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!

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NYU Langone Medical Center Press Release

Scientists Synthesize First Functional “Designer” Chromosome in Yeast

Study reports major advance in synthetic biology

March 27, 2014 (All day)

An international team of scientists led by Jef Boeke, PhD, director of NYU Langone Medical Center’s Institute for Systems Genetics, has synthesized the first functional chromosome in yeast, an important step in the emerging field of synthetic biology, designing microorganisms to produce novel medicines, raw materials for food, and biofuels.

Over the last five years, scientists have built bacterial chromosomes and viral DNA, but this is the first report of an entire eukaryotic chromosome, the threadlike structure that carries genes in the nucleus of all plant and animal cells, built from scratch. Researchers say their team’s global effort also marks one of the most significant advances in yeast genetics since 1996, when scientists initially mapped out yeast’s entire DNA code, or genetic blueprint.

“Our research moves the needle in synthetic biology from theory to reality,” says Dr. Boeke, a pioneer in synthetic biology who recently joined NYU Langone from Johns Hopkins University.

“This work represents the biggest step yet in an international effort to construct the full genome of synthetic yeast,” says Dr. Boeke. “It is the most extensively altered chromosome ever built. But the milestone that really counts is integrating it into a living yeast cell. We have shown that yeast cells carrying this synthetic chromosome are remarkably normal. They behave almost identically to wild yeast cells, only they now possess new capabilities and can do things that wild yeast cannot.”

In this week’s issue of Science online March 27, the team reports how, using computer-aided design, they built a fully functioning chromosome, which they call synIII, and successfully incorporated it into brewer’s yeast, known scientifically as Saccharomyces cerevisiae.

The seven-year effort to construct synIII tied together some 273, 871 base pairs of DNA, shorter than its native yeast counterpart, which has 316,667 base pairs. Dr. Boeke and his team made more than 500 alterations to its genetic base, removing repeating sections of some 47,841 DNA base pairs, deemed unnecessary to chromosome reproduction and growth. Also removed was what is popularly termed junk DNA, including base pairs known not to encode for any particular proteins, and “jumping gene” segments known to randomly move around and introduce mutations. Other sets of base pairs were added or altered to enable researchers to tag DNA as synthetic or native, and to delete or move genes on synIII.

“When you change the genome you’re gambling. One wrong change can kill the cell,” says Dr. Boeke. “We have made over 50,000 changes to the DNA code in the chromosome and our yeast still live. That is remarkable. It shows that our synthetic chromosome is hardy, and it endows the yeast with new properties.”

The Herculean effort was aided by some 60 undergraduate students enrolled in the “Build a Genome” project, founded by Dr. Boeke at Johns Hopkins. The students pieced together short snippets of the synthetic DNA into stretches of 750 to 1,000 base pairs or more. These pieces were then assembled into larger ones, which were swapped for native yeast DNA, an effort led by Srinivasan Chandrasegaran, PhD, a professor at Johns Hopkins. Chandrasegaran is also the senior investigator of the team’s studies on synIII.

Student participation kicked off what has become an international effort, called Sc2.0 for short, in which several academic researchers have partnered to reconstruct the entire yeast genome, including collaborators at universities in China, Australia, Singapore, the United Kingdom, and elsewhere in the U.S.

Yeast chromosome III was selected for synthesis because it is among the smallest of the 16 yeast chromosomes and controls how yeast cells mate and undergo genetic change. DNA comprises four letter-designated base macromolecules strung together in matching sets, or base pairs, in a pattern of repeating letters. “A” stands for adenine, paired with “T” for thymine; and “C” represents cysteine, paired with “G” for guanine. When stacked, these base pairs form a helical structure of DNA resembling a twisted ladder.

Yeast shares roughly a third of its 6,000 genes—functional units of chromosomal DNA for encoding proteins — with humans. The team was able to manipulate large sections of yeast DNA without compromising chromosomal viability and function using a so-called scrambling technique that allowed the scientists to shuffle genes like a deck of cards, where each gene is a card. “We can pull together any group of cards, shuffle the order and make millions and millions of different decks, all in one small tube of yeast,” Dr. Boeke says. “Now that we can shuffle the genomic deck, it will allow us to ask, can we make a deck of cards with a better hand for making yeast survive under any of a multitude of conditions, such as tolerating higher alcohol levels.”

Using the scrambling technique, researchers say they will be able to more quickly develop synthetic strains of yeast that could be used in the manufacture of rare medicines, such as artemisinin for malaria, or in the production of certain vaccines, including the vaccine for hepatitis B, which is derived from yeast. Synthetic yeast, they say, could also be used to bolster development of more efficient biofuels, such as alcohol, butanol, and biodiesel.

The study will also likely spur laboratory investigations into specific gene function and interactions between genes, adds Dr. Boeke, in an effort to understand how whole networks of genes specify individual biological behaviors.

Their initial success rebuilding a functioning chromosome will likely lead to the construction of other yeast chromosomes (yeast has a total of 16 chromosomes, compared to humans’ 23 pairs), and move genetic research one step closer to constructing the organism’s entire functioning genome, says Dr. Boeke.

Dr. Boeke says the international team’s next steps involve synthesizing larger yeast chromosomes, faster and cheaper. His team, with further support from Build a Genome students, is already working on assembling base pairs in chunks of more than 10,000 base pairs. They also plan studies of synIII where they scramble the chromosome, removing, duplicating, or changing gene order.

Detailing the Landmark Research Process

Before testing the scrambling technique, researchers first assessed synIII’s reproductive fitness,  comparing its growth and viability in its unscrambled from  — from a single cell to a colony of many cells — with that of native yeast III. Yeast proliferation was gauged under 19 different environmental conditions, including changes in temperature, acidity, and hydrogen peroxide, a DNA-damaging chemical. Growth rates remained the same for all but one condition.

Further tests of unscrambled synIII, involving some 30 different colonies after 125 cell divisions, showed that its genetic structure remained intact as it reproduced. According to Dr. Boeke, individual chromosome loss of one in a million cell divisions is normal as cells divide. Chromosome loss rates for synIII were only marginally higher than for native yeast III.

To test the scrambling technique, researchers successfully converted a non-mating cell with synIII to a cell that could mate by eliminating the gene that prevented it from mating.

Funding support for these experiments was provided by National Science Foundation, the National Institutes of Health, and Microsoft. Corresponding federal grant numbers are MCB-0718846 and GM-077291. Additional funding support was provided by fellowships from La Fondation pour la Recherche Médicale, Pasteur-Roux, National Sciences and Engineering Research Council of Canada, U.S. Department of Energy, and grants from the Exploratory Research Grant from the Maryland Stem Cell Research Fund and the Johns Hopkins University Applied Physics Laboratory.

Besides the teams at NYU Langone and Johns Hopkins, other scientific teams involved in the global Sc2.0 research effort are based at Loyola University in Baltimore, Md; BGI in Shenzhen, China; Tianjin University in China; Tsinghua University in China; MacQuarie University in Sydney, Australia; the Australian Wine Institute in Adelaide, Australia; the National University of Singapore; Imperial College, London, England; and the University of Edinburgh in Scotland.

£1 Million from BBSRC and EPSRC for Synthetic Yeast

David Willetts, Minister for Universities and Science, announced nearly £1M funding for synthetic yeast at the Sixth International Meeting on Synthetic Biology (SB6.0) at Imperial College London on Thursday (July 11). David Willetts said: Sc2.0 project “is truly groundbreaking and pushes the boundaries of synthetic biology. Thanks to this investment, UK scientists will be at the centre of an international effort using yeast – which gives us everything from beer to biofuels – to provide new research techniques and unparalleled insights into genetics. This will impact important industrial sectors like life sciences and agriculture.” Funding for the yeast project is part of a £60M package for synthetic biology.

Dr.Tom Ellis, Lecturer in Synthetic Biology at Imperial College London, said: “We are excited to be welcoming our new international consortium partners to London to discuss Sc2.0. Having recently secured funding for the UK to be part of this ground-breaking project, we are looking forward to getting started and being part of the action. It’s a perfect fit for our work in synthetic biology here at Imperial, where we really view yeast as a tiny factory that can be tooled-up to produce new molecules. A synthetic genome will allow us to reprogram yeast and our goal is to use it to produce new antibiotics as resistance arises to existing ones.”

When completed, synthetic yeast will be the first time scientists have built the whole genome of a eukaryotic organism – those organisms, like animals and plants, which store DNA within a nucleus. Scientists can then design different strains of synthetic yeast that contain genes to make commercially valuable products such as chemicals, vaccines or biofuels.

Professor Boeke, the overall head of the project at Johns Hopkins Medical School in Baltimore, said: “Sc2.0, once completed, will provide unparalleled opportunities for asking profound questions about biology in new and interesting ways, such as: How much genome scrambling generates a new species? How many genes can we delete from the genome and still have a healthy yeast? And how can an organism adapt its gene networks to cope with the loss of an important gene? Moreover, genome scrambling may find many uses in biotechnology, for example in the development of yeast that can tolerate higher ethanol levels.”

Alongside BBSRC and EPSRC, major funders for the Sc2.0 consortium members in their respective countries include the US National Science Foundation (NSF), the US Department of Energy, China’s Ministry of Science and Technology (MoST) and the Tsinghua University Initiative Scientific Research Program.

More related news:

http://www.guardian.co.uk/science/2013/jul/11/uk-project-synthetic-organism
http://www.epsrc.ac.uk/newsevents/news/2013/Pages/syntheticbiologyprogress.aspx
http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_10-7-2013-12-14-56
http://www.bbsrc.ac.uk/news/research-technologies/2013/130711-pr-funding-to-build-worldfirst-synthetic-yeast.aspx
https://www.gov.uk/government/news/over-60-million-for-synthetic-biology

2nd International Synthetic Yeast Genome (Sc2.0) Consortium Meeting, London, UK, July 12, 2013

We are pleased to announce that this summer on Friday 12th July, we will be hosting the 2nd International Synthetic Yeast Genome (Sc2.0) Consortium Meeting here in the UK at Imperial College London. This day-long meeting is now open for registration.  Notably it will be held the day after the SB6.0 meeting, so it will be easy to attend both.

The Synthetic Yeast Genome Project (Sc2.0) is synthesizing and constructing a modified version of the S. 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 S. cerevisiae genome and opportunities to use the strains and tools of the project. 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://syntheticyeast.eventbrite.com/

Rumor has it microbrew beer samples will be available – as it should be for a yeast meeting. See you in London?

Collaboration with Dalton School – high school science students

Over 150 students have participated in the Build-A-Genome course at Johns Hopkins University since its inception 5 years ago. This hands-on experience with the Sc2.0 project allows participants, including high school students, undergraduates, and faculty members, to gain extensive experience in the fields of synthetic and molecular biology and demonstrates the unique didactic potential of Sc2.0. This year we extended our effort in this arena and engaged in a formal collaboration with the Dalton School, a private high school in Manhattan. Working with Dr. Jennifer Hackett, a former PhD student at Johns Hopkins University and now teacher at Dalton, 9 talented grade ten biology students built 80 Cre-EBD constructs that will be used to activate SCRaMbLE, the inducible evolution system encoded by the Sc2.0 genome. The students assembled these constructs using ‘yeast Golden Gate’ (yGG), our standardized assembly method that enables fast and efficient construction of S. cerevisiae transcription units. Importantly, the students transformed these constructs into a yeast strain encoding a synthetic chromosome and subsequently induced SCRaMbLE; these students are now some of the only people in the world who have inducibly evolved a synthetic yeast chromosome.

Dr. Jenny Hackett (right) and eight of her students. Pictured behind are data from a SCRaMbLe induction experiment.

The First International Coordination Meeting on the Synthetic Yeast Project to Propel Synthetic Biology Forward

The first international meeting on Synthetic Yeast Genome, Sc2.0 project participants:

Funders: NSF (USA); MoST (China); NSFC (China); BBSRC (UK); Council of Scientific and Industrial Research (India); Hong Kong Research Grants Council

Academia: Johns Hopkins University (USA); BGI, Tianjin University, Tsinghua University (China); Imperial College London, The University of Edinburgh (UK); Institute of Genomics and Integrative Biology, Pondicherry University (India); Hong Kong University, Hong Kong University of Science and Technology, Chinese University of Hong Kong (Hong Kong); Institut Pasteur (France); Catholic U Louvain la Neuve (Belgium)

April 17, 2012, China  – The international coordination meeting on the synthetic yeast project (Sc2.0 PROJECT), co-organized by Johns Hopkins University (JHU), BGI and Tsinghua University with the support of National Science Foundation (NSF), was held at the Wenjin Hotel, Beijing, China. This was the first international research coordination meeting on the synthetic yeast project aiming to develop new technological strategies and effective approaches to promote further research on this project as well as to boost the development of synthetic biology.

The meeting was attended by over 40 officials and experts from governments, outstanding scientific research institutes and colleges, including Ministry of Science and Technology, China, The National Science Foundation of China, The National Science Foundation (NSF), U.S.A., Biotechnology and Biological Sciences Research Council (BBSRC), United Kingdom, Council of Scientific and Industrial Research, India, Tianjin University, China, Hong Kong University, China, among others. At this meeting, Johns Hopkins University and The Centre for Synthetic Biology and Innovation (CSynBI) at Imperial College London signed a collaborative research agreement for their role in the Sc2.0 PROJECT. Imperial College will initiate the complete synthesis of yeast chromosome 11, bringing genome-scale synthetic biology to the UK for the first time.

Synthetic biology is a new emerging discipline, which is motivated by advances in molecular cell sciences, systems biology and the advent of two foundational technologies, DNA sequencing and DNA synthesis. The purpose of synthetic biology is to design synthetic biological systems by utilizing systematically engineered micro-organisms for the production of biofuels and drugs, providing a unique opportunity for researchers to study many profound life science questions and generate vital industrial applications.

The Sc2.0 PROJECT, initiated by Johns Hopkins University School of Medicine, is the first synthetic eukaryotic cell genome project. As one of the principal investigators of the project, Dr. Jef Boeke, Director of the High Throughput Biology Center, Johns Hopkins University School of Medicine, delivered a detailed presentation on the overview of the project and its profound impact in the field of synthetic biology. He said, “This meeting provides an opportunity for further boosting the research and applications of the Sc2.0 PROJECT. With the achievements of this project, I believe that we can seek much better solutions to face the challenges of the future, such as world energy shortage.”

After that, experts in different organizations, combining experimental studies with the prospective for synthetic biology, gave excellent presentations and participated in active discussions. Professor Guanhua Xu, Chairman of Advisory Group on The Fifth Major Project of Chinese National Programs for Fundamental Research and Development (973 Program), stated, “The accomplishment of Sc2.0 project will serve as a landmark for important milestones in the development of synthetic biology.”

Professor Huanming Yang, Chairman of BGI, said, “The rapid development of high-throughput sequencing technologies have led to a revolution in OMIC-related areas, which also greatly facilitates the studies on synthetic biology. With solidarity and international cooperation, I believe we will be able to explore more opportunities for valuable research in human disease and biomedical areas.”

Build-A-Genome course goes global!

Our popular undergraduate course — Build A Genome (BAG) just opens its 2012 spring session. We welcome 15 students from Johns Hopkins University, 22 students from Loyola University Maryland, and 2 Chinese scholars who traveled across the world from Tianjin University. Dr. Wenzheng Zhang and Wei Liu, representing Dr. Yingjin Yuan of the Department of Chemical Engineering, will be taking the course at JHU and then will return to Tianjin University to set up and help teach “Build-A-Genome China” in the fall of 2012. It is hoped that Build-A-Genome China will become a part of the regular curriculum for Chemical Engineering students, all of whom will there by be directly contributing to the International Sc2.0 project.  This will be the first international appearance of the Build-A-Genome course, facilitated by a web-enabled international database portal to the BioStudio / Build-A-Genome Database, developed by Dr. Giovanni Stracquadanio of JHU.

The new development of Build A Genome is an important component of a recent collaboration agreement on Synthetic Biology research and education between Johns Hopkins University and Tianjin University. Vice Provost for International Programs Pamela Cranston signed the agreement on behalf of Johns Hopkins University together with the President of Tianjin University, Dr. Jiajun Li in November, 2011.

Johns Hopkins’ Man-Made Yeast Go Global

Released: 12/5/2011 9:55 PM EST
Source: Johns Hopkins Medicine

Researchers at the Johns Hopkins University School of Medicine who recently reported the design and creation of a man-made yeast chromosome have now signed on some international collaborators at BGI, a genomics company headquartered in Beijing, China. The newly formed relationship brings together the Johns Hopkins project with some of the world’s experts in so-called next generation genome sequencing in an effort to speed the understanding of how genomes are built and organized and how they function.

“Next generation sequencing plays a key role in synthetic genomics, enabling large-scale processing with lower costs and higher efficiency,” says Jef Boeke, Ph.D., professor of molecular biology and genetics and director of the Johns Hopkins Institute for Basic Biomedical Science’s High Throughput Biology Center. “With BGI’s expertise in genome sequencing and bioinformatics,

we are confident we can make very rapid progress in the SC2.0 PROJECT to facilitate further studies of how synthetic genomes evolve.”

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BGI Announces Collaboration with Johns Hopkins University on Synthetic Yeast Project to Accelerate the Development of Synthetic Biology

November 14th, 2011, Shenzhen, China – BGI the world’s largest genomic organization and Johns Hopkins University (JHU), today signed a collaborative research agreement for the synthetic yeast project (SC2.0 PROJECT), an ambitious synthetic biology project which seeks to re-design and synthesize the yeast genome. This project was initiated by JHU and serves as part of JHU’s synthetic biology program.

In addition to the research collaboration of SC2.0 PROJECT, BGI’s researchers will have the opportunity to access the synthetic biology expertise of JHU. They can attend for internship the undergraduate course, “Build-A-Genome,” associated with the project at JHU. During the course, they can perform synthesis of segments of the synthetic yeast genome by themselves.

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“Synthetic” chromosome permits rapid, on-demand “evolution” of yeast

In the quest to understand genomes—how they’re built, how they’re organized and what makes them work—a team of Johns Hopkins researchers has engineered from scratch a computer-designed yeast chromosome and incorporated into their creation a new system that lets scientists intentionally rearrange the yeast’s genetic material. A report of their work appears September 14 as an Advance Online Publication in the journal Nature.

“We have created a research tool that not only lets us learn more about yeast biology and genome biology, but also holds out the possibility of someday designing genomes for specific purposes, like making new vaccines or medications,” says Jef D. Boeke, Ph.D., Sc.D., professor of molecular biology and genetics, and director of the High Throughput Biology Center at the Johns Hopkins University School of Medicine.

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