SynBioFromLeukipposInstitute

Ever since it was discovered that the level of calcium ions inside a cell can oscillate (Woods et al., 1986), biologists have been intrigued by the periodic nature of many cellular signals. While we are slowly starting to grasp the many and varied roles that these periodic oscillations play in cellular communication, an open question remains: how are networks of genes able to generate sustained oscillations? Now, in eLife, Sebastian Maerkl and co-workers – including Henrike Niederholtmeyer and Zachary Sun as joint first authors – report that they have used a synthetic biology approach to reveal how simple gene circuits can produce robust oscillations in cells (Niederholtmeyer et al., 2015).

Initially, it was argued that periodic oscillations in the level of calcium ions and other cellular components had no role in signaling, but decades of research has revealed that periodic signals are better at relaying information than non-periodic signals (Rapp, 1987; Behar and Hoffman, 2010; Purvis and Lahav, 2013; Levine et al., 2013). Both types of signal can encode information in the size (amplitude) of the signal, but the frequency and phase of periodic signals can also encode information. As a result, periodic signals may be able to regulate complex cell processes more precisely than non-periodic signals. Importantly, recent advances in single-cell analysis and optogenetics have resulted in numerous in-depth studies that reveal how critical events, such as the determination of cell fate and multicellular communication, are controlled by periodic signals (the review by Sonnen and Auleha, 2014 describes other examples).

Mathematical analysis shows that an essential element of an oscillating circuit is an inhibitory feedback loop: if the activity of one gene in such a feedback loop increases, it activates other genes in the circuit that ultimately inhibit it (Rapp, 1987; Novak and Tyson, 2008; Purcell et al., 2010). This feedback loop needs to have an in-built time delay to enable the activities of the genes in the circuit to fluctuate in regular cycles.

The rise of synthetic biology has made it possible to design and construct synthetic networks in living cells that perform a specific role. In an early example of this, researchers at Princeton reported that they had constructed an oscillatory gene network in E. coli based on a cyclic network of three genes called the repressilator (Elowitz and Leibler, 2000; Figure 1). Theory predicts that the repressilator and other ring oscillators that have an odd number of genes (nodes) should be capable of producing sustained oscillations. However, since designing, building and testing new gene networks in living cells is a lengthy process, ring oscillators with more than three nodes have not been reported.

Inside and outside of the classroom, MIT professor Joseph Jacobson has become a prominent figure in — and advocate for — the emerging field of synthetic biology.
As head of the Molecular Machines group at the MIT Media Lab, Jacobson’s work has focused on, among other things, developing technologies for the rapid fabrication of DNA molecules. In 2009, he spun out some of his work into Gen9, which aims to boost synthetic-biology innovation by offering scientists more cost-effective tools and resources.
Headquartered in Cambridge, Massachusetts, Gen9 has developed a method for synthesizing DNA on silicon chips, which significantly cuts costs and accelerates the creation and testing of genes. Commercially available since 2013, the platform is now being used by dozens of scientists and commercial firms worldwide.
Synthetic biologists synthesize genes by combining strands of DNA. These new genes can be inserted into microorganisms such as yeast and bacteria. Using this approach, scientists can tinker with the cells’ metabolic pathways, enabling the microbes to perform new functions, including testing new antibodies, sensing chemicals in an environment, or creating biofuels.
But conventional gene-synthesizing methods can be time-consuming and costly. Chemical-based processes, for instance, cost roughly 20 cents per base pair — DNA’s key building block — and produce one strand of DNA at a time. This adds up in time and money when synthesizing genes comprising 100,000 base pairs.
Gen9’s chip-based DNA, however, drops the price to roughly 2 cents per base pair, Jacobson says. Additionally, hundreds of thousands of base pairs can be tested and compiled in parallel, as opposed to testing and compiling each pair individually through conventional methods.
This means faster testing and development of new pathways — which usually takes many years — for applications such as advanced therapeutics, and more effective enzymes for detergents, food processing, and biofuels, Jacobson says. “If you can build thousands of pathways on a chip in parallel, and can test them all at once, you get to a working metabolic pathway much faster,” he says.
Over the years, Jacobson and Gen9 have earned many awards and honors. In November, Jacobson was also inducted into the National Inventors Hall of Fame for co-inventing E Ink, the electronic ink used for Amazon’s Kindle e-reader display.
Scaling gene synthesizing
Throughout the early-and mid-2000s, a few important pieces of research came together to allow for the scaling up of gene synthesis, which ultimately led to Gen9.
First, Jacobson and his students Chris Emig and Brian Chow began developing chips with thousands of “spots,” which each contained about 100 million copies of a different DNA sequence.
Then, Jacobson and another student, David Kong, created a process that used a certain enzyme as a catalyst to assemble those small DNA fragments into larger DNA strands inside microfluidics devices — “which was the first microfluidics assembly of DNA ever,” Jacobson says.
Despite the novelty, however, the process still wasn’t entirely cost effective. On average, it produced a 99 percent yield, meaning that about 1 percent of the base pairs didn’t match when constructing larger strands. That’s not so bad for making genes with 100 base pairs. “But if you want to make something that’s 10,000 or 100,000 bases long, that’s no good anymore,” Jacobson says.
Around 2004, Jacobson and then-postdoc Peter Carr, along with several other students, found a way to drastically increase yields by taking a cue from a natural error-correcting protein, Mut-S, which recognizes mismatches in DNA base pairing that occur when two DNA strands form a double helix. For synthetic DNA, the protein can detect and extract mismatches arising in base pairs synthesized on the chip, improving yields. In a paper published that year in Nucleic Acids Research, the researchers wrote that this process reduces the frequency of errors, from one in every 100 base pairs to around one in every 10,000.
With these innovations, Jacobson launched Gen9 with two co-founders: George Church of Harvard University, who was also working on synthesizing DNA on microchips, and Drew Endy of Stanford University, a world leader in synthetic-biology innovations.
Together with employees, they created a platform called BioFab and several other tools for synthetic biologists. Today, clients use an online portal to order gene sequences. Then Gen9 designs and fabricates those sequences on chips and delivers them to customers. Recently, the startup updated the portal to allow drag-and-drop capabilities and options for editing and storing gene sequences.  
This allows users to “make these very extensive libraries that have been inaccessible previously,” Jacobson says.
Fueling big ideas
Many published studies have already used Gen9’s tools, several of which are posted to the startup’s website. Notable ones, Jacobson says, include designing proteins for therapeutics. In those cases, the researcher needs to make 10 million or 100 million versions of a protein, each comprising maybe 50,000 pieces of DNA, to see which ones work best.
Instead of making and testing DNA sequences one at a time with conventional methods, Gen9 lets researchers test hundreds of thousands of sequences at once on a chip. This should increase chances of finding the right protein, more quickly. “If you just have one shot you’re very unlikely to hit the target,” Jacobson says. “If you have thousands or tens of thousands of shots on a goal, you have a much better chance of success.”
Currently, all the world’s synthetic-biology methods produce only about 300 million bases per year. About 10 of the chips Gen9 uses to make DNA can hold the same amount of content, Jacobson says. In principle, he says, the platform used to make Gen9’s chips — based on collaboration with manufacturing firm Agilent — could produce enough chips to cover about 200 billion bases. This is about the equivalent capacity of GenBank, an open-access database of DNA bases and gene sequences that has been constantly updated since the 1980s.
Such technology could soon be worth a pretty penny: According to a study published in November by MarketsandMarkets, a major marketing research firm, the market for synthesizing short DNA strands is expected to reach roughly $1.9 billion by 2020.
Still, Gen9 is pushing to drop costs for synthesis to under 1 cent per base pair, Jacobson says. Additionally, for the past few years, the startup has hosted an annual G-Prize Competition, which awards 1 million base pairs of DNA to researchers with creative synthetic-biology ideas. That’s a prize worth roughly $100,000.
The aim, Jacobson says, is to remove cost barriers for synthetic biologists to boost innovation. “People have lots of ideas but are unable to try out those ideas because of cost,” he says. “This encourages people to think about bigger and bigger ideas.”

The intellectual property, genetic resource prior informed consent, and access & benefit sharing landscape is currently in flux. The new laws and agreements being developed at the national and international levels could have implications for synthetic biology researchers.

Digital DNA: The Nagoya Protocol, Intellectual Property Treaties, and Synthetic Biology looks at current challenges for the intellectual property protection of synthetic biology outputs, implementation issues concerning the Nagoya Protocol on Access and Benefit Sharing to the Convention on Biological Diversity, and possible interactions between the requirements of the Protocol and the World Trade Organization’s Agreement on Trade Related Aspects of Intellectual Property (TRIPS).

The report also explores emerging concerns regarding synthetic biology and “digital biopiracy” in relation to non-commercial research projects. Finally, it presents highlights of negotiations in the World Intellectual Property Organization Intergovernmental Committee on Intellectual Property, Genetic Resources, Traditional Knowledge, and Folklore, which may relate to both the Nagoya Protocol and TRIPS and thus may be relevant for researchers, particularly those working in the area of synthetic biology.

The momentum of developments in bioengineering has left life scientists breathless. CRISPR, the gene editing tech that has been adopted almost universally among biotech labs, has been stealing all the headlines with talk of designer babies. But behind the glitz, a steady stream of software, services, and machines have been coming out that make genetic engineering easier, more reliable, and more automated. The latest innovation comes out of a collaboration between a biologist, a designer, and an engineer at University of Pennsylvania. They created a desktop machine that automates genetic engineering—no hands required.
“You can hit play and just get your product out at the end,” says Karen Hogan, co-inventor of the Biorealize Microbial Design Studio and biology lab coordinator at UPenn.

Space synthetic biology is a branch of biotechnology dedicated to engineering biological systems for space exploration, industry and science. There is significant public and private interest in designing robust and reliable organisms that can assist on long-duration astronaut missions. Recent work has also demonstrated that such synthetic biology is a feasible payload minimization and life support approach as well. This article identifies the challenges and opportunities that lie ahead in the field of space synthetic biology, while highlighting relevant progress. It also outlines anticipated broader benefits from this field, because space engineering advances will drive technological innovation on Earth.

Advanced Lecture Course on Systems Biology

There is enormous potential in combining the capabilities of the biological and the solid state to create hybrid engineered systems. While there have been recent efforts to harness power from naturally occurring potentials in living systems in plants and animals to power complementary metal-oxide-semiconductor integrated circuits, here we report the first successful effort to isolate the energetics of an electrogenic ion pump in an engineered in vitro environment to power such an artificial system. An integrated circuit is powered by adenosine triphosphate through the action of Na+/K+ adenosine triphosphatases in an integrated in vitro lipid bilayer membrane. The ion pumps (active in the membrane at numbers exceeding 2 × 106 mm−2) are able to sustain a short-circuit current of 32.6 pA mm−2 and an open-circuit voltage of 78 mV, providing for a maximum power transfer of 1.27 pW mm−2 from a single bilayer. Two series-stacked bilayers provide a voltage sufficient to operate an integrated circuit with a conversion efficiency of chemical to electrical energy of 14.9%.