SynBioFromLeukipposInstitute

Researchers have found a way to modify antibiotics using synthetic enzymes, allowing them to rationally design new drugs from modified natural compounds.

The dawn of cheap genome editing techniques such as CRISPR understandably have people across the political spectrum worried about what a future of designer babies, more pathogenic viruses, deextincted species, clones, and glow-in-the-dark sushi might look like. But does putting limits on genetic engineering violate scientists' constitutional rights?

The First Amendment has been interpreted by the Supreme Court to encompass not just the freedom of speech, but also the freedom of expression and expressive conduct, which likely includes acts of science, according to Alta Charo, a bioethicist and law professor at University of Wisconsin Law School.

We invariably imagine electronic devices to be made from silicon chips, with which computers store and process information as binary digits (zeros and ones) represented by tiny electrical charges. But it need not be this way: among the alternatives to silicon are organic mediums such as DNA.

DNA computing was first demonstrated in 1994 by Leonard Adleman who encoded and solved the travelling salesman problem, a maths problem to find the most efficient route for a salesman to take between hypothetical cities, entirely in DNA.

Deoxyribonucleaic acid, DNA, can store vast amounts of information encoded as sequences of the molecules, known as nucleotides, cytosine (C), guanine (G), adenine (A), or thymine (T). The complexity and enormous variance of different species’ genetic codes demonstrates how much information can be stored within DNA encoded using CGAT, and this capacity can be put to use in computing.

DNA molecules can be used to process information, using a bonding process between DNA pairs known as hybridisation. This takes single strands of DNA as input and produces subsequent strands of DNA through transformation as output.

Since Adleman’s experiment, many DNA-based “circuits” have been proposed that implement computational methods such as Boolean logic, arithmetical formulas, and neural network computation. Called molecular programming, this approach applies concepts and designs customary to computing to nano-scale approaches appropriate for working with DNA.

A group of nine TU Delft students participating in the upcoming iGem Synthetic Biology Competition have built the first 3D printer capable of creating customizable and reproducible bacterial biofilm, and they’ve made it almost entirely out of the children’s toy K’nex. This development could allow scientists to more effectively study the disease-causing bacteria and devise better methods for removing it. 3Ders.org spoke with Hector Sanguesa Ferrer, one of the students who developed the Biolinker 3D printer, in order to get a better understanding of their goals and how they were accomplished.

The “$1,000 genome” has been one of the most visible tech goals in the last 10 years, even sporting its own XPrize for a short time. It refers to the ability to “sequence,” or de-code, the total genetic information encoded in the DNA (genome) of a single human, at a cost of $1,000. It’s a daunting task, given that the genome is made up of 3 billion base pairs whose exact sequence needs to be determined.

But why $1,000? Many experts feel this is the cost at which it becomes feasible to sequence human genomes on a large scale. The data could then be used to improve clinical diagnosis and treatment of rare and new disorders suspected of having genetic causes. Illumina hit the $1,000 mark in January of 2014.

Their instruments are capable of sequencing 18,000 human genomes per year. Many individual genomes have now been sequenced and have proved invaluable for finding causal genetic mutations for such diseases as schizophrenia and autism. The sequencing of the genome has played a role in personalized genomics, genetic testing and forensic science, just to name a few. This very significant breakthrough in DNA sequencing capability heralds a new era in medicine.

Sequencing DNA can be thought of as the “reading” step, which gives us the information that codes for life. The next step is to “write” new genetic information by synthesizing genes. As researchers, whether the field is agricultural biology, medicine, academia or industrial chemical, the cycle of research is the same — design, build, test — and it repeats until a solution is identified.

This process continues as it has for many years, but there is a bottleneck in the synthesis of genes. It is a time-consuming and expensive proposition, and researchers in a variety of industries are frustrated with the existing process. That’s where synthetic biology (synbio for short) comes in.

Over the last three decades, cloning has been the method of writing genetic material de novo (DNA, RNA and proteins) in all industries using biological materials. This includes industrial chemistry, agricultural biotechnology, medicine and academia. Rapid and affordable access to large quantities of genetic material will drive advances in synthetic biology, which promises to improve health, help clean up the environment, feed the world, and create new industries and jobs.

When did you first hear the phrase "synthetic biology"? Was it many years ago, or did it just happen when you clicked on this blog?
Synthetic biology — or SynBio — involves the engineering of biological systems to create useful products or functions through thoughtful tinkering with DNA. Commercial applications span several industries: energy, chemicals, materials, pharma, food, agriculture, diagnostics, probiotics, antibiotics, and gene therapy — just to name a few. According to one analysis from 2014, the global SynBio market was valued at $3.0 billion in 2013 and is estimated to reach $38.7 billion by 2020.
I first heard about SynBio in 2009 and am now a researcher in this field. In this post, I will describe a representative set of SynBio start-ups alongside a personal narrative of my expanding interest in the field. Despite what little I know, I will also speculate on what may lie ahead. If you are a fan of science, a SynBio student or practitioner, or an investor in start-ups, then this post is especially for you.
Fuels and SynBio Start-ups v1.0
In 2004, I wrote to the Houston Museum of Natural Science about my desire to help cure what I called "The Black Plague of Black Gold." I was a high school junior in the Energy Corridor of West Houston and wanted to help end our reliance on petroleum.
Five years later, I worked part-time in a lab at the University of Texas cultivating strains of algae that naturally accumulate oil. We wanted to harvest the oil as a potential biofuel, and I wondered how we could coax the algae into producing more of it. I was a chemical engineering major and did not know much about biology. But then I heard about a start-up that was doing "synthetic biology" to make renewable fuels. The six year old company was Amyris.
Amyris genetically engineers yeast to produce a chemical called farnesene from sugar. Farnesene can be used as biodiesel or as jet fuel. I was amazed at the time to see that they also engineer yeast to produce artemisinic acid, an immediate precursor to an antimalarial drug. Natural yeast strains do not contain farnesene, artemisinic acid, or anything chemically similar.
Over the next few weeks, I found out about other start-ups that engineer microbes ranging from algae to E. coli in order to produce biofuels from sugar. Among these companies are Synthetic Genomics, Solazyme, Joule Unlimited, and LS9 (now REG Life Sciences).
SynBio fuel efforts seemed to receive validation in the marketplace. For example, in June 2009, oil and gas giant ExxonMobil invested $300 million into Synthetic Genomics as part of an R&D partnership to develop biofuels. Amyris became publicly traded the following year.
Higher Value Products and SynBio Start-ups v2.0
The apparent commercial success of SynBio fuel start-ups influenced my decision to join a SynBio lab in graduate school in early 2011. Once there, I realized that microbes could be engineered to produce essentially any of the numerous products that are ordinarily derived from petroleum. And in order to provide a path towards complete independence from petroleum, it is important to find sustainable routes to make these products in addition to fuels. The use of microbes that are engineered to efficiently convert renewable inputs to products at high yields is an elegant strategy for many products. However, based on rough economic considerations, I gradually began to question whether fuels were practical targets for SynBio start-ups.
The "carbon value chain" is a concept that categorizes carbon-containing products based on their price per mass. Although other variables, such as market size and maximum theoretical yield, are important, the carbon value chain offers quick insight into the largest margins that SynBio companies can realize on processes that generally all use sugar ($0.25-$0.50/kg) as an input. The image below depicts approximate current bulk prices for rough categories of potential SynBio products.

Not unlike the booming technology companies that first launched in Silicon Valley garages decades ago, the next step in the evolution of synthetic biology is being built by citizen scientists in their homes or communal labs. One local man is hoping to bring this new wave of scientific exploration to Charlottesville.
Known as do-it-yourself biology, or biohacking, scientists and science enthusiasts are breaking from traditional laboratory environments to practice a variety of scientific disciplines in their garages and kitchens, conducting their own projects and using their own hardware. As this movement continues to grow, lab spaces for members of the community have begun popping up in densely populated cities around the country — and soon, Charlottesville may have one of its own.
University of Virginia graduate Shaun Moshasha is still nailing down the details on a space for Charlottesville Open Bio Labs, a “community bioscience center” aimed at engaging local residents in the practice of biohacking. He started the nonprofit organization with Michael Lake in early 2014, and has been slowly bringing together the area’s scientific community in the form of meet-ups and, just weeks ago, a foray into experimentation in the form of an inaugural cloning class.
“We want Charlottesville Open Bio Labs to enhance the accessibility of STEM (science, technology, engineering and mathematics) education and bioscience to everybody — make people realize that it’s not as daunting or inaccessible as people think,” Moshasha said.