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Tuesday, 30 December 2014

Synthetic DNA and artificial cell  what are the ethical issues its application in the real life and in human disease at cost of 400 million dollars Research"

Authors are
o*Professor Pranab Kumar Bhattacharya MD(cal univ) FIC path(Ind),Professor Dept of pathology
*Rupak Bhattacharya Bsc(cal.univ )MSc(JU), **Ritwik Bhattacharya, **Somayak Bhattacharya BSC (HM)(IGNOU)  MSc( PUSHA) - Asst Lecturer of IHM Ahemadabad India - Residences 7/51 Purbapalli,Sodepur, Kol­110, ***Miss Upasana Bhattacharya - “  Only Daughter of Prof PK Bhattacharya  **Dalia Mukherjee BA(hons) cal Univ, Miss Oindrila Mukherjee, Miss Ayshi Mukherjee    Dr Hriday Das MD(cal.Univ ) DTM&H(cal Univ) Dr Tarun Biswas MBBS(cal Univ) Dept of Pathology
*Previously  at Institute of Post Graduate Medical Education Research 244 AJC Bose Road kol-20 West Bengal, India, Now Posted as Professor&HOD of Pathology  at Murshidabad District Medical College Behrampore Murshidabad West Bengal
Published online 24 May 2010 | Nature | doi:10.1038/news.2010.261

A synthetic creation story Claims of 'synthetic life' reflect only our changing conception of what life is and how it might be made, says Philip Ball. Philip Ball Last week's announcement of the 'chemical synthesis of a living organism' by Craig Venter and his colleagues at the J. Craig Venter Institute1heads up a very long tradition. Claims such as this have been made throughout history.That's not to cast aspersions on the new results. One can challenge the idea that Venter's bacterium stands apart from Darwinian evolution, modelled as it is on Mycoplasma mycoides.It is nonetheless an unprecedented triumph of biotechnological ingenuity.
But, set in a historical context, what the researchers have achieved is not so much a 'synthesis
of life' as a semi-synthetic recreation of what we currently deem life to be. And, as with
previous efforts, it should leave us questioning the adequacy of that view.
To see that the new results reiterate a perennial theme, consider the headline of the Boston
Herald in 1899: "Creation of Life. Lower Animals Produced by Chemical Means." The article
described how German biologist Jacques Loeb induced an unfertilized sea-urchin egg to divide
and develop into a larva by treating it with salts. Loeb went on to talk in earnest about "the artificial production of living matter", and he was not alone in blending his discovery with speculations about the de novo creation of life. In 1912, the physiologist Edward Albert Schäfer alluded optimistically to Loeb's results in his presidential address to the British Association, in which he expressed great optimism about "the possibility of the synthesis of living matter"2 .Such claims are commonly seen to imply that artificial human life is next on the agenda. It wasa sign of the times that the New York Times credulously reported in 1910 that, "Prof.Herrera, a Mexican scientist, has succeeded in forming a human embryo by chemical combination". It is surely no coincidence that many media reports have compared Venter to Frankenstein, or that the British newspaper The Observer mistakenly suggested he has"succeeded in 'creating' human life for the first time".
What is life?
Beliefs about the feasibility of making artificial organisms have always been governed by the
prevailing view of what life is. When the Universe was seen as an intrinsically fecund matrix,
25-5-2010 A synthetic creation story : Nature Ne……/news.2010.261.html 1/7“'Life' in biology,rather like 'force'in physics, is aterm carried over from a time when scientists thought quite differently,when it served as a makes hift bridge over the inexplicable.”permitting bees and vermin to emerge from rotten flesh by spontaneous generation, it seemed natural to imagine that sentient beings might issue forth from insensate matter. Mechanical models of biology developed during the seventeenth century fostered the idea that a 'spark of life' — after the discovery of electricity, literally that — might animate a suitably arranged assembly of organic parts. The blossoming of chemistry and evolutionary theory in the nineteenth century, meanwhile, spurred a conviction that it was all about getting the recipe right, so that nature's diverse grandeur sprung from primordial colloidal jelly called protoplasm. Yet each apparent leap forwards in this endeavor more or less coincided with a realization that the problem is not so simple. Protoplasm appeared as organic chemists were beginning to erode the concept of vital ism and to appreciate the baffling constitution of organic matter. The claims of Loeb and Schäfer came just before tools for visualizing the sub cellular world began to show the incredible complexity of life's micro structure. And it was the same story for the next big splash in 'making life', when in 1953 Harold Urey and Stanley Miller announced their celebrated 'prebiotic soup' experiment, in which they conjured amino acids from simple raw materials. Some press reports regarded this as a new genesis, in principle if not in practice. Yet that same year saw the game-changing discovery oflife's informational basis in the work of Crick and Watson. Now life was not so much about molecules, but about cracking, and perhaps then rewriting, the genetic code.No more codes Which brings us to Venter et al. Now that the field of genomics has fostered the belief that in sequencing genomes we are reading a 'book of life', it's easy to see why 'booting up' a wholly synthetic genome in a bacterial host should be popularly deemed a synthesis of life itself. Here the membranes, the cytoplasm — everything except the genes — are mere peripherals to the hard drive of life, whose algorithmic instructions need only be rejigged to produce new organisms. But this latest work should encourage us to lay aside the very concepts of an 'artificial organism'and a 'synthesis of life'. Life is not a thing one makes, nor is it even a process that arises or is set in motion. It is a property we may chooseto bestow, more or less colloquially, on certain organizations of matter.25-5-2010 A synthetic creation story : Nature News……/news.2010.261.html 2/7#10725
Comment  No#10725
Title­"Synthetic DNA and artificial cell – what are the ethical issues its application in the
real life and in human disease at cost of 400 million dollars Research"
o*Professor Pranab Kumar Bhattacharya MD(cal) FIC path(Ind),Professor Dept of pathology
oRupak Bhattacharya Bsc(cal)MSc(JU), Ritwik Bhattacharya, Somayak Bhattacharya MBA 7/51 Purbapalli,Sodepur, Kol­110, Miss Upasana Bhattacharya – daughter of Prof PK Bhattacharya Dr. Avisnata Das MBBs(cal) Dalia Mukherjee BA(hons) cal Miss Oindrila Mukherjee, Mrs Chandrani Dutta BSC(Zoology)* Dr Hriday Das MD(cal) DTM&H(cal) *Dr Tarun Biswas MBBS(cal) Dept of Pathology
*Institute of Post Graduate Medical Education Research 244a AJC Bose Road kol-20 West Bengal,
25-5-2010 A synthetic creation story : Nature Ne……/news.2010.261.html 3/7 India

Artificial life is a field of study and an associated art form which examine systems related to life, its
processes, and its evolution through simulations using computer models, robotics, and biochemistry.
There are three main kinds of artificial life named for their approaches: soft from software; hard , from hardware; and wet, from biochemistry molecules. Artificial life imitates traditional biology by trying to recreate biological phenomena. Artificial life has had a controversial history. John Maynard Smith11 criticized certain artificial life work in 1994 as "fact-free science". However, the recent publication of artificial life articles in widely read world’s top impact factor and coveted science journals such as Science and Nature is evident that artificial life techniques are becoming more accepted in the mainstream­as synthetic biology, at least as a method of studying Darwin’s Chemical evolution. Synthetic and self replicating DNA or RNA is part of such an artificial life and tool for studying evolution of life in earth. Evolving such an artificial DNA in laboratory was thus for long years before attempt of research since Watson and Crick Double Helix. The artificial DNA-like molecule directed the synthesis of copies of itself and then copies of the copies, mimicking the natural process of evolution as it was first outlined by Charles Darwin. A polynucleotide is a building block of DNA, or a "letter" in the genetic alphabet used to write the "book" describing our genetic inheritance. The first Synthetic Virus was done in 2002 in stony brook university Newyork by a team of scientist led by Eckarde wimmr (Science, 9 August 2002, p. 1016) Benner and Michael Sismour- two Graduate student of university of California in 2004 first made a synthetic DNA of 12 nucleotides of a virus but it could not however copied itself. In 2010, The first synthetic and self replicating DNA /cell as a bacterium has been claimed by Professor Dr C J Venter of J. Craig Venter Institute (JCVI) in Rockville, Maryland, and San Diego, California, [ He was best known for his work with the Human Genome Project] is successful and same is published in journal the science[ 1]. The cell is claimed totally derived from a synthetic chromosome [They bought it from a company more than 1000 -1080-base sequences that covered the whole M. mycoides genome], made with four bottles of chemicals on a chemical synthesizer, starting with information and using genetic code created by a super computer. The Venterâ team [20 members team] synthesized the largest piece of DNA so far ” a million units in length ” and in making it accurate enough to substitute for the cell  own DNA at cost of $40 million research. Venter's team said they worked with a synthetic version of the DNA from a small bacterium called Mycoplasma mycoides which was transplanted into another bacterium called Mycoplasma capricolum, which had most of its insides DNA removed. The new microbe came to life and began replicating in the lab dish. Specifically, the team showed that the artificially created DNAlike molecule containing six gene ­building nucleotides – instead of the four found in natural DNA –could support the molecular "photocopying" operation known as polymerase chain reaction. The genome Dr. Venter synthesized is copied from a natural bacterium that infects goats. 580,000 DNA units in length, of a small bacterium, Mycoplasma genitalium. His goal however was to make cells that might take carbon dioxide out of the atmosphere and produce methaneose .Replacing the genome of any bacterial cell with one from another species by transplanting a whole genome as naked DNA is however a long known method as gene cloning[3] / and or gene transfer mechanism called genome transplant. Gene cloning will result a new species[ 2] De novo synthesis of a self replicating bacterial or human DNA is here an increasingly valuable resource for a broad research and future application. Synthesis of Gene /DNA is also not new but an old concept. Synthesis of gene length (1-3Kb) DNA is however very common. The Process of Synthetic DNA construction involves the assembly of Overlapping Oligonucleotides into contiguous fragments of dsDNA using PCR based and or ligation based methods[4 ,5] or by Pair wise Selection assembly(PSA) methods for large scale long length automated synthetic DNA production more then 91Kb DNA6, where A target assembly sequence is broken down into sub-fragments that are synthesized with flanking tags .At PSA level 0, sub-fragments are inserted into one of two PSA vectors where tags activate two, diver gently oriented select-able 25-5-2010 A synthetic creation story : Nature Ne……/news.2010.261.html 4/markers . Level 0 sub-fragment pairs are excised so that only one activation tag is retained for each sub-fragment. Subsequent pair ligation occurs in a second PSA vector where tags activate a second set of select-able markers , producing a PSA level 1 product. This hierarchical process is repeated, switching between two vectors with different selectable markers, until the full-length product is assembled 6.Recently, recombination-based methods were also used range of applications to construct a 134-kb fragment in Bacillus subtilis and 583- Kb fragment of Saccharomyces cerevisiae Synthetic DNA (7,8 ). While synthesis of gene ­length DNA (13 kb) is common, the ability to quickly and cost effectively assemble longer-length DNA (>10 kb) remained of course a challenge. 256 orthologous
genes shared by the Gram-negative Haemophilus influenzae and the Gram-positive bacterial life
Mycoplasma genitalium genomes are a close approximation of a minimal gene set . The Mollicutes,
generically known as the mycoplasmas, are the best experimental platform for experimentally defining a minimal gene set. Mycoplasmas are obligate parasites that live in relatively unchanging nichesrequiring little adaptive capability. M. genitalium, a human urogenital pathogen, is the extreme manifestation of this genomic parsimony, having only 482 protein-coding genes and the smallest genome, at 580 kb, of any known free-living organism capable of being grown in axenic culture[9]
Mycoplasma genitalium has the smallest genome of any organism that can be grown in pure culture. It has a minimal metabolism and little genomic redundancy. Consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. To construct synthetic DNA of Mycoplasma genetelium it is always very essential to identify and delete all the putative nonessential gene, isolation and characterization of trasposon mutants and mixture of mutant genes butpreservation and non-disruptions of DNA recombination & six DNA repair gene like recA,recU, DNA hellicase gene like ruvA, ruvB DNA Glycosylase gene mute M which excises oxidized purine from DNA and DNA damage inducible gene[10]In 1995, a team led by the trio Venter, Smith and Hutchison sequenced the 600,000-base chromosome of bacterium Mycoplasma genitalium, the smallest genome of a free-living organism. The microbe has about 500 genes, and researchers found they could delete100 individual genes without ill effect (Science, 14 February 2003, p. 1006) In 2007, Venter, Smith,Hutchison, and colleagues finally demonstrated that they could transplant natural chromosomes fromone microbial species to another (Science, 3 August 2007, p. 632). By 2008, they showed that theycould make an artificial chromosome that matched M. genitalium's but also contained "watermark"DNA sequences that would enable them to tell the synthetic genome from the natural one (Science, 29February 2008, p. 1215) The first Synthetic Virus was done in 2002 in stony brook university Newyork by a team of scientist led by Eckarde wimmr (Science, 9 August 2002, p. 1016)
The synthetic genome created by Venter's team is almost identical to that of a natural bacterium. It
was achieved at great expense; an estimated $40 million, and effort, 20 people working for more than
a decade. Dr. Venter took a first step toward this goal three years ago, showing that the natural DNA
from one bacterium could be inserted into another and that it would take over the host cell’s
operation. He said that before copying the DNA, he excised 14 genes likely to be pathogenic, so the
new bacterium, even if it escaped, would be unlikely to cause goats harm.Dr. Venter calls the result synthetic cell and is presenting the research as a landmark achievement that will open the way to creating useful microbes from scratch to make products like biofuels. At a press conference Thursday, Dr. Venter described the converted cell as “the first self replicating species weâve had on the planet Though the scientists claim for creation of artificial living cell “He has not created life, only mimicked it,â€what we want to say There remains much about the ethical issues to be solved
1] Consequence of progress in the new field of synthetic biology is an emerging view of cells as
assemblages of parts that can be put together to produce an organism with a desired phenotype
2].Over the long term, the approach will be used to synthesize increasingly novel designed genomes,
and may be a tool for bioterrorism and we need protections from military or terrorist misuse and
25-5-2010 A synthetic creation story :
3]. Will the newer synthetic biology help human mankind by detecting where is the defect lies the
human genome that give rise cancer or in formulation of new drug or vaccine?
4]. is it a step towards ... creation of living beings or artificial life with capacities and natures that could
never have naturally evolved."
5]. In Future Can some one will design for Human clone?
Nature Ne……/news.2010.261.html 5/7 comment 2010-05-25 08:14:52 AM  Posted by: Prof. Pranab Kumar Bhattacharya
1] Elizabeth Pennisi Synthetic Genome Brings New Life to Bacterium News of the Week Genomics:
Science 21 May 2010:Vol. 328. no. 5981, pp. 958 – 959 DOI: 10.1126/science.328.5981.958

2] R. L. Warren, J. D. Freeman, R. C. Levesque, D. E. Smailus, S. Flibotte, and R. A. Holt Transcriptionsof foreign DNA in Escherichia coli Genome Res. 18, 1798-1805. 2008

3] G. A. Benders, V. N. Noskov, E. A. Denisova, C. Lartigue, D . G. Gibson, N. AssadGarcia,
R. Y. Chuang, W. Carrera, M. Moodie, M. A. Algire, et a Cloning wholebacterial genomes in yeast. Nucleic Acids Res. 38, 2558-2569 2010

4] Tian,J., Gong,H., Sheng,N., Zhou,X., Gulari,E., Gao,X. andChurch,G. (2004) Accurate multiplex
gene synthesis fromprogrammable DNA microchips. Nature, 432, 1050–1054.

5] Mandecki,W. and Bolling,T.J. (1988) FokI method of genesynthesis. Gene, 68, 101–107.

6] *, William J. Blake Brad A. Chapman, Anuradha Zindal, Michael E. Lee, Shaun M. Lippow and BrianM. Baynes , Pair wise selection assembly for sequence-independent construction of long-length DNANucleic Acids Research, 2010, Vol. 38, No. 8P 2594–2602 Published online 1 March 2010

7] Gibson,D.G., Young,L., Chuang,R.Y., Venter,J.C.,Hutchison,C.A. III and Smith,H.O. (2009)
Enzymatic assembly ofDNA molecules up to several hundred kilo bases. Nat. Methods, 6, 343â

8] Gibson,D.G., Benders,G.A., Andrews-Pfannkoch,C.,Denisova,E.A., Baden-Tillson,H., Zaveri,J.,
Stockwell,T.B., Brownley,A., Thomas,D.W., Algire,M.A. et al Complete chemical synthesis, assembly,and cloning of a Mycoplasma genitalium genome., Science 319, 1215–1220.2008

9] Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A.,Fleischmann, R. D., Bult, C. J.,Kerlavage, A. R., Sutton, G., Kelley, J. M., et al. 1995) Science 270, 397–403.1995

10] John I. Glass, Nacyra Assad-Garcia, Nina Alperovich, Shibu Yooseph, Matthew R. Lewis, Mahir
Maruf,Clyde A. Hutchison III, Hamilton O. Smith*, and J. Craig Venter Essential genes of a minimal
bacterium, proceeding Nat Academy Science USA PNAS _ January 10, 2006 _ vol. 103 ,425-30

11] Horgan, J. 1995. From Complexity to Perplexity. Scientific American. p107
 This comment is cited by 2
1] Synthetic Cells and Their Regulatory Challenges by J C Varela - Eur. J. Risk Reg., 2010 - Hein Online

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