A Giant Leap for Synthetic Genes

Science magazine has just published the latest tour de force in building genetic machinery from the ground-up since Mycoplasma laboratorium (“Mycoplasma of the laboratory”), dubbed Synthia by some. M. lab, the “synthetic cell,” represented a major milestone in the synthesis of functional DNA, which was announced just four years ago [1]. Craig Venter’s group from the JCVI had reported the complete chemical synthesis of a chromosome that was able to support living, bacterial Mycoplasma genitalium cells.
This time in 2014, a different team of scientists synthesized a chromosome that can support living yeast cells [2]. The ultimate goal of the  Synthetic Yeast 2.0 project (http://syntheticyeast.org) is to build the entire genetic make-up of a yeast cell and use it to boot-up Sc2.0. How ambitious is this endeavor? For reference, M. lab is a tiny bacterium that measures about 0.1 micrometer across and carries 0.58 million letters, or nucleotides (A’s, T’s, C’s, and G’s), in its complete genetic code. Sc2.0 will measure a whopping 10 micrometers across (the width of 100 M. labs). The chromosome that the yeast team built, chromosome number 3, consists of 0.27 million letters. All together, the genetic code of Sc2.0 may add up to 14 million letters.
This accomplishment has major implications for human cell engineering, and for understanding life. Compared to mycoplasma, the internal organization of yeast cells more closely matches human cells. Furthermore, the yeast team added many unique, synthetic features to the yeast chromosome and demonstrated that this chromosome could still support life. The function of the new features is to aid the process of clipping out portions of the chromosome at specific sites in order to discover what happens to yeast after you eliminate presumably “non-essential” stuff.
This demonstration that a huge synthetic chromosome can reside peacefully amongst the other 15 native chromosomes inside a eukaryotic cell is a major milestone for synthetic biology. We (humans) are also eukaryotes. The yeast team’s work is an important step for advancing human cell engineering. The work helps to determine to what extent a eukaryote will tolerate artificial genetic “plug-ins”. Now that the size limit is bigger than ever reported, we can build more complex and more useful synthetic systems. The work will also help us to finally answer the vexing question of whether our “junk” DNA is essential for life, or perhaps just an evolutionary artifact.
Very impressive work scientifically, but what moves me the most is the personality of the endeavor. Jef Boeke had organized this effort around an undergraduate lab course called “Build-a-Genome” (or BAG) to give college students an authentic graduate-level research experience [3]. Students were assigned chunks of the synthetic chromosome to build. I can only imagine how amazed they must be to see the impact that the end-product has had on basic research and synthetic biology.
The international yeast team includes scientists from Johns Hopkins University, The Carnegie Institution of Washington, New York University, and Loyola University in the USA, Institut Pasteur and Université Pierre et Marie Curie in France, the University of Edinburgh in Scotland, and Pondicherry Biotech in India. One of the leaders of this effort, Jef Boeke, was interviewed on NPR’s Science Friday [4]. Yizhi “Patrick” Cai, who happens to be an alum of the widely popular International Genetically Engineered Machines Competition (iGEM), was recently awarded a grant of 1.8 million pounds to establish the new Edinburgh Genome Foundry.
Congratulations team yeast! Only 15 more chromosomes to go…
1. Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R.-Y., Algire, M. A., et al. (2010). Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science, 329(5987), 52–56. doi:10.1126/science.1190719
2. Annaluru, N., Muller, H., Mitchell, L. A., Ramalingam, S., Stracquadanio, G., Richardson, S. M., et al. (2014). Total Synthesis of a Functional Designer Eukaryotic Chromosome. Science. doi:10.1126/science.1249252
3. Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course. (2009). Genetics, 181(1), 13–21. doi:10.1534/genetics.108.096784
4. Engineering Life Through Biology. NPR’s Science Friday, http://www.sciencefriday.com/guests/jef-boeke.html#page/full-width-list/1

Haynes Lab Students to Present Research at UC Berkeley

Congratulations to the following Haynes Lab students who will present posters at the 2014 Spring Synthetic Biology Engineering Research Center (SynBERC) Retreat on March 24 – 26 at UC Berkeley.

  • Rene Davis (PhD student) – “Investigating quorum sensing orthogonality using a modular, Escherichia coli-based platform” Authors: Rene Davis and Karmella A. Haynes
  • David Barclay (Undergrad, FURI) – “Epigenetic engineering of pancreatic cells with DNA-packing actuators and sensors” Authors: David Barclay, Behzad Damadzadeh, and Karmella A. Haynes
  • Matsemela “Zazu” Moloi (Undergrad, SynBERC Scholars Program) – “Teaching Digital PCR with OpenPCR and a Blue Light Fluorimeter” Authors: Matsemela Moloi, Hiram Rivera-Passapera, Kathryn Scheckel, and Karmella A. Haynes
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Rene Davis receives a 2014 ARCS Award

In recognition of her outstanding scientific achievements, Rene Davis, has been awarded $7,000 from the Phoenix Chapter of ARCS Foundation, Inc. for the 2014-2015 academic year. Rene’s “Papadopoulos Scholar” award is sponsored by Dr. and Mrs. Stephen Papadopoulos from Paradise Valley, AZ. We thank them for their generous support of cutting-edge science and training of a talented future innovator. Rene will present a poster at the annual awards dinner at the Arizona Biltmore, Gold Room on April 25th.

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ASU iGEM 2014 – Now Accepting Applications!

We are recruiting new members for the International Genetically Engineered Machines competition, iGEM. Never heard of iGEM before? Visit http://igem.org/About for more information and some examples of award-winning team projects.

What does the ASU iGEM experience look like?

  • Spring – meet with your teammates and advisors, develop a project idea, meet other budding teams across the Southwest
  • Summer (May – August) – use DNA as building blocks to develop a living cell that carries out an engineered function, such as blinking, toggle-switching, generating valuable chemical compounds…yes, biology can do that. Apply graphic design/ web page building to communicate the team’s project to the world, scientists, non-scientists, and students. Think forward…prepare to explain what impact your invention will have on a world in which your synthetic organism has not yet become a part of society.
  • Fall (October) – bring your results to the most exciting student research jamboree in the world, which takes place in Boston, MA. Return to ASU as celebrated heroes of bioengineering!

We are seeking undergraduate applicants with a minimum of some coursework that is relevant to synthetic biology (e.g., biology, molecular biology, circuit design, applied math/ calculus, relevant humanities course, graphic design, etc.).

You should definitely consider registering for Dr. Haynes’ course Molecular Synthetic Biology, or at least attend our research article discussions.

DEADLINE EXTENSION: Please complete the application online by Friday, February 21st. Send inquiries to the lead faculty advisor Dr. Haynes. DO NOT send your c.v./ resume/ or transcript at this time. We may ask for these items later in the selection process. We will follow up in early February and hold an in-person, group interview of the finalists in late February/ early March.

If you are not an undergraduate but want to get involved, please e-mail Dr. Karmella Haynes.

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Karmella Haynes is the December 2013 “Scientist to Watch”, The Scientist Magazine

Karmella Haynes was selected as The Scientist magazine’s December Scientist to Watch.

“In 2011, at the Fifth International Meeting on Synthetic Biology in Stanford, California, Karmella Haynes arrived at the designated spot to display her poster. Rather than standing idly by, however, she set the board on an easel, whipped out a paintbrush, and turned science into art.”

Read the full article, Turning the Dials, written by Kerry Grens, at The Scientist online.

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Biomedical engineering project aimed at improving diabetes treatment

This ASU News article covers a new project in the Haynes lab that aims to apply synthetic chromatin to pancreas cell development, with implications for understanding and treating diabetes.

“In her synthetic biology lab, Karmella Haynes focuses much of her effort on developing better ways of exploring how human body cells work – or don’t work like they should. She’ll be applying her expertise in that area to a major new research endeavor to produce more effective treatments for diabetes. The project is being undertaken by the national Synthetic Biology Engineering Research Center (SynBERC), which is supported by the National Science Foundation (NSF). SynBERC members include the Massachusetts Institute of Technology (MIT), Harvard Medical School and Stanford University.”

The original article, written by Joe Kullman, is at the ASU News website.

The story is also featured here:
Full Circle – by Joe Kullman, Nov 21, 2013 
IDT DNA – post on Twitter 

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David Barclay Receives a FURI Fellowship

Haynes lab undergraduate researcher David Barclay (BME) was awarded a Fulton Undergraduate Research Initiative (FURI) fellowship for Spring 2014. Congrats, David!

ARCS Foundation Phoenix ASU Scholar Rene Davis Shares Her Summer Experience

Recently, Haynes lab PhD student Rene Davis wrote a letter to the ARCS Foundation thanking them for their support ($7000 in 2013) and sharing her fantastic experience as a teaching assistant at the 2013 Cold Spring Harbor Laboratory summer course in Synthetic Biology. ARCS published her letter on their website in the Scholar Spotlight section. You can read Rene’s letter here.

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ASU Homecoming DNA Booth

Students from synthetic biology labs at ASU organized a booth for the Engineering section of the annual ASU homecoming block party, which received thousands of visitors on Saturday afternoon. The “Machines for Visualizing DNA” booth was led by Haynes lab PhD student Rene Davis.


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Synthetic Biology Faculty Search at ASU

The Ira A. Fulton Schools of Engineering at Arizona State University are seeking applicants for tenure-track/tenured faculty positions in Synthetic/ Systems Biology to grow our efforts in the important thrust area of health. Areas of interest include, but are not limited to, therapeutics, stem cells/ regenerative medicine, cellular biomechanics/ engineering and cell signaling. Review of applications will begin December 1, 2013; if not filled, reviews will occur on the 1st and 15th of the month thereafter until the search is closed. Please read the Synthetic/ Systems Biology announcement for application details. A parallel faculty search is described in the Molecular, Cellular, and Tissue Engineering announcement.

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