Posts in category Synthetic Biology & Bioenergy

New Method for Genome-wide Engineering of Viruses

Researchers at JCVI have been developing synthetic genomics assembly methods since 2000, addressing fundamental biological questions. Together, with researchers at Oregon Health and Science University, Johns Hopkins University School of Medicine, Synthetic Genomics, Inc., and Vir Biotechnology, Inc. (formerly TomegaVax, Inc.), the team has made another major advance in this field.

Building upon past advancements, a protocol has been developed whereby we are able to engineer genome variants of large DNA viruses by breaking the original genome up into smaller, overlapping pieces, that can then be independently modified, and then reassembled back into full-length virus genomes.

This allows for quick assembly of genome variants that can be used to understand the function of genes and gene combinations in viruses. Previous genetic systems for large DNA viruses, such as herpesviruses and poxviruses, required you to make one change at a time, making the new system significantly more efficient.

In our study, we used herpes simplex virus type 1 (HSV-1) and human cytomegalovirus (HCMV), both members of the herpesvirus family. Herpesviruses can cause a range of diseases and symptoms, including cold sores, congenital birth defects, and cancer.

Fluorescence microscopy shows an HSV-1 genome engineered to express a fusion of viral protein VP16 and fluorescent protein Cerulean. Image by Peter Grzesik with assistance from The Johns Hopkins University Integrated Imaging Center.

Herpesviruses have extremely large genomes. HCMV is about 230,000 base pairs, the largest genome of any virus known to infect humans, and carries over 100 genes. Many of the functions of these genes are not yet known. We believe that our system will allow for a combinatorial approach to herpesvirus genetics that was not possible previously.

Rapid engineering of herpesviruses could also lead to new therapeutics and vaccines. For most herpesviruses, there are no effective vaccines. Improved genetics may allow us to rationally design and attenuate the virus, which would lead directly to vaccine strains.

Herpesviruses could be developed as delivery systems for gene therapy. Herpesviruses could also be developed to treat cancer as oncolytic viruses, which are viruses that attack cancer cells. An HSV-1-based oncolytic virus has already been approved by the FDA to treat melanoma and rapid engineering strategies could help generate oncolytic viruses to treat other cancers.

We believe this method to assemble and engineer virus genomes will be applicable to many different viruses and help expand our understanding of the basic biology of other viruses that are difficult to work with currently.

You can read more about this in the two original papers, and a just published commentary.

Genome-wide engineering of an infectious clone of herpes simplex virus type 1 using synthetic genomics assembly methods

Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination

Commentary: Synthetic genome engineering gets infectious

JCVI Launches New Internship Partnership with Smithsonian Science Education Center

Are you passionate about science education? If so, we have a unique hands-on opportunity for you to be a part of real teams of scientists and educators. This opportunity doesn’t require any previous lab experience, and is open to undergraduate and graduate students in the United States.

The internship will be split between the J. Craig Venter Institute (JCVI) and the Smithsonian Science Education Center (SSEC). At JCVI you will participate in cutting-edge research. This will dovetail into curriculum enhancement previously developed at the SSEC, which aligns with the U.N.’s Global Sustainability Development Goals (SDGs).

This is an excellent opportunity for both science majors who may be interested in pursuing a path in education, and for education majors looking to gain valuable experience in a professional laboratory.

Space-fill drawing of the outside of one Zika virus particle, and a cross-section through another as it interacts with a cell. Image courtesy David Goodsell.

What will do you?

At the JCVI, you will work on a part of a larger project geared towards the development of rapid tests for virus genes that suppress host antiviral defenses. The project, which will focus on the mosquito-borne Zika Virus Disease, will use synthetic biology techniques to help scientists identify virulent strains.

At the SSEC, you will work with curriculum developers and experts in the field of global science education to support the development and rollout of the SSEC’s curriculum module “Zika!,” which helps students understand mosquito-borne diseases through inquiry-based science education methods.

The outcomes of this internship will lead to not only a better understanding of current research being done in the field, but will also result in the development of effective ways to communicate scientific research to the public.

Apply on our website today!

June Grant Update

Congratulations to our JCVI Principal Investigators for the several successful grants that were awarded or that we received notification of in the month of June. All of the following PIs received official confirmation of awards to be made to them. Christopher Dupont, John Glass, Granger Sutton, Daniel Gibson, Charles Merryman, Rembert Pieper, Richard Scheuermann, Christopher Town, Reed Shabman, Orianna Bretschger, Sanjay Vashee and Sarah Highlander to the sum of $6,365,099. The topics of these awards ranged from synthetic approaches to studying the human microbiome, vaccine development, protein modeling, studies on tuberculosis strain diversity, and immune profiling.

Of notable mention are the awards to be made to Sanjay Vashee $1,879,282 from the NSF (BREAD supplement that will allow for an extension of the current program focused on developing a synthetic vaccine for Bovine pleuropneumonia), Reed Shabman from DHS ($1,135,654; The development and validation of sequence subtraction databases to improve virus discovery through next generation sequencing – special acknowledgement to Tim Stockwell and Derek Harkins for their contributions to this proposal), and to Chris Town from NSF ($883,704; Federated Plant Data Base Initiative for Legumes).

A sincere Congratulations to the team.

JCVI Scientists Join NASA-Funded Astrobiology Research Teams

Scientists from J. Craig Venter Institute are part of teams awarded grants from NASA to “study the origins, evolution, distribution, and future life in the universe.” Dr. Christopher Dupont is part of a team led by the University of California, Riverside and will study chemical energy stored in rocks as a potential power source, while Dr. Shino Ishii will work with a team from NASA’s Jet Propulsion Laboratory looking at the habitability of extraterrestrial icy worlds.

Artist concept of an early Earth

Artist concept of an early Earth. Image Credit: NASA

From NASA’s Press Release:

NASA’s Jet Propulsion Laboratory, Pasadena, California. Team lead is Isik Kanik. Research will conduct laboratory experiments and field research in environments on Earth, such as The Cedars in Northern California, to understand the habitability of extraterrestrial icy worlds such as Europa, Ganymede and Enceladus.

University of California, Riverside. Team lead is Timothy Lyons. Research will examine the history of oxygen in Earth’s atmosphere and ocean between 3.2 and 0.7 billion years ago. This is a time range in which the amount of oxygen present is thought to have increased from almost nothing to the amounts present today. This work will address the question of how Earth has remained persistently inhabited through most of its dynamic history and would provide NASA exploration scientists a template to investigate the presence of habitable conditions on Mars and other planetary bodies.

See the complete release.

The 2014 Summer Internship Application is Open and Announcing the Genomics Scholar Program

The 2014 Summer Internship Application is now open.   Last summer, we hosted 49 interns from a pool of 424 applicants. They presented their research in the First Annual Summer Internship Poster Sessions held in San Diego and Rockville. The posters were judged by a team of volunteer JCVI scientists and the poster sessions were open to all employees, interns and their guests to share what great work they all participated in this summer.

 

 

2013 Intern Poster Session

2013 Intern Poster Session

We are also excited to announce the new Genomics Scholar Program beginning this summer and also accepting applications.  The Genomic Scholar Program (GSP) is a targeted research experience program to community college students in Rockville. Our program incorporates multiple avenues of support for students through the research experience with the Principal Investigators as mentors, and supplemental professional development provided by the JCVI.  Additionally, selected students will have the opportunity to participate in undergraduate research conferences.

The GSP is supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health under award number R25DK098111.

NASA and JCVI host symposium on the evolution of Earth and Life

On May 12th and 13th, the J. Craig Venter Institute in San Diego will be hosting a NASA Astrobiology Institute-funded symposium titled “Paleobiology in the genomics era.” Paleobiology is the study of the origins and evolution of life and, by nature, is interdisciplinary. The goal is to bring together scientists united by this common interest but differentiated by expertise.  A major intellectual challenge to paleobiology is the close interaction between environment and life.  As life evolved, it changed the environment and suffered the consequences.  One of the most extreme examples is the invention of oxygenic photosynthesis by blue-green algae cyanobacteria; the sunlight-fueled production of dramatically changed the availability of crucial elements of life, like nitrogen, sulfur, iron, zinc, copper, and other trace metals.  Genome-based analyses showed that these environmental changes modulated the emergence of metal-requiring proteins.  For example, proteins that bind Fe evolved when the earth was Fe rich. Essentially, one biological event changed the environment, which in turn induced a subsequent biological change; a feedback cycle between biota and planet.

In order to study these interactions in a robust fashion, numerous lines of evidence must be integrated, despite originating from disparate fields like organic and inorganic geochemistry (oils and metals in rocks), micropaleontology (tiny fossils), and evolutionary biology.  Recent years have observed the emergence and maturation of synthetic biology and computational biology, two fields with tremendous potential for the formulation and testing of hypotheses about the evolution of life. To facilitate a dialog between these fields, myself, along with Ariel Anbar from Arizona State University, and John Peters and Eric Boyd from Montana State University, have invited experts to present their work as it pertains to paleobiology.  The topic list almost appears schizophrenic, with numerous hard-core geochemical talks being followed presentations on molecular genetics, synthetic biology, metagenomics, and comparative genomics.   This was intentional. I hope to feel intellectually challenged in the fashion of a 1st year graduate student and further hope that I’m not the only one.  A major wild card at the moment is the identity of over 2/3rd of the attendees.  With travel grants available for graduate students, post-doctoral researchers, and faculty, we hope to incorporate novel perspectives not covered by the confirmed speakers.

While the content of the meeting is exciting, the format is pretty sweet too. As part of NASA’s Workshop Without Walls series, the meeting will be webcast live with an accompanying live stream chat.  Thus, people will be able to see the presentations and pose questions and comments during the attendant discussions.  Previous workshops have often had hundreds of live viewers throughout the meeting, despite only dozens of in situ attendees.   The actual energy savings for a single meeting are modest in isolation; imagine 250 people not flying 500 miles and you basically have a single 737 flight that remains grounded.  However, the future of environmentally-friendly science requires important preliminary steps to change dominant trends.  Similarly, the talks will be streamed live without charge and deposited in the open access scientific podcast site, Scivee.tv; economic barriers to information exchange are removed.

Needless to say, I’m looking forward to this meeting. Organizing something like this is an absolute undertaking. The number of details that need attention is astounding.  And if you think I actually could do that, you don’t know me.  Numerous people at JCVI have provided invaluable assistance, including Matt LaPointe and Jasmine Pollard, Robert Friedman, Dave Negrotto, and Jody Wilson.  It would also have no chance of happening if it not for Pat Goley, who has handed the numerous (re: uncountable) details I’ve lapsed on.

Check out the NASA page for the meeting and webcast registration.

http://astrobiology.nasa.gov/nai/geobiology2011

A Look Back at 2010 at the JCVI…

As the J. Craig Venter Institute (JCVI) soars into its 19th year, we reflect on the past year of highlights and accomplishments to mark the close 2010 and look forward to more significant scientific advances in 2011.

JCVI Top 10 of 2010 …

1. First Synthetic Cell: Fifteen years in the making, 2010 brought to bear with huge anticipation the successful construction of the first self-replicating, synthetic bacterial cell. The work was published in Science in May. The synthetic cell called Mycoplasma mycoides JCVI-syn1.0 is the proof of principle that genomes can be designed in the computer, chemically made in the laboratory and transplanted into a recipient cell to produce a new self-replicating cell controlled only by an artificial genome. Although the first synthetic cell was not designed to produce a specific bioproduct, the team has shown that this can be done and the potential benefits are numerous. The research team, lead by JCVI President Craig Venter, Hamilton Smith, Clyde Hutchison, and Daniel Gibson, envision a future where the rapid design and production of biological products using synthetic biology techniques will be used to produce clean fuels, medicines, and other bioproducts. Throughout the course of this work, the JCVI Policy group has extensively engaged in outside review of the ethical and societal implications of this work, including advising the new Presidential Commission on Bioethics on their recommendations for oversight.

M. mycoides JCVI-syn1

M. mycoides JCVI-syn1

2. Synthetic Vaccines: Following on the heels of the announcement of the first synthetic cell, the company Synthetic Genomics Inc. and JCVI announced in October the formation of a new company, Synthetic Genomics Vaccines Inc. (SGVI). The privately held company is focused on developing next generation vaccines that can be rapidly produced and tested, which is especially important for outbreaks of new infectious diseases. SGVI also announced a three-year collaboration with Novartis to apply synthetic genomics technologies to accelerate the production of the influenza (flu) seed strains required for vaccine manufacturing. The seed strain is the starter culture of a virus, and is the base from which larger quantities of the vaccine virus can be grown. Under this collaboration, Novartis and SGVI will work to develop a “bank” of synthetically constructed seed viruses ready to go into production as soon as WHO makes recommendations on the flu strains. The technology could reduce vaccine production time by up to two months, which is particularly critical in the event of a pandemic.

3. Hydra Genome – one of the animal kingdom’s earliest common ancestors: JCVI scientists along with more than 70 other researchers from around the world, have sequenced and analyzed the genome of Hydra magnipapillata, a fresh water member of the cnidaria– stinging animals that include jellyfish, sea anemones and corals. The research, published in the March 14 edition of Nature, was co-led by Ewen F. Kirkness, JCVI, Jarrod A. Chapman, Department of Energy Joint Genome Institute, and Oleg Simakov, University of California, Berkeley. This is the second sequenced cnidarian genome, following that of a sea anemone, Nematostella vectensis, in 2007. The ancestors of these two species diverged more than 500 million years ago, and comparison of their genomes has revealed common features of the earliest animals that gave rise to the diversity of animals on Earth today. The team found clear evidence for conserved genome structure between the Hydra and other animals, like humans. Unexpectedly, the sequencing also revealed a novel bacterium that lives in close association with the Hydra.

4. Uncovering the Human Microbiome: Microbes are living within and on the human body and this collective community is called the human microbiome. JCVI Scientists, as one component of the large scale NIH Roadmap Human Microbiome Project, and along with colleagues at three other genome centers sequenced the genomes of ~180 microbes from the human body, published in the May 21 edition of Science. At the JCVI we anticipate sequencing an additional 400 species over the next few months. Colleagues at the JCVI are also using single cell approaches to isolate new strains that have not been cultured – isolates whose genomes will also be completely sequenced. The role these microbes play in human health and disease is still relatively unknown and these approaches are allowing us to gain a greater understanding of these enigmatic species.

5. Body Louse Genome: A global research team led by Ewen Kirkness and colleagues from JCVI published a study in the Proceedings of the National Academy of Sciences in June describing the sequencing and analysis of the human body louse, Pediculus humanus humanus, a human parasite responsible for the transmission of bacteria that cause epidemic typhus, relapsing fever and trench fever. Detailed analysis of the genome was then conducted by a large international group of 71 scientists, coordinated by Barry Pittendrigh, University of Illinois, and Professor Evgeny Zdobnov, University of Geneva Medical School. Comparative studies of the body louse genome with other species revealed features that will enhance our understanding of the relationships between disease-vector insects, the pathogens they transmit, and the human hosts. In addition to the targeted louse genome, the project unexpectedly yielded the complete genome sequence of a bacterial species, Riesia, that lives in close association with lice, and which is essential for survival of the insects. The researchers believe that the genome will be a valuable reference for evolutionary studies of insect species, especially in the areas related to insect growth and development.

6. Castor Bean Genome Sequencing: A research team co-led by Agnes P. Chan and colleagues from JCVI and Jonathan Crabtree and others at the Institute for Genome Sciences, University of Maryland School of Medicine, published the sequence and analysis of the castor bean (Ricinus communis) genome in Nature Biotechnology in August. Because of the potential use of castor bean as a biofuel and its production of the potent toxin ricin, the team focused efforts on analysis of genes related to oil and ricin production. The analyses could be important for comparative studies with other oilseed crops, and could also allow for genetic engineering of castor bean to produce oil without ricin. Identifying and understanding the ricin–producing gene family in castor bean will be important in preventing and dealing with potential bioterrorism events. Genomics enables enhanced diagnostic and forensic methods for the detection of ricin and precise identification of strains and geographical origins. As a next step, the group suggests further comparative genomic studies with the close relative cassava, a major crop in the developing world, to further elucidate their disease resistance aspects.

7. Science Education: JCVI was an Official Partner of the inaugural USA Science and Engineering Festival held on the National Mall in Washington, DC in October. The Festival, which was the country’s first national science festival, included over 500 of the country’s leading science and engineering organizations with the aim to reignite the interest of our nation’s youth in the sciences. The JCVI ‘Discover Genomes’ Bus was showcased during a two-day expo and some of the research being done at JCVI was presented to around 1700 visitors by our scientists and staff.

There were lines all day!

8. Viral Genomics– In 2010 the JCVI has published over 1600 influenza genomes and over 75% of all published flu genomes to date have been sequenced by the JCVI, totaling over 6000 genomes. This year the diversity of viral genomes we have sequenced has significantly expanded under the NIH Genomic Sequencing Center for Infectious Diseases contract. Some of the projects include viruses causing diseases such as measles, mumps, rubella, encephalitis, SARS, and the common cold, just to name a few. The viral group has annotated and published 79 Rotavirus (stomach flu) and 33 Coronavirus genomes (includes SARS and common cold) this year and many more will be published in 2011. The pace of sequencing and finishing genomes has also increased this year as a result of adoption of nextgen platforms (e.g. Illumina/454 and Illumina/Solexa) and the development of more efficient methodologies to increase productivity while reducing costs.

9. Marine Microbial Genome Sequencing Project: JCVI scientists have continued their quest to isolate and sequencing microbes living in global ocean waters to discover new genes and enzymes, and to help understand the role microbes play in the ocean ecosystem. Shibu Yooseph, Kenneth Nealson and colleagues at JCVI published an analysis of 137 known marine microbial genomes living in the global ocean surface in Nature in November. These genomes were compared to metagenomic samples of ocean waters of 10.97 million sequences of JCVI’s Sorcerer II Global Ocean Sampling (GOS) metagenomic data and thousands of 16S rRNA sequences. The marine genomes were collected as part of the Gordon and Betty Moore Foundation-funded Marine Microbial Genome Sequencing Project, a project coordinated by JCVI that has a primary goal of obtaining whole genome sequences of ecologically important microbes from a variety of diverse, global marine environments. The work provides a good example of combining metagenomic data with sequenced genomes data to study microbial communities and to generate testable hypotheses in microbial ecology.

10. Sorcerer II Global Ocean Sampling Expedition: On December 17th 2010 Sorcerer II arrived in Florida after spending the last two years with her crew collecting samples in The Baltic, Mediterranean and Black Seas. Funded generously by the Beyster Family Foundation Fund, The San Diego Foundation, and Life Technologies Foundation, Sorcerer II has sailed ~28,000 nautical miles since departing San Diego in March 2009. During this time 212 samples were collected and over 5,100 liters of sea water was filtered and sent to JCVI for analysis of the microbial life contained within these samples. The JCVI established strong collaborations with scientists in all 16 countries in which samples were collected, which will lead to joint publications and future collaborative studies in the new year. Read more.

Sunrise in the Ligurian Sea

Looking Forward to 2011…

Ten-year anniversary of the Human Genome Project: To commemorate the anniversary of the publications of the first human genome sequences in 2001, JCVI and Nature are hosting a conference and celebration in February 2011 titled – Human Genomics: The Next 10 Years. The conference will look forward to the promises of human genomics for the next 10 years, with sessions on medical advances related to genomics; the technological and ethical challenges of human genomics; personalized and familial genomics; the human microbiome project; variation in the human genome; and making sense of the genetic code. This conference will be a great way to jump into the new year and inspire the grandiose ideas and achievements that genomic scientists will accomplish over the years to come.

Scientist Spotlight: Hamilton O. Smith and Clyde A. Hutchison III

Two of the superstars of science at the helm of the effort to make a synthetic cell (a cell with a completely man-made set of genetic instructions) are Hamilton Smith and Clyde Hutchison, or Ham and Clyde as they are affectionately known to colleagues. Since 2003 when they started working together here at JCVI one rarely hears about one without the other – always together and cracking jokes amidst discussing the complexities that define their ultimate quest: To understand, “What is Life?” I like to think of them as the Abbott and Costello or Laurel and Hardy of science. A colleague said they reminded him of Statler and Waldorf – the muppet men on the balcony heckling the other characters –although Ham and Clyde are neither ornery nor disagreeable but their subtle banter with each other is hilarious. They play off each other perfectly and I had the pleasure of interviewing them for a more personal piece to coincide with the landmark announcement of their trailblazing work to make first living synthetic cell.

Hamilton Smith and Clyde Hutchison III

Hamilton Smith and Clyde Hutchison III

So I was to begin the interview diligently with a list of well thought out and leading questions that fed nicely into the next. Those quickly went out the window when Ham and Clyde walked into the room (them in San Diego and me in Rockville over a videoconference). “I cleaned the stain off my cuff!” declared Clyde holding up his sleeve, and “we wore our good suit jackets,” thinking I would be interviewing them in person. “Will this be recorded by video?” “No, no audio or video” I replied, “so you can say anything you’d like to and I’ll capture what I can with my pen.” They started talking before I could pose a question and I settled back for a hugely enlightening hour of landmark scientific achievements and hilarious stories. The Early Years Ham grew up primarily in New York and Illinois with a family who valued education and encouraged his interests in science and medicine. His father was a professor of education and his mother an aspiring writer. Ham was a mathematics major at the University of Illinois with an interest in neurophysiology, and attended medical school at Johns Hopkins University where he later would spend the majority of his career doing research. In 1978 he won the Nobel Prize in Physiology or Medicine for his work on restriction endonucleases (enzymes made by bacteria that cut DNA in specific places; the isolation of these enzymes provided a vital tool for molecular biology research). When asked how the Nobel had affected him Ham said modestly, “Getting the Nobel was a nice thing. I became nervous about how I should behave. I always looked up to Nobel Laureates but didn’t’ feel like I was one of them.” One of the perks he said was that he could “apply for any grant and get it!” Ham lamented that “Clyde should have gotten the prize in 1993 with Michael Smith” for their work on site directed mutagenesis. But Clyde is not the kinda guy who promotes himself like you need to for things like this,” said Ham. Clyde hastily added, almost interrupting him, “Ham isn’t the type either but he had good promoters.” But apparently his parents weren’t one of them! Clyde relayed a story about how Ham’s parents found out about the prize when they were listening to a radio show and heard the announcement that Hamilton Smith from Johns Hopkins received the Nobel Prize. His mother turned to his father and said, “I didn’t know there were two Hamilton Smiths at Johns Hopkins!” Ham slightly corrected Clyde’s story and said it was more like, Do you suppose there is another Hamilton Smith at JHU?” Modesty and humility are in his genes. Clyde also had a very supportive family who nurtured his interest in science at a young age. His father was a chemist and physicist. “A chemical physicist” said Clyde, “rather than a physical chemist.” Being a physical scientist his father looked down on biology as “messy business.” Although Clyde was a physics undergrad at Yale he eventually ended up in biology and joked that, “It allowed me to do science but rebel against my father.” Most kids rebel by getting tattoos or ditching school, but apparently Clyde wasn’t like most kids. Clyde’s entry into biology was serendipitous. He was on a scholarship at Yale and in order to maintain it he had to have a part time job. The first year everyone was put in the dining hall, but the 2nd year he lined up a job with an astrophysicist involved in radiotelescopes. By the time Clyde returned to school from summer break the professor gave the job to someone else. Clyde pleaded with school administrators for a science job and got into the Biophysics department working with then postdoc Carl Woese who discovered the 3rd branch of life- Archaea- and that piqued Clyde’s interest in biology. Clyde later moved to North Carolina and spent over 37 years at the University of North Carolina, Chapel Hill building an illustrious research career. How They Met In 1973 Ham and Clyde were both independently invited to a conference on restriction enzymes in Belgium and stayed in a monastery. “We don’t really remember meeting each other,” said Ham but he distinctively remembers the communal bathroom (back then a novelty). It wasn’t until 20 years later that the two made a real connection. Craig Venter and Ham met in Bilbao, Spain in 1993 at a meeting. Craig gave a presentation on his Expressed Sequence Tag (EST) work at NIH. Ham said they met in the hotel bar and from that time on they liked each other as their science interests were similar. Craig soon afterward asked Ham to be on the Scientific Advisory Council for TIGR (The Institute for Genomic Research). “I saw the sequencing lab and that instantly convinced me” said Ham. “The biggest I’d ever seen! I was impressed by [the technology] he had.” Around 1994 Ham called Clyde to collaborate on a sequencing project. Craig, Ham and the team at TIGR had just sequenced the first bacterial genome, Haemophilus Influenzae. Ham noticed Clyde’s work on Mycoplasma genitalium and since it’s the smallest known bacterial genome he thought it would be a good candidate for their next sequencing project. That simple project would eventually turn into the quest to create a synthetic cell. Ham said that “synthetic genomes were discussed” by he, Clyde, and Craig starting around 1996. Then, with a wink, Ham said that he “made an offer Clyde couldn’t refuse” and they collaborated to sequence M. genitalium. Clyde split his time between TIGR and UNC, while Ham and Craig slowly wooed him into joining full time in 2003. After sequencing the M. genitalium genome (published in 1995), they began work on the “minimal genome project.” The goal of this project was to see how many genes are necessary to sustain life, and in this case they studied the genes essential for the growth of M. genitalium because it is a bacterium with the smallest genome known. This work was published in the journal Science in 1999. At the same time a group of bioethicists from the University of Pennsylvania published the results of their ethical review of this work. By July 1998 Ham retired from JHU to work full time at TIGR. He was there only a month before leaving for Celera, the biotech company Craig founded to sequence the first human genome. Ham and Craig were at Celera from 1998-2002 and had the idea to do the synthetic cell from Clyde’s work then but put it on hold for four years until after the draft human genome was finished. Early in 2002 Craig left Celera and founded two new institutes: the Institute for Biological Energy Alternatives (IBEA), and The Center for the Advancement of Genomics. Ham resigned from Celera to join IBEA (where he became scientific director) and “cashed in my stock” he laughed only half-joking. Ham and Clyde finally started working closely in 2003 when Clyde moved full time to work at IBEA, and since then have been inseparable. Clyde and Ham both did phage work in graduate school. Clyde worked primarily on phiX174, a phage virus that infects E. Coli. They thought this would be a good first target to test their new synthetic biology technology. They received a Department of Energy (DOE) grant to synthesize phiX in the lab and worked on it during the summer 2003. “Both of us moved into the Marriot Residents Inn and worked 12 hours a day on the synthesis of phiX” said Ham. He proudly added that Craig said, “We were the best postdocs he ever had!” Considering Ham was in his early seventies then and Clyde was not far behind, that was a pretty impressive claim! The synthesis of phiX was published in 2003 and laid the ground work for synthesis of a larger genome — that of a mycoplasma bacterial species. One of the keys to working together so well is how they complement each other both personally and professionally. When asked about how they would characterize the other, Ham divulged the important attributes first, “Clyde likes martinis and I like manhattans!“ he blurted out smiling. Ham continued, “I like his sense of humor very much. He’s very precise in his speech and thinking, whereas I get a little more disorderly. But our approach to science is very similar.” Clyde added that “Ham is great at coming up with things that should have been obvious to everyone but aren’t.” Key to Success I wanted to know what makes these two extraordinary men tick. What motivates and inspires their drive and successes — Good mentors? Good luck? Sacrifices? Hard work and determination? Or just a good time to be in biology? Clyde said simply, “You have to want to do good things, and have a motivation to do interesting science. We both have an aptitude for it, but need to just do things and see what happens.” So they appear to be open to risks and new adventures in their careers, maybe they could even be described as mavericks as Craig has been called. Ham said, “If I hadn’t met Craig I’d be retired and living on the farm (his wife of 53 years maintains the farm in rural Maryland). “Craig has given me the opportunity to continue [doing science]. Clyde added that “being at the JCVI (J. Craig Venter Institute) has made it possible to do things we couldn’t do otherwise in an academic setting.” For example, Ham said, “When sequencing first took off in the late 80s a lot of good scientists didn’t see value [with pure data collection]. I’ve always said “sequence, sequence, sequence” then later we can figure out what to do. “It’s the code of life!” Ham performed his first sequencing experiment in 1976 using the Maxim-Gilbert method and realized its potential back then. “But I was sequencing before Ham,” said Clyde who trumped him in that area by doing a sabbatical in Fred Sanger’s lab in 1975. Speaking of aptitude, science isn’t the only activity at which Ham and Clyde excel. Ham played classical piano starting age 7 or 8. He never practiced and said he was a lousy pupil. Every 6 months or so his mother said he could quit. At age 12 a friend took him to a music store where he heard the Pathetique Sonata by Rubenstein that he had struggled to play and when he heard it for the first time he felt an instant change – he started practicing 3-4 hours a day up to 8 hours a day during the summer. It’s not a surprise that this type of diligence contributed to his later successes in life. Presumably complimenting Ham’s ability to tickle the ivories, Clyde said, “He’s remarkably fast with his hands and can shuck edamame faster than anyone.” Ham added that “I was the fastest newspaper shuffler and hand-bill stuffer in high school.” He would race his friends to finish the chores. Clyde also took classical piano lessons as a kid but quit after a few years to take up the saxaphone and clarinet. He listened to jazz alot and learned how to play in his forties, going on to perform regularly in clubs in North Carolina. Although he stopped taking formal piano lessons as a youth he has kept up with it to this day. He is now playing solo piano accompanied by computerized bass and drum every Thursday in a restaurant in La Jolla called Bernini’s Bistro. What is Life? To finish up the interview I wanted them to leave us parting words of wisdom and so asked, “When you look back on your illustrious careers do you think about how far science has come or how far we have to go to understanding “What is life?” Ham: “It’s hard for me to believe how far we’ve come. If you think about how far things have come since sequencing the first mycoplasma genome (15 years ago) it’s hard to conceptualize what it will be like in 15 years.” Clyde: ”We grew up reading Dick Tracy with his wrist radio, and the iPhone makes the wrist radio look like trash.” When I asked what he meant by a wrist radio, he explained that the comic book character, Dick Tracy, used it to communicate. Ham added that if you sent in cereal box tops they would send you a wrist radio. “It didn’t work of course but you pretend,” he smiled. Ham and Clyde then started to banter about the fantasy uses of wrist watch radios. I threw out an analogy I was familiar with – the legendary 80s show, “Knight Rider” and the “Kit” car that David Hasselholf could summon on his wrist watch. They nodded in familiarity and added that some cars today can parallel park themselves. Getting back to the question of “What is life” I asked them if synthetic biology will provide more for us initially as a research tool in molecular biology or as a chassis for production of bioproducts. “Both” they chimed together. Clyde remarked, “It will have a lot of basic science value that will allow us to get at questions that motivated us in the beginning such as, what are the minimal number of genes essential for life?” “It will promote a better understanding of cells” added Ham. There will be practical applications too, Clyde continued, but “this synthetic cell [M. mycoides ] is not a good production host to make useful bioproducts since it’s expensive to grow and fastidious (requires special nutrients).” “But it provides the proof of principle that it can be done,” Ham exclaimed. We’ve developed a bunch of methods that we can build whatever chromosome we want as long as we know the DNA sequence, said Clyde. Using synthetic genomics “we can take apart a cell and figure out what every gene does in that cell. There is currently no cell we can fully understand,” said Ham. We can reduce the number of genes we don’t know down to a dozen or so and once we’ve done this “then I retire” Ham grinned. I ended the interview asking which comedian duo they thought they most resembled- Abbott and Costello or Laurel and Hardy. They both kind of shook their head not thinking that was a good analogy. But that same moment (just before the videoconference equipment unexpectedly cut off our connection), Clyde said with a laugh, “Neither, but maybe the Keystone Cops!” There they ended the interview as they began – being unduly modest, charmingly funny and easy. And to think these two individuals have been key figures in science, whose work has spanned both the dawn of molecular biology continuing through to the dawn of a new frontier in science- writing the code of life.