CSHL Synthetic Biology Course – 2015

The 2015 Cold Spring Harbor Summer Course in Synthetic Biology will take place July 27 – August 10.The course will focus on how the complexity of biological systems, combined with traditional engineering approaches, results in the emergence of new design principles for synthetic biology. The Course centers around an immersive laboratory experience. Here, students will work in teams to learn the practical and theoretical underpinnings of cutting edge research in the area of Synthetic Biology. Broadly, we will explore how cellular regulation – transcriptional, translational, post-translational, and epigenetic – can be used to engineer cells to accomplish well-defined goals.

Instructors for 2015:
John Dueber,University of California, Berkeley
Mary Dunlop, University of Vermont
Karmella Haynes, Arizona State University
Julius Lucks, Cornell University
Pamela Peralta-Yahya, Georgia Institute of Technology
Stanley Qi, Stanford University 

Read Instructor bios at  https://cshlsynbio.wordpress.com/instructors2015/

Invited Speakers are current leaders in synthetic biology, who will present seminars on their research, industrial developments, and other recent developments in the field. Students will have the opportunity to interact with the speakers in an intimate setting:
Elisa Franco, University of California, Riverside
Emma Frow, Arizona State University
Mo Khalil, Boston University
Nathan Hilton, Joint BioEnergy Institute
Thomas Knight, Ginkgo BioWorks
Vincent Noireaux, University of Minnesota
Pamela Silver, Harvard Medical School
Danielle Tullman-Erceck, University of California, Berkeley

An up-to-date Speakers list is available at https://cshlsynbio.wordpress.com/speakers/

For more information about the course and instruction on how to apply, visit http://cshlsynbio.wordpress.com.

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Review on Engineered Quorum Sensing Published in Frontiers

Figure 2. Homoserine lactone (HSL)-based genetic wiring supports the function of sophisticated synthetic systems.

Can the natural diversity of quorum-sensing advance synthetic biology?” a review written by Rene Davis (Biological Design PhD student, SBHSE), Ryan Muller (Undergraduate, SOLS), and Dr. Karmella Haynes (SBHSE) was accepted by the journal Frontiers in Bioengineering and Biotechnology. This article is part of the research topic “Synthetic Biology: engineering complexity and refactoring cell capabilities.”

View the article at this link: http://journal.frontiersin.org/article/10.3389/fbioe.2015.00030/full

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Haynes Lab Students Present Research at IBE

On March 5 – 7, Cameron Gardner (BME, SBHSE) and Jimmy Xu (BME, SBHSE) presented their work on synthetic biology at the Institute of Biological Engineering 2015 Annual Conference in St. Louis, MO. Cameron Gardner presented his human cell research with a poster titled “Isolation and Testing of Synthetic Polycomb Transcription Factors”. Jimmy Xu presented his work in developing a synthetic biology project kit for high schools with a poster titled ”Massively Open Online Research for Secondary Education in Synthetic Biology.”

Cameron Gardner is supported by FURI.
Jimmy Xu is supported by NSF CBET.
The Institute of Biological Engineering (IBE) is a professional organization which encourages inquiry and interest in biological engineering.

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Haynes Receives NIH K-Award

Dr. Karmella Haynes is the recipient of a Mentored Research Scientist Development Award to Promote Diversity (K01) from the National Cancer Institute (NCI) of the National Institutes of Health (NIH).

Karmella Haynes wants to help the body fight cancer by designing proteins to stop the disease. “We have the ability to build new synthetic proteins by borrowing pieces of the natural DNA-folding proteins. The new synthetic proteins are designed to counteract cancer-associated chromatin folding,” Haynes explained. Supported by a grant from National Cancer Institute through the National Institutes of Health (NIH), she is working on a technique for effectively introducing the engineered proteins into chromatin structures.

~~~Building Proteins to Counteract Cancer. Joe Kullman, ASU News.

Related news articles:

  1. Kullan, J. (2014) Building Proteins to Counteract Cancer. ASU Engineering Full Circle. http://fullcircle.asu.edu/2014/11/11439/
    • Also in: ASU News [now] Science & Tech. https://asunews.asu.edu/20141110-haynes-proteins-fight-cancer
    • Also in: ASU Inner Circle Fulton Schools News Roundup. http://innercircle.engineering.asu.edu/2014/11/10/fulton-schools-news-roundup-23/
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Haynes Lab Students Present Research at Synberc MIT Event

Over the weekend of September 26 – 28, Rene Davis (Biological Design PhD, SBHSE) and David Barclay (BME, SBHSE) presented their work on engineering chromatin in mammalian cells at the Synthetic Biology Engineering Research Center‘s Fall 2014 Retreat at the Massachusetts Institute of Technology. Rene Davis presented a talk on “Mammalian Cell Engineering and Chromatin,” which started with an overview of the chromatin engineering projects in the Haynes lab, followed by details of her own new project that investigates the impact of chromatin on genome engineering. David Barclay presented a poster, titled “A synthetic fusion protein for epigenetic control of pancreatic cell function,” which gave an update on his progress with experiments that are a key part of the Synberc “Programmable Organoids” collaboration with MIT and Harvard.

Synberc is an NSF-funded and Industry-supported center that provides full travel support twice a year for students from Synberc labs to share their research in synthetic biology. 

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Synthetic Biology meets Capitol Hill

From ASU News: “ASU professor speaks to Congress about supporting synthetic biology research

“Karmella Haynes was among scientists and engineers to address national leaders at a recent U.S. Congressional briefing on issues raised by the emerging field of synthetic biology… The rapid advance of synthetic biology has prompted discussions about how to weigh the benefits of the research against potential social and ethical implications, and concerns about safety… Haynes and two colleagues – Steve Evans [Dow AgroSciences] and Jay Keasling [Director of Synberc] – gave presentations on those questions to staff members representing members of Congress, National Science Foundation officials, science journalists and other interested parties.”

Remarks were given by U.S. Representative Eric Swalwell of California. The session was moderated by Pramod Khargonekar, NSF assistant director for Engineering.


  1. ASU News. ASU professor speaks to Congress about supporting synthetic biology research. https://asunews.asu.edu/20140718-haynes-congress-briefing-bioengineering
  2. National Science Foundation. Media advisory: Learn the latest on synthetic biology at a June 26 Capitol Hill briefing. http://www.nsf.gov/news/news_summ.jsp?cntn_id=131810
  3. Genome Compiler. Leading scientists address congress on future of synthetic biology. http://www.genomecompiler.com/leading-scientists-address-congress-on-future-of-synthetic-biology/
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GMO Labeling: a (chance for) victory for GMO’s

Think of the worst thing that the food industry has done with genetically modified foods (GMOs). If you say “sell them at all,” I’d disagree. I enjoy genetically modified foods, and they rely less on pesticides than “organically” grown foods. More on that later.

The worst thing that industry has done regarding GMOs is hide the fact that they are GMOs. There is a strong public belief that there is something toxic about GMOs, and nondisclosure only fuels public suspicions. This is why as a pro-GMO consumer, I am actually happy to hear about Vermont’s recent legislation [1] that requires any foods that contain GMOs be labeled as such. Now that genetic modification has been asked to come out of the closet, we can all learn the facts about various GMOs, and stop limiting our knowledge to scary catch-phrases and sound bytes like “Frankenfood.”

This brings me back to the previous point about pesticides. According to the US Environmental Protection Agency (EPA) [2], ”organically grown” food uses no synthetic fertilizers or pesticides, but pesticides derived from natural sources (e.g., biological pesticides) may be used in producing organically grown food. The US Department of Agriculture’s Organic Foods Program [3] will allow foods to bear their certified organic label even if food pests and diseases have been managed with “application of nonsynthetic biological, botanical, or mineral inputs.”

In conversations with some acquaintances, it is as if they fantasize that organic farmers are roving the fields each day, gingerly collecting crop-eating bugs from the plants into a jar and releasing them into the forest. At the end of the day, GMO, organic, or local*, no farmer wants to lose crops to enemies such as pests and disease. That farmer is going to use the least expensive and most effective method to poison bugs. That’s just how agriculture works.

The thing that sets the GMO approach apart in the human struggle to protect crops is that it uses DNA biochemistry to make crop-protecting changes within plants. These new traits can be inherited from plant to plant. Some GMOs don’t need any pesticides, synthetic or “botanical,” to keep bugs away. Some are even designed to grow happily in the presence of less fertilizer. This reduces the amount of chemical run-off into the environment. In some cases, GMOs are even made to increase the nutritional value of plants (e.g., golden rice [4]).

Unfortunately, the food industry has taken defensive actions in response to the Vermont bill. Companies, including Ben & Jerry’s, have started pulling some GMO products from their foods [5]. Fabulous! Now our fat, salt, and cholesterol can be more “organic.” 

On the positive side, now that a label will make GMOs highly visible, we can all observe first-hand that GMOs, by virtue of being genetically altered, cause no harm to human health. Through conversations with each other around food, I can talk to more friends about how transferring an anti-browning gene into an apple [6] is no more “Frankenstein” than slicing up a lemon and squeezing its juices unnaturally onto cut apples. We can distinguish political and economic from scientific arguments. People who oppose GMO and those who support GMO can both shop with confidence. Hopefully, as the public becomes more educated about the science, people will be able to support or oppose specific engineered foods, rather than being forced to accept or reject any and all GMOs across the board. 

*Footnote: I support (reasonably priced) local food because it reduces the need to ship produce across the country, not because I believe it is somehow “healthier.” Now, if only I could find local GMOs…


  1. NPR Blog. Bracing For A Battle, Vermont Passes GMO Labeling Bill. http://www.npr.org/blogs/thesalt/2014/04/24/306442972/bracing-for-a-battle-vermont-passes-gmo-labeling-bill
  2. Environmental Protection Agency. Pesticides and Food: What “Organically Grown” Means. http://www.epa.gov/pesticides/food/organics.htm
  3. US Department of Agriculture. Electronic code of federal regulation: 205.206 - Crop pest, weed, and disease management practice standard. http://www.ecfr.gov/cgi-bin/text-idx?SID=db18e8182c5d577eff51a071cff3dbee&node=7:
  4. Golden Rice Project. The science of golden rice. http://www.goldenrice.org/Content2-How/how1_sci.php
  5. NPR Blog. Some Food Companies Are Quietly Dumping GMO Ingredients. http://www.npr.org/blogs/thesalt/2014/07/22/333725880/some-food-producers-are-quietly-dumping-gmo-ingredients
  6. Huffington Post. USDA asked to approve non-browning GMO apple. http://www.huffingtonpost.com/2010/11/29/non-browning-gmo-apple-usda_n_789123.html
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Professional bullying: personal comments on the recent assault of Dr. Ore

Unfortunately, the disingenuous practice of disguising emotion-driven assaults with a veil of rules and laws is widespread, even amongst esteemed protectors, leaders, and professionals. This is what happened recently when a Tempe Police officer exploited his authority and applied excessive force in apprehending ASU Professor Ersula Ore for jay-walking in an area where the street is currently blocked off and there is no through-traffic on May 20, 2014. I have walked this exact area myself, just North of the Tempe campus. The very likely chance that this could have been me is chilling. View the video of her assault here: https://www.youtube.com/watch?v=XQJD2pqhMA4#t=145

After I posted a response to a very lazily-written, one-sided news article on the internet, an instigator from the comment thread emerged from the shadows to send a message via Facebook to inform me that Dr. Ore was simply an “uppity thing” (referring to her as “it”) that got what she deserved. The last time that “uppity” was a crime that warranted police brutality was back in the pre-Civil Rights era, when that “crime” mostly applied to black people. I am not sure how the internet troll managed to find a time machine back in 1950, but welcome to 2014, time-traveler.

Imagine that you are a student in one of my classes. You didn’t study as much as you should have for one of the exams, and wrote a lot of incorrect responses to pretty easy questions. You receive your graded exam not only with a D scrawled in red at the top, but a nice illustration of your head on the body of a mule alongside a quoted Miriam-Webster’s definition of idiot written in the margins, ending with with a phrase such as “drop out and just save your parents or the government some money, you worthless failure.”

Think very carefully before you answer the following question. Would you shrug your shoulders and admit that you really deserved ALL of that for not studying? The D, maybe, but the written abuse along with it? I may not know you personally, but I highly doubt it.

Now, imagine that you approach me regarding this excessive feedback.

Professor: “I am the professor and you are being insolent.”
You: “Are you serious?”
Professor: “Shut up or I’ll slam your grade down to the level of an F.”

Understandably, you go immediately to the Dean with the graded exam in order to address the unprofessional and excessive manner in which you were “evaluated” by me, the professor. I hear about this from the Dean, and then use every logical loop-hole in my syllabus to score your assignments as low as possible so that you fail the course, and then I report you to the Dean for attempting to slander my character (verbal assault of a professor).

Now if things aren’t already bad enough, the Dean’s written response to you looks something like this…

“Administrative authorities have reviewed the unfortunate circumstances surrounding your course failure and have found that the professor involved did not violate protocol and no evidence was found of emotional motivation by the ASU faculty involved.”

Imagine that an account of the incident has spread around campus, and you receive an e-mail from someone you do not know that says that you are just some uppity little college snot that got what you deserved because you didn’t study.

Here’s a question to ponder: what on earth would provoke a trained professional to go to extra lengths to demean a person who he/she is expected to serve the best interests of? Perhaps a deeply-engrained nasty attitude, over-inflated sense of self-importance, or extreme insecurity? Perhaps an inability to see particular people as nothing more than insolent beasts who need to be taught a lesson every once in a while? Thankfully, my character and upbringing place me well above that base level of thinking. Unfortunately, a Tempe police officer who we have entrusted to protect and serve still has some growing up to do.

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Haynes Receives Grant from Women and Philanthropy

Getting a grant is extremely exciting, especially for a young PI who has to find support after she has exhausted her start-up funds. In addition to receiving new funding, something else truly amazing happened. My science-communication skills were challenged like they had never been before. I got a very broad audience excited about synthetic biology…something that I believed only scientists and students could ever truly get excited about. The Women and Philanthropy grant application experience was worlds apart from what I am used to…scientifically convincing a panel of scientists that I am a scientist worth her salt who can science, science, science, and science. Instead, I had to identify the real impact that my work would have on my University, community, and the world; how stakeholders who are often taken for granted (the public) would benefit from the work.

I first put pen to paper to materialize my ideas for enabling distributed characterization of bioenginered parts at the 2012 Synthetic Biology Leadership Excellence Accelerator Program (SynBioLEAP), held in Arlington, VA (SynBioLEAP White Paper – “Incentive-Driven Information Sharing for Engineering Biology”). Since then I have been seeking out support and collaborators. After an unsuccessful attempt to get the project funded by the NSF as part of a Career proposal, I tried another route.

Women have an unconventional approach to science that is not always supported by funding agencies with less broad views on how science and research should be approached.

Dr. Peggy Rismiller

I sought out a collaboration with Catherine Seiler, curator of the amazing DNA plasmid repository DNASU, which is just across the street from my building on Arizona State University’s Tempe campus. A few brainstorming sessions later the blueprint for “SB.ASU” (Synthetic Biology at ASU) was born. We formed a three-woman team, along with my graduate student Rene Davis, to apply for support from Women and Philanthropy.

The project aims take DNA parts repositories to a new level. We will develop a tool that gathers real experiences from research labs to describe how those parts function in living cells. Bioengineering needs functional data to move forward with rational design of new technologies to build new tools for biomedical and energy needs. We anticipate that the project will reduce the time, cost, and guesswork involved in bioengineering. Read more about the project in ASU Full Circle’s article by Joe Kullman.

Related articles
1. ASU full Circle. Haynes looks to create a global resource for synthetic biology researchers. http://fullcircle.asu.edu/2014/05/10501/

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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