GP-W & SC2.0 MEETING

Registration is now open for the 2019 GP-WRITE & 8TH ANNUAL SC2.0 MEETING
Hosted by the Institute for Systems Genetics at NYU Langone Health

November 11-14
REGISTER

Synthetic genomics is an emerging field driven by the rapidly decreasing cost of gene synthesis, scalable DNA assembly technologies, and the ever-increasing amount of genome sequence data. To date, convergence of these technologies has enabled total genome synthesis projects targeting viral, bacterial and yeast genomes.

This meeting will bring together global leaders in the field of genome writing, focusing on achievements to date, and more importantly, what’s coming up next.  Major topics will include whole genome engineering efforts via bottom-up design and total synthesis, as well as top down, massively parallelized genome editing by designer nucleases.

The Genome Project-write (GP-write) is an open, international research project led by a multi-disciplinary group of scientific leaders who will oversee a reduction in the costs of engineering and testing large genomes in cell lines more than 1,000-fold within ten years.

The Synthetic Yeast Genome Project, Sc2.0, is an international and collaborative effort aiming to design and build the 16 synthetic chromosomes of the world’s first designer eukaryotic cell.

7th international yeast 2.0 and synthetic genomes conference

Synthetic Biology is widely believed to have the potential to make the most profound impact on the way we solve the many grand challenges facing humanity over the next 50 years. Conferences, such as this one, which bring together individuals involved in this field from around the world, are crucial to supercharge the intellectual horsepower required to ‘join the dots’.

The 7th Yeast 2.0 and Synthetic Genomes conference, to be held in the spectacular city of Sydney in November 2018, will provide delegates the opportunity to hear speakers who have made or have the potential to make significant impacts in the synthetic biology world.  Synthetic genomics takes science and technology into a whole new dimension, and will provide the impetus to propel the bioeconomy, to meet the complex needs of a rapidly greying global population.  The conference program will highlight work currently being undertaken in the most crucial areas, and delegates will have ample opportunity to network with colleagues, to exchange ideas and to forge new collaborations.

This conference also acts as a pivotal moment for the international Yeast 2.0 project.  This history-in-the-making project will open-up the possibility of producing energy-rich molecules for renewable biofuels and sustainable industrial chemicals; compounds for the bio-remediation of polluted environments; novel antibiotics, vaccines and personalised medicines; and adequate nutritious and safe food supplies to meet the future demands of a global population of 10 billion people of which two-thirds will be over the age of 60 by 2050.

We invite you to join with us for this very special conference (registration), and look forward to welcoming you to Sydney in November 2018.

Professor Sakkie Pretorius

Chairman

Conference Planning Committee

Conference website: https://iysgc2018.com/

6th Annual Sc2.0 Meeting, Singapore

The Synthetic Yeast Genome Project (Sc2.0) is the world’s first synthetic eukaryotic genome project that aims to create a novel, rationalized version of the genome of the yeast species Saccharomyces cerevisiae. In a truly global collaborative effort, research teams across the world have embarked on the challenging but exciting task of building 16 designer synthetic chromosomes encompassing ~ 12 million base pairs of DNA.

From 13-16 June 2017, international synthetic biology communities will convene in Singapore for SB7.0. The Seventh International Meeting for Synthetic Biology where several esteemed members of the Sc2.0 consortium will be speaking. The conference presents an opportune time for members of the Sc2.0 consortium to gather once again to discuss the progress on our concerted efforts on the Synthetic Yeast Genome Project and how we can lend support to one another to forge ahead towards finishing the world’s first synthetic eukaryotic genome together.

Location: National University of Singapore, Kent Ridge Guild House, 9 Kent Ridge Drive, 119241, Singapore

To register or looking for more details: https://www.eventbrite.sg/e/6th-annual-sc20-meeting-singapore-tickets-32810369699

Sc2.0 project hits new milestone: 5 additional chromosomes completed!

The global Sc2.0 team has built five new synthetic yeast chromosomes, meaning that 30 percent of S.cerevisiae’s genetic material has now been swapped out for engineered replacements. This is one of several findings of a package of seven papers published March 10 as the cover story for Science.

An international team of more than 200 authors produced the latest work from the Synthetic Yeast Project (Sc2.0). By the end of this year, this international consortium hopes to have designed and built synthetic versions all 16 chromosomes – the structures that contain DNA – for S. cerevisiae.

Like computer programmers, scientists add swaths of synthetic DNA to – or remove stretches from – human, plant, bacterial or yeast chromosomes in hopes of averting disease, manufacturing medicines, or making food more nutritious. Yeast has long served as an important research model because their cells share many features with human cells, but are simpler and easier to study.

“This work sets the stage for completion of designer, synthetic genomes to address unmet needs in medicine and industry,” says Jef Boeke, the Sc2.0 project director.  “Beyond any one application, the papers confirm that newly created systems and software can answer basic questions about the nature of genetic machinery by reprogramming chromosomes in living cells.”

In March 2014, Sc2.0 successfully assembled the first synthetic yeast chromosome (synthetic chromosome 3 or synIII) comprising 272,871 base pairs, the chemical units that make up the DNA code. The new round of papers consists of an overview and five papers describing the first assembly of synthetic yeast chromosomes synII, synV, synVI, synX, and synXII. A seventh paper provides a first look at the 3D structures of synthetic chromosomes in the cell nucleus which mimic their native counterparts with remarkable fidelity.

Many technologies developed in Sc2.0 serve as the foundation for GP–write, a related initiative aiming to synthesize complete sets of human and plant chromosomes (genomes) in the next ten years. GP-write will hold its next meeting in New York City on May 9-10, 2017; please visit this site for more information.  

 

Global Production

 

To begin synthesizing a yeast chromosome, researchers must first plan thousands of changes, some of which empower them to move around pieces of chromosomes in a kind of fast, high-powered evolution. Other changes remove stretches of DNA code found to be unlikely to have a functional role by past efforts. The BioStudio software was developed by a team at Johns Hopkins led by Joel Bader.

 

With the edits made, the team starts to assemble edited, synthetic DNA sequences into ever larger chunks, which are finally introduced into yeast cells, where cellular machinery finishes building the chromosome. A major innovation captured in the current round of papers involves this last step.

 

Previously, researchers were required to finish building one piece of a chromosome before they could start work on the next. Sequential requirements are bottlenecks, says Boeke, which slow processes and increase cost. The current round of papers features several efforts to “parallelize” the assembly of synthetic chromosomes.

Labs around the globe each synthesized different pieces in strains of yeast that were then mated (crossed) to quickly yield thriving yeast, not just with an entire synthetic chromosome, but in some instances with more than one. Specifically, a paper led by author Leslie Mitchell, PhD, a post-doctoral fellow from Boeke’s lab at NYU Langone, described the construction of a strain containing three synthetic chromosomes.

“Steps can be accomplished at the same time in many locales and then assembled at the end, like networking laptops to create a global super computer,” says Mitchell.

Along the way, the global team honed a number of innovations and came to understand yeast biology better. A team at Tsinghua University, for instance, led an effort where six teams built in pieces synthetic chromosome XII (synXII), which was then assembled into a final molecule more than a million base pairs (a megabase) in length. This largest synthetic chromosome to date is still 1/3,000 of what would be needed to build a human genome molecule, so new techniques will be needed.

In addition, experiments demonstrated that drastic changes can be made to the genomes of yeast without killing them, says Boeke. Yeast strains, for instance, survived experiments where sections of DNA code were moved from one chromosome to another, or even swapped between yeast species, with little effect. Genetically pliable (plastic) organisms make good platforms for the dramatic engineering that may be needed for future applications. The search for differences between the wild type and synthetic chromosomes was taken to new heights by the BGI/Edinburgh effort on synII, which used a “Transomic” approach to deeply profile the DNA, RNA protein and even metabolomics and phenomics, and confirm the “yeastiness” of the altered strain and its chromosomes.

 

The package of seven newly published had authors from ten universities in several countries, including the US (NYU Langone, Johns Hopkins), China (Tsinghua, Tianjin), France (Institut Pasteur, Sorbonne Universités), and Scotland (Edinburgh); along with authors from key industry partners: BGI, the leading Chinese genomics company, and US/China-based Genscript.

 

Led by the School of Chemical Engineering and Technology at Tianjin University in China, the paper describing the synthesis of SynV is noteworthy in that is was done by undergraduate students as part of “Build-a-Genome China”, a class first taught in the United States at Johns Hopkins, where Boeke worked before coming to NYU Langone. This is part of an emerging global network of “chromosome foundries,” says Boeke, “which is building the next generation of synthetic biologists along with chromosomes.” The Tianjin group also notably completed two chromosomes, and developed powerful methods for “debugging” errors found in synthetic chromosomes.
In addition to Boeke and Mitchell, lead organizers for the current studies included Ying-Jin Yuan of Tianjin and Junbiao Dai of Tsinghua University, Joel Bader from Johns Hopkins, Romain Koszul at the Institut Pasteur, Yizhi Cai at the University of Edinburgh, and Huanming Yang at BGI. The US studies were supported principally by the National Science Foundation. Other key funding sources were the China National High Technology Research and Development Program, the National Science Foundation of China, the Chinese Ministry of Science and Technology, the UK Biotechnology and Biological Sciences Research Council, and ERASynBio.

 

Links to seven papers:

5th Annual Sc2.0 and Synthetic Genomes Conference, Edinburgh, UK on July 8-9, 2016

smallyeast

On July 8th-9th 2016 scientists from around the world will convene in Edinburgh at Dynamic Earth to discuss the progress of the international synthetic yeast genome project as well as other advances in genome engineering including genome assembly methodologies, mammalian synthetic biology, lab automation and software development for synthetic biology (for more details, go to conference website: http://syngenomesconf.cailab.org).

For the past four years, the conference has focused on the ongoing Synthetic Yeast Genome Project (Sc2.0). As the world’s first synthetic, designer eukaryotic genome project, the Synthetic Yeast Genome Project has garnered global attention. The Sc2.0 international consortium is building 16 designer synthetic chromosomes encompassing ~12 million base pairs of DNA, and we are around halfway through this very exciting project.

The conference has been expanded to include a focus on Synthetic Genomes and Engineering Biology. This is a hot topic and we are thrilled to announce that this year’s program will include at least one new panel discussion as well as Keynotes from leaders in the field including Jasper Rine (UC-Berkeley), Pam Silver (Harvard), Maitreya Dunham (University of Washington) and Jim Collins (MIT). The meeting will also feature panel speakers, demonstrations of the latest in lab automation, updates from the DNA synthesis industry and an exciting poster session.

Finally, delegates will be able to experience at first hand some local yeast strains in action with a glass or two of the local craft beers. During the event delegates will also get to enjoy many of the premiere foods for which Scotland has an international reputation.

There will be plenty of opportunity to burn off any additional calories at a lively traditional Ceilidh after the conference dinner and by strolling around the beautiful old city of Edinburgh during the long midsummer days! This meeting is being sponsored by LabCyte, BBSRC, Twist Bioscience, Autodesk, Gen9, Thermo Fisher Scientific, Synthetic Genomics, SULSA, the US National Science Foundation, the University of Edinburgh, New York University, and the UK Centre for Mammalian Synthetic Biology.

New York Genome Center (NYGC) hosts 4th International Sc2.0 and synthetic Genomes meeting

sc2-meeting-2015The fourth international meeting of our group was held at the NYGC in lower Manhattan on July 16-17, 2015, and organized by Jef Boeke, Nancy J. Kelley and Leslie Mitchell. At the last meeting, our group decided to expand to a two day meeting and also to expand the topic area to include discussion and presentations on other synthetic genomes. Jef Boeke kicked off the meeting with an overview of the Sc2 project, and there were two nuts and bolts workshops where each team explained progress and challenges. Highlights included panel discussions on synthetic genomes and society and discussions of what is the next multicellular genome that should be synthesized. Sessions highlighting the relationship of yeast genomes to the flavors and behaviors of certain alcoholic beverages were discussed by Daniel Johnson and Sakkie Pretorius of the Australian Wine Research Institute and by Troels Prahl of White Labs with his colleague Toby Richardson of Synthetic Genomics Inc. Representatives of DNA synthesis and robotics and instrument companies were also in attendance. A very exciting meeting all around! We hope to see you in Edinburgh next year:

5th International Sc2.0 and Synthetic Genomes meeting, Dynamic Earth, Edinburgh, July 8-9, 2016, Main Organizer: Patrick Cai. Keynote speakers are Jasper Rine and Jim Collins.

Build-a-Genome Network Workshop, Aug 14-16 Loyola University Maryland, Baltimore MD

The Build-a-Genome (BAG) course offers undergraduate students an exceptional opportunity to participate in the cutting-edge research of the Synthetic Yeast Project. BAG offers students an authentic laboratory experience where they perform fundamental techniques in synthetic genomics, present and critique their data, and troubleshoot experiments until successful. By completion of the course, students who worked on synthetic chromosome III became so fluent in molecular and synthetic biology techniques that they produced numerous synthetic chromosome “building blocks” and earned authorship on that milestone research paper. After being established at Johns Hopkins University, BAG franchises were established at Loyola University Maryland and Tianjin University in China. Thanks to funding from the National Science Foundation RCN-UBE program, the Build-a-Genome Network has now been established with the goal of broadening the number of colleges and universities that offer the BAG course.

A national workshop for the Build-a-Genome Network will be held from August 14th to 16th at Loyola University Maryland in Baltimore. This meeting will:

(1) Introduce new members to the Synthetic Yeast Project and the BAG workflow through a series of talks, hands-on bioinformatics exercises, and wet-lab activities.
(2) Discuss strategies for adapting the BAG course to diverse undergraduate institutions. We seek to preserve the most attractive features of the BAG course while confronting the logistical hurdles that may arise when implementing research-intensive courses at undergraduate institutions.
(3) Develop course learning objectives and assessment tools for different variations of the BAG course.

These activities will create a network of expertise and “ready-to-implement” frameworks, both of which will allow network participants to implement the BAG curriculum (or similar synthetic genomics projects) at a broad range of academic institutions. For more information please contact Rob Newman (rhnewman@ncat.edu), Eric Cooper (ecooper@hartwick.edu), or Lisa Scheifele (lzscheifele@loyola.edu).

First SAVI-sponsored joint US-China paper on Sc2.0 published

Two graduate students from Tianjin University, Qiuhui Lin and Jia Bin, from the laboratory of Yingjin Yuan at Tianjin University traveled to Johns Hopkins University where they worked in the lab of Jef Boeke for several months, in an effort to exchange scientific information, and develop new methods.  Working with postdoctoral fellow Leslie Mitchell and graduate students Jingchuan Luo and Zhuwei Xu they developed efficient and standardized methods for assembling “Minichunks” of 2.5-4 kb, stringing together Building Blocks previously made by JHU “Build A Genome” students. Then the “RADOM” method, which produces up to 10 kb fragments “in yeasto”, used the Build A Genome Class, led by Karen Zeller, as a testbed, and the workflow was implemented in BioStudioDb by Kun Yang.  The work is published in ACS SynBio and sponsored by the NSF SAVI program..
The RADOM method

The RADOM method

3d International Synthetic Yeast Genome (Sc2.0) Consortium Meeting, Taormina, Italy on June 20, 2014 – sponsored by NSF SAVI

We are pleased to announce that this summer on June 20th, we will be hosting the 3d International Synthetic Yeast Genome (Sc2.0) Consortium Meeting at the Hotel Villa Diodoro, Sicily, Italy. This day-long meeting is now open for registration.  Notably it will be held the day after the International Synthetic and Systems Biology Summer School, so it will be easy to attend both activities.

The Synthetic Yeast Genome Project (Sc2.0) is synthesizing and constructing a modified version of the Saccharomyces cerevisiae genome to test biological questions and give new functions.

We will be bringing those around the world involved in the Sc2.0 project together to discuss progress on the synthetic genome, opportunities to use the strains and tools of the project, and related projects in synbio and sysbio. This meeting is open to all interested in Sc2.0 and we encourage you (and your colleagues) to register if you’d like to attend.

http://syntheticyeast3.eventbrite.com/

Please note the happy smiling faces of the participants at the 2d Sc2.0 meeting in London — this time we will sample some Sicilian beers and maybe even wines!

IMG_0159