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10 Years of PLOS Synbio Publications

The PLOS Synbio Collection organizes the synthetic biology papers from across the PLOS family of journals into nine categories. The collection includes publications going back to December 2006 so this month we’re celebrating 10 years of synbio articles. Here I’ll give you a quick rundown of history with some highlights from the PLOS Synbio Collection.

The Launch

In 2012, PLOS launched the Synthetic Biology Collection to showcase synbio papers published with PLOS. At the start, there were already over 50 papers with some going all the way back to the first issue of PLOS One in 2006.

https://blogs.staging.plos.org/everyone/2012/08/15/plos-one-launches-synthetic-biology-collection/

Synbio papers published with PLOS have covered a broad range of the field, since PLOS One accepts all fields of science and journals like PLOS Computational Biology and PLOS Biology focus on areas that include particular aspects of synthetic biology. Originally, PLOS One was the main home of the Synbio Collection but it has expanded to all PLOS journals.

An early example in PLOS One is the 2007 paper, “High-Yield Hydrogen Production from Starch and Water by a Synthetic Enzymatic Pathway”. They tested hydrogen production using 13 purified enzymes in a continuous flow system. This functioning enzymatic pathway points toward more synthetic biology innovation because it does not occur in nature and worked by making use of enzymes from a variety of organisms. Optimizing a host or cell-free system is still a challenge for synthetic biology production of high value products.

Another example of what synbio you could find early in PLOS is “Design principles for riboswitch function“. This work used mathematical modeling to analyze the relevant rate constants and constraints that guide how a riboswitch can be engineered for specific purposes. Since its publication in 2009, lots of work has been done to build on this understanding of riboswitch function to give us new genetic parts.

beisel_fig_1
Reproduced figure 1 from Beisel et al. Figure 1.’ Kinetic models for riboswitches functioning through three distinct regulatory mechanisms.’ http://dx.doi.org/10.1371/journal.pcbi.1000363.g001

 

Other work has provided key experimental methods for the community. Both the Modular Cloning (MoClo) and the GoldenBraid cloning systems were published in PLOS One. These popular methods provide modular cloning techniques for multigene systems and have enabled more efficient assembly of large or combinatorial genetic constructs.

cloning_strategies
Modified figure 1 from Weber et al. (http://dx.doi.org/10.1371/journal.pone.0016765.g001) and figure 3 from Sarrion-Perdigones et al. (http://dx.doi.org/10.1371/journal.pone.0021622.g003)

At its start the collection held all of the synbio papers in one place, but it quickly grew to the point where it was difficult for the editors to put all of the relevant papers in one place. Both finding all of the right papers to include and making the collection easy to navigate required some changes.

Updates and Expansion

In 2014, the collection editors rolled out some updates including dividing the collection into eight sections to make browsing easier and introducing the idea of “community-driven editing”.  The sections allow readers to find papers specific to the area of synthetic biology they would like to read about. The community-driven editing means that you can let us know if an article published with PLOS should be included in the collection.

Gyorgy_fig_2
Modified figure 2 from Gyorgy et al.

The update also brought the inclusion of the full suite of PLOS journals. This brought in papers like “Modular Composition of Gene Transcription Networks” published in PLOS Computational Biology by my former lab-mate and co-advisor. Their modeling work focused on the effects of retroactivity, a phenomenon in which the connection in a network cause a load on each other the affects the original unconnected  dynamics. Work like this can inform how synthetic gene networks scale up and provide more breadth to the collection. The hope with each update is to engage the synbio community more and provide a space for open sharing.

iGEM Collection

The newest innovation to PLOS synbio publishing is the PLOS iGEM collection. The International Genetically Engineered Machine (iGEM) Foundation runs an annual competition in which thousands of students design and build their own synbio projects. Now, the final results of those projects can be included in this new model of open publishing that encourages community editing.

https://blogs.staging.plos.org/collections/plos-igem-collection/

After the iGEM competition is over, all students can submit to the PLOS iGEM Collection or teams will still have the option to submit full research articles to PLOS ONE. This exciting iGEM collection is in its second year with 2015 results online. An example of the 2015 student work is the Chinese University of Hong Kong’s engineering of Azotobacter vinelandii. This bacterium is a fairly unique lab organism because it can fix nitrogen while growing aerobically and has been used to study nitrogen fixation. Their project characterized Biobrick constructs and tried to put the magnetosome biogenesis machinery from Magnetospirillum gryphiswaldense to A. vinelandii.

abstract-690x320
Graphical abstract for iGEM REPORT: Characterization of Azotobacter vinelandii and Kits for Its Synthetic Biology Applications

The iGEM collection is continuing for iGEM 2016, and a peer-review jamboree will be happening next month to go over the submissions from this year’s iGEM teams.

Looking Forward

PLOS is still welcoming synbio submissions and always let us know if there’s a published paper that should be included in the collection. The collection is now up to nine sections because fields like “genome editing” have grown to warrant their own spot. The rise of CRISPR technologies like Cas9 have had huge impacts in synthetic biology and that’s reflected in the PLOS Synbio Collection.

For instance, one group of researchers created a biophysical model of Cas9 interactions that identifies DNA supercoiling as a way to control Cas9 binding. They use this modeling insight to propose new ways to design target sights with less unwanted off-target activity.

 

journal.pcbi.1004724.g001
Modified Figure 1 from Farasat et al. ‘The multi-step mechanism responsible for Cas9-mediated DNA site cleavage.’

You’ll find many other papers in the collection and you can even find PLOS synbio papers highlighted when you sign up for our blog newsletter (see the upper-right part of this page). Be sure to take a look at the full synbio collection and always let us know if there’s a PLOS paper that should be included. Also let us know your thoughts and your favorite papers in the PLOS Synbio Collection using #PLOSSynbio10years.

 

 

References

Beisel, Chase L., and Christina D. Smolke. “Design principles for riboswitch function.” PLoS Comput Biol 5.4 (2009): e1000363.

Farasat, Iman, and Howard M. Salis. “A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation.” PLoS Comput Biol 12.1 (2016): e1004724.

Gorochowski, Thomas E., et al. “BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.” PloS one 7.8 (2012): e42790.

Gyorgy, Andras, and Domitilla Del Vecchio. “Modular composition of gene transcription networks.” PLoS Comput Biol 10.3 (2014): e1003486.

King Pong Leung, Jacky Fong Chuen Loo, Leo Chi U Seak, Tung Faat Lai, Kevin Yuk Lap Yip, Siu Kai Kong, Ting Fung Chan, King Ming Chan. “Characterization of Azotobacter vinelandii and Kits for Its Synthetic Biology Applications” PLOS iGEM Collection

Sarrion-Perdigones, Alejandro, et al. “GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules.” PloS one 6.7 (2011): e21622.

Weber, Ernst, et al. “A modular cloning system for standardized assembly of multigene constructs.” PloS one 6.2 (2011): e16765.

 

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