Synthetic biology

“Genetic engineering techniques are abysmally primitive, akin to swapping random parts between random cars to produce a better car. Yet our ignorance will fade; biological engineering will become a reality relatively soon.” – Letter to New York Times, 12 December 2000, by Rob Carlson, synthetic biologist and senior scientist in electrical engineering, University of Washington
Synthetic biology (also known as Synthetic Genomics, Synbio, Systems Biology or Constructive Biology) is construction of new biological parts/systems that donot exist in co-existing natural world or to manipulate the existing ones to perform special human desirable tasks. Synbio is inspired by the advancement of nanoscale biology, computing and engineering. Just about anyone has the potential to construct genes or entire genomes from scratch using a laptop, gene sequence information and synthetic DNA

Synthia

In 2010, scientists of the J. Craig Venter Institute, announced that they had created the only first synthetic bacterial genome, and they had added it to a cell that has no DNA. The resulting bacterium was thus named Synthia by them and is now known as the world's first synthetic life form. Mycoplasma laboratorium is a planned partially synthetic species of bacterium derived from the genome of Mycoplasma genitalium. This effort in synthetic biology is being undertaken at the J. Craig Venter Institute by a team of approximately twenty scientists headed by Nobel laureate Hamilton Smith, and including DNA researcher Craig Venter and microbiologist Clyde A. Hutchison III.

Pat Mooney, of the ETC group, a technology watchdog with a special interest in synthetic biology, said: 'This is a Pandora's box moment - like the splitting of the atom or the cloning of Dolly the sheep, we will all have to deal with the fall-out from this alarming experiment.'

Dr David King, of the Human Genetics Alert watchdog, said: 'What is really dangerous is these scientists' ambitions for total and unrestrained control over nature, which many people describe as 'playing God'.

who is J. Craig Venter..

 

“Within a decade a single person could sequence . . . his or her own DNA within seconds.”

— Rob Carlson,University of Washington.
In 1973 it would take a whole year for a scientist to make eleven base pairs long DNA. Today Khorana’s monumental feat would take minutes and would cost around $200. In the same year that Khorana announced his functional artificial gene (1976),California-based start-up Genentech– the world’s first commercial biotech company – invented a faster, automated method of synthesising genes, and so the gene synthesis industry was born. Now we can send orders to dozens of oligo-sythesizing companies to synthesize our desired DNA sequence. Korea based Bioneer Corporation, for example,has the capacity to produce 20,000 oligos per day.
The world’s first synthetic biology conference convened in June 2004. Two months later, the University of California at Berkeley announced the establishment of the world’s first synthetic biology department. In 2005, three synthetic biology start-ups attracted over $43 million in venture capital.

According to one industry estimate, the current market for gene synthesis is only $30-$40 million per year. Although the United States is currently home to more gene foundries than any other country, the industry is rapidly moving offshore. Most gene synthesis companies produce lengths of DNA smaller than 3kbp at a time (3000 base pairs – a base pair makes one ‘rung’ of the DNA ‘ladder’), however some companies, such as Blue Heron, can synthesise up to 40kbp (40,000 base pairs) of DNA at one go. Some companies boast that there are no technical limits to the length of DNA they can produce (although most sequences are not error-free). GeneArt claims that it can produce a half-million base pairs of DNA per month.
According to engineering professor Drew Endy of Massachusetts Institute of Technology (MIT), “There is no technical barrier to synthesizing plants and animals, it will happen as soon as anyone pays for it.”
Today’s DNA synthesis techniques allow us to put a theoretical price on human life: building the entire enome of a human being – around 3 billion base pairs – could be done today by a bargain basement synthesis company for just over $2.5 billion dollars – well within the reach of several individuals on the planet. Drew Endy of MIT speculates that within 20 years human genomes will be synthesised from scratch.

What does synthetic biology mean for bioweapons?

In 2002, Dr. Eckard Wimmer and his team at the State University of New York at Stony Brook, mail-ordered short sequences of synthetic DNA strands (oligonucleotides) and pasted them together into a functional version of poliovirus. (They injected their de novo virus into to confirm that the pathogen worked.”) When this extreme genetic engineering feat was announced to the world, Wimmer and his team were attacked for their irresponsible work which could be inspiration for terrorists to make a bioweapon. According to Wimmer, the experiment was to illustrate the possibility of constructing such a dangerous pathogen using mail-order parts.
In the last century(1918-1919) H1N1 killed around 50 million people worldwide – higher than that of World War I. In the 1950s when H1N1 strain was eradicated from the earth efforts to reconstruct the highly communcable virus begun. In 1997, Dr. Jeffrey Taubenberger of the US Armed Forces Institute of Pathology in Washington, DC succeeded in recovering and sequencing fragments of the viral RNA from preserved tissues of 1918 flu victims buried in the Alaskan permafrost. Eight years later, Taubenberger’s team and collaborating researchers at Mount Sinai School of Medicine in New York and the US Centers of Disease Control (CDC) in Atlanta announced that they had resurrected the lethal virus. About ten vials of the flu virus were produced with the possibility that more could be made to accommodate research needs.Craig Venter later described the resurrection of the 1918 flu virus as “the first true Jurassic Park scenario”. Two leading technology thinkers, Bill Joy and Ray Kurzweil wrote,“The genome is essentially the design of a weapon of mass destruction. No responsible scientist would advocate publishing precise designs for an atomic bomb…revealing the sequence for the flu virus is even more dangerous.” for publishing the full genome of the 1918 flu virus in the GenBank database.
Richard H. Ebright, a biochemist at Rutgers University, clarified for The Washington Post that it would now be possible and “fully legal for a person to produce full-length 1918 influenza virus or Ebola virus genomes, along with kits containing detailed procedures and all other materials for reconstitution…it is also possible to advertise and to sell the product…” Eckard Wimmer is even more blunt about the potentially deadly combination of accessible genomic data and DNA-synthesizing capabilities: “If some jerk then takes the sequence of [a dangerous pathogen] and synthesizes it, we could be in deep, deep trouble.”
In June 2006, The Guardian (UK) announced that one of its journalists ordered a fragment of synthetic DNA of Variola major (the virus that causes smallpox) from a commercial gene synthesis company and had it delivered to his residential address. The company involved in The Guardian’s investigation, VH Bio Ltd., based in Gateshead, UK, did not screen the requested sequence against the known genome sequences of dangerous microorganisms.

Rebooting Biofuels

“Something I’m really excited about are the synthetic biology projects they’re working on to create new kinds of fuels so we can reduce our dependence on oil and protect our environment.” – Arnold Schwarzenegger, Governor of California. At the US Department of Energy’s (DOE), Patrinos had overseen both the Human Genome Project and more recently the Genomes to Life (GTL) programme – which supports research to focus synthetic biology on the production of biofuels such as ethanol and hydrogen. The current buzz phrase for ethanol is “energy independence.” Environmental groups such as Natural Resources Defense Council (NRDC) are also championing the development of certain types of ethanol that could reduce global emissions of carbon dioxide and prove to be climate-friendly fuel. The biofuel buzz is about to become a boom because the US government mandates that at least 30 percent of transport uel be derived from biofuels (mostly ethanol) by 2030 –requiring roughly 60 billion gallons of ethanol to be produced per year. Brazil is using sugarcane and corn in US for ethanol production but US corn production is energy intensive, requiring massive inputs of fossil fuels for fertilisers, pesticides, tractors, post-harvest processing and transport. The synthetic biology approach is to custom design a microorganism that can utilize wide range of cellulosic biomass to produce ethanol with high yield. A team from the University of Stellenbosch (South Africa), collaborating with engineering professor Lee Lynd at Dartmouth University (USA), has engineered a yeast that can survive on cellulose alone, breaking down the plant’s cell walls and fermenting the derived sugars into ethanol. Meanwhile, Lynd’s group at Dartmouth is working with a modified bacterium that thrives in high-temperature environments and produces only ethanol in the process of fermentation. Lynd hopes to commercialise his technology at a start-up company called Mascoma in Cambridge, Massachusetts (USA). Chairing Mascoma’s board of directors is venture capitalist and ethanol evangelist, Vinod Khosla, also funds another synthetic biology energy company known as LS9, based in the San Francisco Bay area (CA, USA). Similarly, at Purdue University’s Energy Center, Senior Research Scientist, Dr. Nancy Ho, has developed a modified yeast that can produce 40 percent more ethanol from biomass than naturally occurring yeast, and the Nobel Prize-winning head of the prestigious Lawrence Berkeley Lab, Dr. Steven Chu, who grabbed headlines last year when he suggested that synthetic biology could be used to rewire the genetic networks in a cellulose-crunching bug found in the gut of termites. As a first step, the Berkeley Lab is sequencing microorganisms living in the termite’s gut, to identify genes responsible for degrading cellulose.

Synthetic Biology and Intellectual monopoly

Patents have already been granted on many of the products and processes involved in synthetic biology.
Examples include
• Patents on methods of building synthetic DNA strands (US 6,521,427, “Method for the complete chemical synthesis and assembly of genes and genomes,” assigned to Egea Biosciences, a subsidiary of Johnson & Johnson)
• Patents on synthetic cell machinery such as modified ribosomes (WIPO Patent WO05123766A2: “Methods
Of Making Nanotechnological And Macromolecular Biomimetic Structures,” awarded to Alexander Sunguroff)
• Patents on genes or parts of genes represented by their sequencing information (“DNA and Patent Law,” on the Internet: http://www.thebiotechclub.org/industry/ articles/dnapatentlaw.php)
• Patents for the engineering of biosynthetic pathways (WIPO Patent WO05033287A3: “Methods For Identifying A Biosynthetic Pathway Gene Product” claimed by The Regents of the University of California, or US20060079476A1, US patent application entitled, “Method for enhancing production of isoprenoid compounds.”)
• Patents on new and existing proteins and amino acids (WIPO Patent WO06091231A2: “Biosynthetic Polypeptides Utilizing Non-Naturally Encoded Amino Acids” (2006) awarded to Ambrx, Inc)
• Patents on novel nucleotides that augment and replace the letters of DNA (US 5,126,439, “Artificial DNA base pair analogues,” awarded to Harry P. Rappaport; and S.Benner, US Patent 6,617,106, “Methods for preparing oligonucleotides containing non-standard nucleotides.”)

Biosafety and Synbio

Is it safe ? Are they under human control ? Are the precautions more than sufficient to ensure best safety ? People are filled with so many similar questions when it comes to using the products of synbio. “An engineer’s approach to looking at a biological system is refreshing but it doesn’t make it more predictable. The engineers can come and rewire this and that. But biological systems are not simple…And the engineers will find out that the bacteria are just laughing at them.” – Eckard Wimmer, molecular geneticist at the State University of New York at Stony Brook, who synthesised poliovirus. Biological systems are extremely complicated and so far we have reached but still so less we have understood and yet the synbio practitioners don’t hesitate to quote that safety is assured assuming an impossible achievement of mastery over their art when it is wel known that living systems evolve and mutate. Only recently have scientists rejected conventional wisdom about genetic inheritance: no single gene exclusively governs the molecular processes that give rise to a particular inherited trait. They have also discovered that the vast “non-coding” sequences of DNA (so-called “junk” DNA), long considered irrelevant because they yield no proteins, may actually play indispensable roles in affecting an organism’s function, health and heredity. Under such circumstances there is high possibility that many of the scientific assumptions will be rejected and corrected with new ones which may change the whole scenario.

The expansion of genetic code..

The expansion of genetic code is becoming more popular in Synthetic biology. The major benefits associated with it is that it offers one of the best platfortm for transformation of numerous chemical reactions and various processes from the chemical synthetic laboratory into the biology and biochemistry of living cells.

Human gene therapy

Genetic engineering procedures

There are three basic requirements for Genetic engineering requires : the gene which is to be transferred, a host cell where the gene has to be inserted, and a vector through which the transfer of gene is made to the host cell . 

Say, for example, the gene for making insulin has to be inserted into a bacterial cell. Insulin is a naturally occurring protein made by cells in the pancreas in humans and other mammals which carries out the breakdown of complex carbohydrates(sugar) in the blood to glucose. Diabetic people dont the ability to make insulin or they form insufficient amount of insulin. So, the first step  is to obtain a copy of the insulin gene. This copy can be obtained from a natural source, or it can be manufactured in a laboratory.

DNA being injected into a mouse embryo. (Reproduced by permission of Phototake .) (from the DNA in a pancreas, for example)

 The second step is to insert the gene of interest, here insulin gene,  into the vector. The term vector means any living or nonliving particles which will carry the gene of interest from one organism or place to another. The most common vector used in genetic engineering is a circular form of DNA known as a plasmid. Endonucleases are the enzymes that are used to cut the plasmid molecule open at almost any point as per the need of  the scientist. Once the plasmid has been cut open, ligase enzyme is used to ligate the cut portion. This is done to attach the insulin gene itself to the plasmid before the plasmid is reclosed. Thus formed plasmid is called the hybrid plasmid which now contains the gene whose product (insulin) is desired. It can be inserted into the host cell, where it begins to function just like all the other genes that make up the cell in the following ways

1. Transformation
2. Conjugation
3. Transduction  
4. Recombination 

In this case, however, transformation of the insulin gene is done to competent bacterial cells. In addition to normal bacterial functions, the host cell also  produces insulin, due to the inserted gene.

Apart from transformation of competent cells, different physical methods can be used for gene transfer like:

• Transformation by electroportation,  
• Micro particle bombardment technique for gene transfer, 
• PEG (Polyethylene Glycol) mediated gene transfer, 
• Liposome mediated gene transfer, 
• Ultrasound mediated gene transfer and   

different plant viruses like Caulimovirus and Gemini virus and bacteria like Agrobacterium can be used for the process of gene transformation.