SynBioFromLeukipposInstitute
108.7K views | +10 today
Follow
 
Scooped by Gerd Moe-Behrens
onto SynBioFromLeukipposInstitute
Scoop.it!

Self-Assembled DNA Crystals: The Impact on Resolution of 5'-Phosphates and the DNA Source

Self-Assembled DNA Crystals: The Impact on Resolution of 5'-Phosphates and the DNA Source | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Ruojie Sha , Jens J. Birktoft , Nam Nguyen , Arun Richard Chandrasekaran, Jianping Zheng , Xinshuai Zhao , Chengde Mao , and Nadrian Charles Seeman

"Designed self-assembled DNA crystals consist of rigid DNA motifs that are held together by cohesive sticky-ended interactions. A prominent application of such systems is that they might be able to act as macromolecular hosts for macromolecular guests, thereby alleviating the crystallization problem of structural biology. We have recently demonstrated that it is indeed possible to design and construct such crystals and to determine their structures by X-ray diffraction procedures. To act as useful hosts that organize biological macromolecules for crystallographic purposes, maximizing the resolution of the crystals will maximize the utility of the approach. The structures reported so far have diffracted only to about 4 Å, so we have examined two factors that might have impact on the resolution. We find no difference in the resolution whether the DNA is synthetic or PCR-generated. However, we find that the presence of a phosphate on the 5' end of the strands improves the resolution of the crystals markedly."

 http://bit.ly/WMt8Wx

about the illustration:
The woodcut Depth (pictured) by M. C. Escher reportedly inspired Nadrian Seeman to consider using three-dimensional lattices of DNA to orient hard-to-crystallize molecules. This led to the beginning of the field of DNA nanotechnology.
http://bit.ly/13LEjFV

more...
Luís Bastos's curator insight, January 18, 2013 12:58 PM

by
Ruojie Sha , Jens J. Birktoft , Nam Nguyen , Arun Richard Chandrasekaran, Jianping Zheng , Xinshuai Zhao , Chengde Mao , and Nadrian Charles Seeman

"Designed self-assembled DNA crystals consist of rigid DNA motifs that are held together by cohesive sticky-ended interactions. A prominent application of such systems is that they might be able to act as macromolecular hosts for macromolecular guests, thereby alleviating the crystallization problem of structural biology. We have recently demonstrated that it is indeed possible to design and construct such crystals and to determine their structures by X-ray diffraction procedures. To act as useful hosts that organize biological macromolecules for crystallographic purposes, maximizing the resolution of the crystals will maximize the utility of the approach. The structures reported so far have diffracted only to about 4 Å, so we have examined two factors that might have impact on the resolution. We find no difference in the resolution whether the DNA is synthetic or PCR-generated. However, we find that the presence of a phosphate on the 5' end of the strands improves the resolution of the crystals markedly."

 http://bit.ly/WMt8Wx

about the illustration:
The woodcut Depth (pictured) by M. C. Escher reportedly inspired Nadrian Seeman to consider using three-dimensional lattices of DNA to orient hard-to-crystallize molecules. This led to the beginning of the field of DNA nanotechnology.
http://bit.ly/13LEjFV

SynBioFromLeukipposInstitute
Your new post is loading...
Your new post is loading...
Scooped by Gerd Moe-Behrens
Scoop.it!

Groundbreaking gene-editing technique that could cure cancer found to have dangerous flaw

Groundbreaking gene-editing technique that could cure cancer found to have dangerous flaw | SynBioFromLeukipposInstitute | Scoop.it
It has been hailed as a cure for cancer and all forms of inherited disease. But scientists have now discovered that a system for editing the genes of living creatures can have a potentially dangerous side-effect – causing unintended mutations. Human trials of the Crispr-Cas9 gene-editing technique are already underway in China and are due to start in the US next year.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Digital-to-Biological Converter for On-Demand Production of Biologics Developed by Synthetic Genomics, Inc. - News Press Release | PharmiWeb.com

Synthetic Genomics, Inc. announced today the publication of a peer reviewed article describing the development and operation of its digital-to-biological converter (DBC) prototype that produced biologic compounds on-demand without any human intervention. The DBC integrates many of the synthetic biology tools developed by Synthetic Genomics for creating high fidelity and complex synthetic DNA all in one fully automated unit.

The paper describing this work is the first peer-reviewed publication of its kind and was published online today in Nature Biotechnology by lead authors Kent S. Boles and Krishna Kannan, and senior authors J. Craig Venter and Daniel G. Gibson.

To demonstrate feasibility, researchers digitally transmitted a file with DNA sequence information to the DBC. The DBC converted that digital sequence into oligonucleotides, and utilized synthetic biology tools developed by Synthetic Genomics such as gene synthesis, error correction, and Gibson Assembly™ methods to create large and complex DNA constructs with high fidelity. Utilizing this DNA as a template, the DBC further produced a series of biological materials without any human intervention, such as RNA, proteins, and viral particles.

"The concept of a DBC presents a new paradigm for the manufacturing of biological materials all starting from transmitted DNA sequences," said Daniel Gibson, Ph.D., vice president of DNA technology at Synthetic Genomics and senior author of the study. "It is easy to imagine numerous high value applications for rapid on-demand production of biological materials in healthcare, such as creating truly personalized therapeutics at a patient's bedside and rapidly generating custom vaccines to counter an infectious disease outbreak."

Biological products created on the DBC included DNA templates for an influenza vaccine, an RNA-based vaccine, antibody polypeptides, and a bacteriophage. The antibody polypeptides synthesized by the DBC included abatacept, ranibizumab, and trastuzumab. Biologics were created in under 2 days, which is several weeks faster than traditional biological manufacturing processes that require extended timelines and external vendors.

"The DBC is the first machine that can receive via the Internet or radio wave, digital biology in the form of DNA sequence enabling reconstitution of components of living systems," said J. Craig Venter, Ph.D., co-founder, chairman, co-chief scientific officer of Synthetic Genomics. "We are excited by the commercial prospects of this revolutionary tool as we believe the DBC represents a major leap forward in advancing new vaccines and biologics."

The DBC contains several components in common with the BioXp™ 3200, the world's first instrument for printing and cloning double stranded DNA. Capabilities on the DBC that are not yet available as integrated components on the BioXp include the conversion of digital code to DNA oligonucleotides using more basic chemical inputs, and the synthesis of proteins from DNA constructs. The BioXp™ 3200 is currently available through Synthetic Genomics' subsidiary, SGI-DNA, to improve the workflow for applications such as molecular cloning, protein production, antibody library generation, and cell engineering.

Synthetic Genomics is continuing to develop the DBC platform for several commercial applications. Continued modifications include implementing new methods for more reliable production of large, error-free, synthetic DNA and reducing dimensions of the instrument to make it more robust and portable.      

The other authors on this paper that have been integral to this work include John Gill, Martina Felderman, Heather Gouvis, Bolyn Hubby, and Kurt I. Kamrud.

The paper is available on the Nature Biotechnology website at http://dx.doi.org/10.1038/nbt.3859.

About SGI-DNA
SGI-DNA, a wholly owned subsidiary of Synthetic Genomics Inc., provides genomic solutions to advance scientific discovery. SGI-DNA's ever expanding suite of products, services, reagents, bioinformatics tools and instrumentation enables scientists to discover, design and build novel solutions for basic research, as well as for biomedical and industrial applications. SGI-DNA's genomic services include whole genome sequencing, DNA synthesis, library design, bioinformatics, cell engineering, and plasmid DNA cloning and purification. SGI-DNA's reagents include a complete suite of Gibson Assembly® and Site Directed Mutagenesis kits as well as optimized cell lines such as Vmax™ a novel, fast growing host system for molecular biology. To further enable synthetic biology workflows, SGI-DNA offers the BioXp™ 3200 System. This fully automated genomics workstation allows the creation of double stranded DNA fragments, automated cloning, Next Generation Sequencing DNA library preparation and cGMP manufacturing of synthetic DNA for clinical trials. Building on scientific breakthroughs from J. Craig Venter, Hamilton Smith, Clyde Hutchison, Daniel Gibson and their teams, SGI-DNA is committed to reducing barriers associated with synthetic biology. More information is available at www.sgidna.com.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications | SynBioFromLeukipposInstitute | Scoop.it
Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Bacteria with multicolor vision

Bacteria with multicolor vision | SynBioFromLeukipposInstitute | Scoop.it
Red, green, and blue light can be used to control gene expression in engineered E. coli.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Genome writing project confronts technology hurdles

More than 250 scientists, entrepreneurs, and ethicists assembled in New York City last week to discuss Genome Project–write (GP-write), which aims to build large stretches of synthetic DNA and put them to work in cells. The still-unfunded project promises better and cheaper DNA-writing technology that could help treat and study diseases or create more sustainable food and energy sources. But questions remain about whether GP-write should pursue an original goal, championed by co-founder and futurist Andrew Hessel, of assembling the 3 billion DNA bases of the human genome. In the meantime, the initiative aims to support technology-advancing "pilot projects" that modify cells from various organisms. But technical challenges—from the cost of DNA synthesis to genetic circuit design—loom large.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Microsoft Reportedly Wants to Use DNA for Cloud Data Storage

Microsoft Reportedly Wants to Use DNA for Cloud Data Storage | SynBioFromLeukipposInstitute | Scoop.it
In the not-so-distant future, next time you want to back up your work to Microsoft’s cloud, you might be storing it on a few snippets of DNA.
more...
Leonid Fridman's curator insight, May 23, 4:57 PM
הנה שימוש בטכנולוגיה בימינו שלנו בעדי לשצור קבצים בעתיד אנחנו נשתמש בדגימת די אן איי
 
Scooped by Gerd Moe-Behrens
Scoop.it!

Synthetic biology: Return to sender

Temporal control of gene expression is critical for cellular function and fate determination. Some genes, such as the Notch effector Hes1, exhibit an oscillating pattern of gene expression, marked by rapid mRNA synthesis and degradation due to negative feedback. Optogenetic approaches have enabled the generation of artificial oscillations with rapid spatial–temporal precision, whereas the use of bioluminescent or fluorescent reporters allows detection of oscillations at the single-cell level. However, it is not clear whether this oscillatory information can be transfe…
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Cell-free synbio: a technology whose time has come | PLOS Synthetic Biology Community

Cell-free synbio: a technology whose time has come | PLOS Synthetic Biology Community | SynBioFromLeukipposInstitute | Scoop.it
‘It’s like instant noodles – just add water’ exclaims Dr. Keith Pardee, now an assistant professor at the University of Toronto. He is describing a small black object developed during his postdoc in the Collins lab. This unassuming device is one of the most advanced biosensors ever built – it is able to detect the presence of the Zika virus. This is achieved by using an RNA toehold switch which provides the molecular precision required to identify and outbreaks and help guide efforts to combat virus’ spread. But things get really interesting when you look at the transformative technology behind the sensor.

 

Rather than use the common approaches of polymerase chain reaction (PCR) or a genetically modified bacteria to detect the virus, Keith decided to use a ‘cell free’ system. The principle is simple: grow up bacteria, smash open the cells, and use the contents to perform reactions in a test tube or on paper (for a guide on how to make extracts see this JoVE article). This has a number of advantages over the alternatives: unlike PCR, the assay can be used in remote locations without the need for expensive lab equipment, thereby allowing instantaneous field testing, and unlike genetically modified bacteria, cell-free systems avoid concerns about uncontrolled escape of genetically modified organisms into the environment.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Towards implementation of cellular automata in Microbial Fuel Cells

Towards implementation of cellular automata in Microbial Fuel Cells | SynBioFromLeukipposInstitute | Scoop.it
The Microbial Fuel Cell (MFC) is a bio-electrochemical transducer converting waste products into electricity using microbial communities. Cellular Automaton (CA) is a uniform array of finite-state machines that update their states in discrete time depending on states of their closest neighbors by the same rule. Arrays of MFCs could, in principle, act as massive-parallel computing devices with local connectivity between elementary processors. We provide a theoretical design of such a parallel processor by implementing CA in MFCs. We have chosen Conway’s Game of Life as the ‘benchmark’ CA because this is the most popular CA which also exhibits an enormously rich spectrum of patterns. Each cell of the Game of Life CA is realized using two MFCs. The MFCs are linked electrically and hydraulically. The model is verified via simulation of an electrical circuit demonstrating equivalent behaviours. The design is a first step towards future implementations of fully autonomous biological computing devices with massive parallelism. The energy independence of such devices counteracts their somewhat slow transitions—compared to silicon circuitry—between the different states during computation.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

“Addressing the ethical issues raised by synthetic human entities with embryo-like features” Human life starts day 0

The "14-day rule" for embryo research stipulates that experiments with intact human embryos must not allow them to develop beyond 14 days or the appearance of the primitive streak. However, recent experiments showing that suitably cultured human pluripotent stem cells can self-organize and recapitulate embryonic features have highlighted difficulties with the 14-day rule and led to calls for its reassessment. Here we argue that these and related experiments raise more foundational issues that cannot be fixed by adjusting the 14-day rule, because the framework underlying the rule cannot adequately describe the ways by which synthetic human entities with embryo-like features (SHEEFs) might develop morally concerning features through altered forms of development. We propose that limits on research with SHEEFs be based as directly as possible on the generation of such features, and recommend that the research and bioethics communities lead a wide-ranging inquiry aimed at mapping out solutions to the ethical problems raised by them.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Programmable DNA-Guided Artificial Restriction Enzymes

Programmable DNA-Guided Artificial Restriction Enzymes | SynBioFromLeukipposInstitute | Scoop.it
Restriction enzymes are essential tools for recombinant DNA technology that have revolutionized modern biological research. However, they have limited sequence specificity and availability. Here we report a Pyrococcus furiosus Argonaute (PfAgo) based platform for generating artificial restriction enzymes (AREs) capable of recognizing and cleaving DNA sequences at virtually any arbitrary site and generating defined sticky ends of varying length. Short DNA guides are used to direct PfAgo to target sites for cleavage at high temperatures (>87 °C) followed by reannealing of the cleaved single stranded DNAs. We used this platform to generate over 18 AREs for DNA fingerprinting and molecular cloning of PCR-amplified or genomic DNAs. These AREs work as efficiently as their naturally occurring counterparts, and some of them even do not have any naturally occurring counterparts, demonstrating easy programmability, generality, versatility, and high efficiency for this new technology.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

SB7.0 - The Seventh International Meeting on Synthetic Biology

The goal of SB7.0 is to unite again the international synthetic biology communities to take a fresh look at the key topics and challenge
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Advances in bacteria cancer therapies using synthetic biology

Synthetic biology aims to apply engineering principles to biology by modulating the behavior of living organisms. An emerging application of this field is the engineering of bacteria as a cancer therapy by programming of therapeutic, safety, and specificity features through genetic modification. Here, we review progress in this engineering including the targeting of bacteria to tumors, specific sensing and response to tumor microenvironments, remote induction methods, and controllable release of therapeutics. We discuss the most prominent bacteria strains used and their specific properties, and the types of therapeutics tested thus far. Finally, we note current challenges such as genetic stability that researchers must address for successful clinical implementation of this novel therapy in humans.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Synthetic biology: “Disco bacteria” could churn out drugs and useful chemicals | The Economist

Synthetic biology: “Disco bacteria” could churn out drugs and useful chemicals | The Economist | SynBioFromLeukipposInstitute | Scoop.it
Coloured light can be used to control how genetically-engineered organisms behave
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Design of synthetic epigenetic circuits featuring memory effects and reversible switching based on DNA methylation

Design of synthetic epigenetic circuits featuring memory effects and reversible switching based on DNA methylation | SynBioFromLeukipposInstitute | Scoop.it
Recording systems would allow synthetic organisms to store a ‘memory’ of a past event for future reference.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Cell-free technology startup founded by former SynBio SRI member awarded funding by RebelBio. — Synthetic Biology in Cambridge

Cell-free technology startup founded by former SynBio SRI member awarded funding by RebelBio. — Synthetic Biology in Cambridge | SynBioFromLeukipposInstitute | Scoop.it
Cell-Free Tech is a brand new start up company specialising in giving people the ability to do biological research, without the need for expensive tools and infrastructure. Based at the Microbiology Department of the University College Cork, Cell-free Tech is part of RebelBio, an accelerator programme that helps life sciences innovators, academics, biomakers and citizen scientists to change the world with biology.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Base‐modified nucleic acids as a powerful tool for synthetic biology and biotechnology

The ability of various nucleoside triphosphate analogs of deoxyguanosine and deoxycytidine with 7-deazadeoxyadenosine (A1) and 5-chlorodeoxyuridine (T1) to serve as substrates for Taq DNA polymerase was evaluated. The triphosphate set constituted of A1, T1, and 7-deazadeoxyguanosine with either 5-methyldeoxy-cytidine or 5-fluorodeoxycytidine was successfully employed in the polymerase chain reaction (PCR) of 1.5 kb fragments as well as random oligonucleotide libraries. Another effective combination of triphosphates for the synthesis of 1 kb PCR product was A1, T1, deoxyinosine, and 5-bromodeoxycytidine. In vivo experiments using an antibiotic-resistant gene containing the latter set demonstrated that the bacterial machinery accepts fully modified sequences as genetic templates. Moreover, the ability of the base-modified segments to selectively protect DNA from cleavage by restriction endonucleases was shown. This evidence can be used to regulate the endonuclease cleavage pattern.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Lab-grown blood stem cells produced at last

Lab-grown blood stem cells produced at last | SynBioFromLeukipposInstitute | Scoop.it
After 20 years of trying, scientists have transformed mature cells into primordial blood cells that regenerate themselves and the components of blood. The work, described today in Nature1, 2, offers hope to people with leukaemia and other blood disorders who need bone-marrow transplants but can’t find a compatible donor. If the findings translate into the clinic, these patients could receive lab-grown versions of their own healthy cells.

One team, led by stem-cell biologist George Daley of Boston Children’s Hospital in Massachusetts, created human cells that act like blood stem cells, although they are not identical to those found in nature1. A second team, led by stem-cell biologist Shahin Rafii of Weill Cornell Medical College in New York City, turned mature cells from mice into fully fledged blood stem cells2.

“For many years, people have figured out parts of this recipe, but they’ve never quite gotten there,” says Mick Bhatia, a stem-cell researcher at McMaster University in Hamilton, Canada, who was not involved with either study. “This is the first time researchers have checked all the boxes and made blood stem cells.”

Daley’s team chose skin cells and other cells taken from adults as their starting material. Using a standard method, they reprogrammed the cells into induced pluripotent stem (iPS) cells, which are capable of producing many other cell types. Until now, however, iPS cells have not been morphed into cells that create blood.

The next step was the novel one: Daley and his colleagues inserted seven transcription factors — genes that control other genes — into the genomes of the iPS cells. Then they injected these modified human cells into mice to develop. Twelve weeks later, the iPS cells had transformed into progenitor cells capable of making the range of cells found in human blood, including immune cells. The progenitor cells are “tantalizingly close” to naturally occurring ‘haemopoetic’ blood stem cells, says Daley.

Bhatia agrees. “It’s pretty convincing that George has figured out how to cook up human haemopoetic stem cells,” he says. “That is the holy grail.”

more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Bacteria can form living materials with liquid crystals, says a new research

Bacteria can form living materials with liquid crystals, says a new research | SynBioFromLeukipposInstitute | Scoop.it
https://t.co/HZNV2j0Sdm
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Interlocked DNA topologies for nanotechnology

Interlocked DNA topologies for nanotechnology | SynBioFromLeukipposInstitute | Scoop.it
Interlocked molecular architectures are well known in supramolecular chemistry and are widely used for various applications like sensors, molecular machines and logic gates. The use of DNA for constructing these interlocked structures has increased significantly within the current decade. Because of Watson–Crick base pairing rules, DNA is an excellent material for the self-assembly of well-defined interlocked nanoarchitectures. These DNA nanostructures exhibit sufficient stability, good solubility in aqueous media, biocompatibility, and can be easily combined with other biomolecules in bio-hybrid nano-assemblies. Therefore, the study of novel DNA-based interlocked systems is of interest for nanotechnology, synthetic biology, supramolecular chemistry, biotechnology, and for sensing purposes. Here we summarize recent developments and applications of interlocked supramolecular architectures made of DNA. Examples illustrating that these systems can be precisely controlled by switching on and off the molecular motion of its mechanically trapped components are discussed. Introducing different triggers into such systems creates molecular assemblies capable of performing logic gate operations and/or catalytic activity control. Interlocked DNA-based nanostructures thus represent promising frameworks for building increasingly complex and dynamic nanomachines with highly controllable functionality.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Biohacking & the Rise of Digital Biology

Biohacking & the Rise of Digital Biology | SynBioFromLeukipposInstitute | Scoop.it
Biohacking and digital biology are taking off with huge promise of positively impacting a wide variety of industries.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Biobrick chain recommendations for genetic circuit design

Synthetic biology databases have collected numerous biobricks to accelerate genetic circuit design. However, selecting biobricks is a tough task. Here, we leverage the fact that these manually designed circuits can provide underlying knowledge to support biobrick selection. We propose to design a recommendation system based on the analysis of available genetic circuits, which can narrow down the biobrick selection range and provide candidate biobricks for users to choose. A recommendation strategy based on a Markov model is established to tackle this issue. Furthermore, a biobrick chain recommendation algorithm Sira is proposed that applies a dynamic programming process on a layered state transition graph to obtain the top k recommendation results. In addition, a weighted filtering strategy, WFSira, is proposed to augment the performance of Sira. The experimental results on the Registry of Standard Biological Parts show that Sira outperforms other algorithms significantly for biobrick recommendations, with approximately 30% improvement in terms of recall rate. It is also able to make biobrick chain recommendations. WFSira can further improve the recall rate of Sira by an average of 7.5% for the top 5 recommendations.
more...
No comment yet.