter medicine to keep an eye on in 2017 and beyond is the use of engineered microbes to produce therapeutics or diagnostic signals within the human body. Living medicines designed to respond to cues in the human body can create new kinds of treatments or diagnostics that would be impossible with a traditional drug.

Our ability to reliably engineer microorganisms to do our bidding (synthetic biology) and our knowledge of the importance of balancing the vast community of bacteria in our gut (human gut microbiome) are both fairly new developments. Beyond just a combination of two buzzwords, synthetic biology applied to the microbes in our gut gives us a new treatment approach that uses a living product instead of a chemical.

Synthetic biologists put bits of DNA in the cells of an organism so that it does some new job in addition to all of its normal functions to survive. Meanwhile, studies of the human gut microbiome have lead to the realization that bacteria may be constantly influencing our health. While this microbiome knowledge has lead to fads in probiotic use, a more powerful application may be using probiotics engineered to address the specific problem for each patient.

Sense and destroy

A clear example of an engineered therapeutic was published in 2011 that created E. coli that could sense and destroy the pathogen Pseudomonas aeruginosa. The researchers from Nanyang Technological University in Singapore put the quorum sensing ability from P. aeruginosa into E. coli and connected it to the production of the toxic proteins called pyocins. So when there’s a quorum of P. aeruginosa, the engineered E. coli turn on pyocin production to kill P. aeruginosa. Figure 1 below shows the overall system.
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Genomic targeting of epigenetic probes using a chemically tailored Cas9 system

Recent advances in the field of programmable DNA-binding proteins have led to the development of facile methods for genomic localization of genetically encodable entities. Despite the extensive utility of these tools, locus-specific delivery of synthetic molecules remains limited by a lack of adequate technologies. Here we combine the flexibility of chemical synthesis with the specificity of a programmable DNA-binding protein by using protein trans-splicing to ligate synthetic elements to a nuclease-deficient Cas9 (dCas9) in vitro and subsequently deliver the dCas9 cargo to live cells. The versatility of this technology is demonstrated by delivering dCas9 fusions that include either the small-molecule bromodomain and extra-terminal family bromodomain inhibitor JQ1 or a peptide-based PRC1 chromodomain ligand, which are capable of recruiting endogenous copies of their cognate binding partners to targeted genomic binding sites. We expect that this technology will allow for the genomic localization of a wide array of small molecules and modified proteinaceous materials.
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Spinning stronger synthetic spider silk

A new method for producing stronger artificial spider silk is reported in a study published online this week in Nature Chemical Biology. Spider silk is an attractive biodegradable material for many different applications, but producing artificial silk with the same properties as natural silk has historically been difficult.

Spider silk is made up of long chains of linked protein molecules. Inside silk glands, the proteins used to make the silk are kept in a very concentrated solution. When spinning silk, the spider secretes the protein solution through a narrow duct. Along the length of this duct, the acidity changes and the pressure increases, causing the protein molecules to link up in the chains that form the silk fiber.

Inspired by the way that spiders spin silk, Jan Johansson, Anna Rising and colleagues designed a spinning device that mimics the narrow duct and acidity changes met by silk protein in spider glands. Using this device on a special protein - a hybrid of two natural silk proteins that can be manufactured in a highly concentrated form - enabled the authors to produce artificial spider silk that has greater strength and elasticity than other artificial silks, and that is nearly as strong as natural spider silk.

The authors note that the biodegradable silk produced by this method is cheaper and easier to obtain than natural spider silk, and will potentially allow for the production of large amounts of silk for applications such as high-performance textiles and advanced medical devices.
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Analyzing native membrane protein assembly in nanodiscs by combined non-covalent mass spectrometry and synthetic biology

Membrane proteins frequently assemble into higher order homo- or hetero-oligomers within their natural lipid environment. This complex formation can modulate their folding, activity as well as substrate selectivity. Non-disruptive methods avoiding critical steps such as membrane disintegration, transfer into artificial environments or chemical modifications are therefore essential to analyze molecular mechanisms of native membrane protein assemblies. The combination of cell-free synthetic biology, nanodisc-technology and non-covalent mass spectrometry provides excellent synergies for the analysis of membrane protein oligomerization within defined membranes. We exemplify our strategy by oligomeric state characterization of various membrane proteins including ion channels, transporters and membrane integrated enzymes assembling up to hexameric complexes. We further indicate a lipid dependent dimer formation of MraY translocase correlating with the enzymatic activity. The detergent free synthesis of membrane protein/nanodisc samples and the analysis by LILBID mass spectrometry provides a versatile platform for the analysis of membrane proteins in a native environment.
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A Blueprint for a Synthetic Genetic Feedback Controller to Reprogram Cell Fate

To artificially reprogram cell fate, experimentalists manipulate the gene regulatory networks (GRNs) that maintain a cell's phenotype. In practice, reprogramming is often performed by constant overexpression of specific transcription factors (TFs). This process can be unreliable and inefficient. Here, we address this problem by introducing a new approach to reprogramming based on mathematical analysis. We demonstrate that reprogramming GRNs using constant overexpression may not succeed in general. Instead, we propose an alternative reprogramming strategy: a synthetic genetic feedback controller that dynamically steers the concentration of a GRN's key TFs to any desired value. The controller works by adjusting TF expression based on the discrepancy between desired and actual TF concentrations. Theory predicts that this reprogramming strategy is guaranteed to succeed, and its performance is independent of the GRN's structure and parameters, provided that feedback gain is sufficiently high. As a case study, we apply the controller to a model of induced pluripotency in stem cells.
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Road to the future of systems biotechnology: CRISPR-Cas-mediated metabolic engineering for recombinant protein production

Road to the future of systems biotechnology: CRISPR-Cas-mediated metabolic engineering for recombinant protein production | SynBioFromLeukipposInstitute | Scoop.it
The rising potential for CRISPR–Cas-mediated genome editing has revolutionized our strategies in basic and practical bioengineering research. It provides a predictable and precise method for genome modification in a robust and reproducible fashion. Emergence of systems biotechnology and synthetic biology approaches coupled with CRISPR–Cas technology could change the future of cell factories to possess some new features which have not been found naturally. We have discussed the possibility and versatile potentials of CRISPR–Cas technology for metabolic engineering of a recombinant host for heterologous protein production. We describe the mechanisms involved in this metabolic engineering approach and present the diverse feature
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CRISPR–Cas9: A European position on genome editing : Nature : Nature Research

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CRISPR 101 eBook: Your Guide to Understanding CRISPR

CRISPR 101 eBook: Your Guide to Understanding CRISPR | SynBioFromLeukipposInstitute | Scoop.it
This eBook looks at how CRISPR is transforming genome engineering and provides crash course in everything a new CRISPR researchers and scientist needs to know.
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Designed cell consortia as fragrance-programmable analog-to-digital converters

Designed cell consortia as fragrance-programmable analog-to-digital converters | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biology advances the rational engineering of mammalian cells to achieve cell-based therapy goals. Synthetic gene networks have nearly reached the complexity of digital electronic circuits and enable single cells to perform programmable arithmetic calculations or to provide dynamic remote control of transgenes through electromagnetic waves. We designed a synthetic multilayered gaseous-fragrance-programmable analog-to-digital converter (ADC) allowing for remote control of digital gene expression with 2-bit AND-, OR- and NOR-gate logic in synchronized cell consortia. The ADC consists of multiple sampling-and-quantization modules sensing analog gaseous fragrance inputs; a gas-to-liquid transducer converting fragrance intensity into diffusible cell-to-cell signaling compounds; a digitization unit with a genetic amplifier circuit to improve the signal-to-noise ratio; and recombinase-based digital expression switches enabling 2-bit processing of logic gates. Synthetic ADCs that can remotely control cellular activities with digital precision may enable the development of novel biosensors and may provide bioelectronic interfaces synchronizing analog metabolic pathways with digital electronics.
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Five big mysteries about CRISPR’s origins

Five big mysteries about CRISPR’s origins | SynBioFromLeukipposInstitute | Scoop.it
Francisco Mojica was not the first to see CRISPR, but he was probably the first to be smitten by it. He remembers the day in 1992 when he got his first glimpse of the microbial immune system that would launch a biotechnology revolution. He was reviewing genome-sequence data from the salt-loving microbe Haloferax mediterranei and noticed 14 unusual DNA sequences, each 30 bases long. They read roughly the same backwards and forwards, and they repeated every 35 bases or so. Soon, he saw more of them. Mojica was entranced, and made the repeats a focus of his research at the University of Alicante in Spain.

It wasn't a popular decision. His lab went years without funding. At meetings, Mojica would grab the biggest bigwigs he could find and ask what they thought of the strange little repeats. “Don't care about repeats so much,” he says that they would warn him. “There are many repeats in many organisms — we've known about them for years and still don't know how many of them work.”
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Tweet from @MITxonedX

MITx on edX on Twitter: "Join us as we explore the field of synthetic biology: … https://t.co/iGIbCi2dUC, see more https://t.co/5KmHKbxNUh
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A New Era of Genome Integration - Simply Cut and Paste! 

Genome integration is a powerful tool in both basic and applied biological research. However, traditional genome integration, which is typically mediated by homologous recombination, has been constrained by low efficiencies and limited host range. In recent years, the emergence of homing endonucleases and programmable nucleases has greatly enhanced integration efficiencies and allowed alternative integration mechanisms such as non-homologous end joining and microhomology-mediated end joining, enabling integration in hosts deficient in homologous recombination. In this review, we will highlight recent advances and breakthroughs in genome integration methods made possible by programmable nucleases, and their new applications in synthetic biology and metabolic engineering.
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Why biology holds the key to the future of design and manufacturing

Why biology holds the key to the future of design and manufacturing | SynBioFromLeukipposInstitute | Scoop.it
Circulate - the go-to location for circular economy related news and insight.
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Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology

The chemical synthesis of DNA oligonucleotides and their assembly into synthons, genes, circuits, and even entire genomes by gene synthesis methods has become an enabling technology for modern molecular biology and enables the design, build, test, learn, and repeat cycle underpinning innovations in synthetic biology. In this perspective, we briefly review the techniques and technologies that enable the synthesis of DNA oligonucleotides and their assembly into larger DNA constructs with a focus on recent advancements that have sought to reduce synthesis cost and increase sequence fidelity. The development of lower-cost methods to produce high-quality synthetic DNA will allow for the exploration of larger biological hypotheses by lowering the cost of use and help to close the DNA read–write cost gap.
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Could tissue engineering mean personalized medicine?

Could tissue engineering mean personalized medicine? | SynBioFromLeukipposInstitute | Scoop.it
Each of our bodies is utterly unique, which is a lovely thought until it comes to treating an illness -- when every body reacts differently, often unpredictably, to standard treatment. Tissue engineer Nina Tandon talks about a possible solution: Using pluripotent stem cells to make personalized models of organs on which to test new drugs and treatments, and storing them on computer chips. (Call it extremely personalized medicine.)
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High efficiency hydrodynamic bacterial electrotransformation

Synthetic biology holds great potential for addressing pressing challenges for mankind and our planet. One technical challenge in tapping into the full potential of synthetic biology is the low efficiency and low throughput of genetic transformation for many types of cells. In this paper, we discuss a novel microfluidic system for improving bacterial electrotransformation efficiency and throughput. Our microfluidic system is comprised of non-uniform constrictions in microchannels to facilitate high electric fields with relatively small applied voltages to induce electroporation. Additionally, the microfluidic device has regions of low electric field to assist in electrophoretic transport of nucleic acids into the cells. The device features hydrodynamically controlled electric fields that allow cells to experience a time dependent electric field that is otherwise difficult to achieve using standard electronics. Results suggest that transformation efficiency can be increased by ∼4×, while throughput can increase by 100-1000× compared to traditional electroporation cuvettes. This work will enable high-throughput and high efficiency genetic transformation of microbes, facilitating accelerated development of genetically engineered organisms.
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Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology

The chemical synthesis of DNA oligonucleotides and their assembly into synthons, genes, circuits, and even entire genomes by gene synthesis methods has become an enabling technology for modern molecular biology and enables the design, build, test, learn, and repeat cycle underpinning innovations in synthetic biology. In this perspective, we briefly review the techniques and technologies that enable the synthesis of DNA oligonucleotides and their assembly into larger DNA constructs with a focus on recent advancements that have sought to reduce synthesis cost and increase sequence fidelity. The development of lower-cost methods to produce high-quality synthetic DNA will allow for the exploration of larger biological hypotheses by lowering the cost of use and help to close the DNA read–write cost gap.
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Synthetic recording and in situ readout of lineage information in single cells

Synthetic recording and in situ readout of lineage information in single cells | SynBioFromLeukipposInstitute | Scoop.it
Reconstructing the lineage relationships and dynamic event histories of individual cells within their native spatial context is a long-standing challenge in biology. Many biological processes of interest occur in optically opaque or physically inaccessible contexts, necessitating approaches other than direct imaging. Here we describe a synthetic system that enables cells to record lineage information and event histories in the genome in a format that can be subsequently read out of single cells in situ. This system, termed memory by engineered mutagenesis with optical in situ readout (MEMOIR), is based on a set of barcoded recording elements termed scratchpads. The state of a given scratchpad can be irreversibly altered by CRISPR/Cas9-based targeted mutagenesis, and later read out in single cells through multiplexed single-molecule RNA fluorescence hybridization (smFISH). Using MEMOIR as a proof of principle, we engineered mouse embryonic stem cells to contain multiple scratchpads and other recording components. In these cells, scratchpads were altered in a progressive and stochastic fashion as the cells proliferated. Analysis of the final states of scratchpads in single cells in situ enabled reconstruction of lineage information from cell colonies. Combining analysis of endogenous gene expression with lineage reconstruction in the same cells further allowed inference of the dynamic rates at which embryonic stem cells switch between two gene expression states. Finally, using simulations, we show how parallel MEMOIR systems operating in the same cell could enable recording and readout of dynamic cellular event histories. MEMOIR thus provides a versatile platform for information recording and in situ, single-cell readout across diverse biological systems.
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