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Scientists Create First Cell Controlled by Synthetic Genome - TøbiasBlack - 2010-05-20
article source: http://abcnews.go.com/Technology/scientists-create-cell-controlled-synthetic-genome/story?id=10692639
ABC News Wrote:It may not quite be "Frankenstein," but for the first time scientists have created an organism controlled by completely manmade DNA.
Using the tools of synthetic biology, scientists from the J. Craig Venter Institute installed a completely artificial genome inside a host cell without DNA. Like the bolt of lightening that awakened Frankenstein, the new genome invigorated the host cell, which began to grow and reproduce, albeit with a few problems.
The research marks a technical milestone in the synthesis and implantation of artificial DNA. Venter, along with dozens of other companies and researchers in the same field, expects the research will lead to cheaper drugs, vaccines and biofuels in several years.
"This is the first synthetic cell that's been made," said Venter. "We call it synthetic because the cell is totally derived from a synthetic chromosome, made with four bottles of chemicals on a chemical synthesizer, starting with information in a computer."
The research, published today in the journal Science, combines two of Venter's past achievements.
In 2007 Venter transplanted the genome of one Mycoplasma bacterium into another. Venter and his colleagues also synthesized a trimmed down, artificial version of Mycoplasma's DNA, a project known as the Minimal Genome Project. Attempts to implant the synthetic DNA all failed, until now.
In the current research Venter and his colleagues, which includes Nobel laureate Hamilton Smith, first synthesized Mycoplasma's full genome. Then they added hundreds of thousands of additional base pairs to "watermark" the DNA to distinguish it from a natural one.
Venter and his colleagues created a special code, similar to Morse code, to "write" within the DNA itself. Instead of dots and dashes, they used the sequence of four DNA nucleotides, thymine (T), guanine (G), cytosine ©, and adenine (A), as a code for any letter, number or punctuation mark. Using the code, the team included the names of the study co-authors, a website, and even several philosophical quotes, complete with punctuation.
DNA Made by Machine
The completed DNA sequence was more than one million base pairs long. The human genome, by comparison, is more than three billion base pairs long.
No machine can turn out a single piece of DNA anywhere close to that long, however. Instead, Venter and his colleagues started with many relatively small pieces of DNA. Then the scientists transferred DNA pieces back and forth between a yeast cell and E. coli bacteria, turning the many short pieces into fewer but longer DNA segments.
opinions guys? I'm already starting to think we're one step closer to Terminator with this mixed with the advent of Ferrofluids.
Scientists Create First Cell Controlled by Synthetic Genome - Swerve - 2010-05-20
You do realize that this is what happens to 97% of soybeans and 60% of corn in regards to American produce. The news always feels that it is necessary to treat it's readers like juvenile school children who haven't grasped the basic fundamentals of biology.
ABC Wrote:Venter and his colleagues created a special code, similar to Morse code, to "write" within the DNA itself. Instead of dots and dashes, they used the sequence of four DNA nucleotides, thymine (T), guanine (G), cytosine ©, and adenine (A), as a code for any letter, number or punctuation mark. Using the code, the team included the names of the study co-authors, a website, and even several philosophical quotes, complete with punctuation.
This is basic genetics, it is not "special code" nor is it similar to "Morse code." It is a piece of DNA that contains a promoter which is activated by...
Scientists Create First Cell Controlled by Synthetic Genome - Alloy - 2010-05-20
Swerve Wrote:You do realize that this is what happens to 97% of soybeans and 60% of corn in regards to American produce. The news always feels that it is necessary to treat it's readers like juvenile school children who haven't grasped the basic fundamentals of biology.
This is basic genetics, it is not "special code" nor is it similar to "Morse code." It is a piece of DNA that contains a promoter which is activated by...
Nope. Genetically MODIFIED cells simply alter an existing DNA and make the cell adapt to it.
These guys created DNA out of scrap, added it to a cell, AND IT WORKED. Using chemicals, these guys CREATED THE VERY BASIS OF LIFE.
Scientists Create First Cell Controlled by Synthetic Genome - Swerve - 2010-05-20
You know that when you modify a cell, you usually are using a DNA created out of scrap by oligo-dT primers and then have genetic recombination using annealing arms between that sequence or the host sequence. Or you can use microorganisms such as bacteria in order to transfer the genetic code. The article itself didn't specify whether the host cell had transcription factors that allowed it to process the DNA. Because it would be impossible for the DNA sequence to express itself without a transcription factor to connect to the promoter sequence and to activate the coding of the genes present in the engineered DNA strand. When we talk about an entirely synthetic cell the news article leaves out details about how much of the host cell was used and what types of enzymes, carbohydrates, and other structures were present before the new strand of DNA was introduced. The following sentence, "No machine can turn out a single piece of DNA anywhere close to that long, however. Instead, Venter and his colleagues started with many relatively small pieces of DNA. Then the scientists transferred DNA pieces back and forth between a yeast cell and E. coli bacteria, turning the many short pieces into fewer but longer DNA segments" indicates the possibility that they were able to identify restriction markers along the chromosome and simply performed numerous gene recombinations with the host strand until they got their completely synthesized DNA strands to replace the host strands. Again this is done often in biotechnology, it's just that no one bothers to transplant a whole genome because it's not very sensible or effective. Only certain genes are targeted for phenotypic attributes such as taste, color, or other factors and then a synthesized strand that is supposed to either disable those genes or insert new features is supposed to replace them via a specific sequence on the engineered plasmid or chromosome. It is an extension of what is normally done on many biotechnologically engineered crop strains in order to form better cultivars. Except they decided to try to do it for the whole genome... instead of focusing on a specific trait.
Scientists Create First Cell Controlled by Synthetic Genome - TøbiasBlack - 2010-05-20
Alloy Wrote:Nope. Genetically MODIFIED cells simply alter an existing DNA and make the cell adapt to it.
These guys created DNA out of scrap, added it to a cell, AND IT WORKED. Using chemicals, these guys CREATED THE VERY BASIS OF LIFE.
^
This, and thank you for clarifying this for me. im a dunce when it comes to actual scientific terms, and trying to reiterate how i interpret things, but thats basically what i meant by that comment "I'm already starting to think we're one step closer to Terminator with this mixed with the advent of Ferrofluids;" nanotechnology will eventually reach a point where computers can be made so small they can be fitted into micromachines. combine that with a liquid metal thats capable of changing its form via magnetic forces, and... computer synthesized cells(?), and you've got the basics of a Terminator by my book. (note: never seen any of the Terminator movies, but i know enough of the lore of the machines.)
Scientists Create First Cell Controlled by Synthetic Genome - TøbiasBlack - 2010-05-20
Sorry for double post, but found this link from a 'friend' on facebook.
http://www.jcvi.org/cms/research/projects/first-self-replicating-synthetic-bacterial-cell/overview/
this is about the same thing, and im reading this one versus just watching the thing on abc world news then c+p'ing the article here.
Scientists Create First Cell Controlled by Synthetic Genome - Swerve - 2010-05-20
TøbiasBlack Wrote:^
This, and thank you for clarifying this for me. im a dunce when it comes to actual scientific terms, and trying to reiterate how i interpret things, but thats basically what i meant by that comment "I'm already starting to think we're one step closer to Terminator with this mixed with the advent of Ferrofluids;" nanotechnology will eventually reach a point where computers can be made so small they can be fitted into micromachines. combine that with a liquid metal thats capable of changing its form via magnetic forces, and... computer synthesized cells(?), and you've got the basics of a Terminator by my book. (note: never seen any of the Terminator movies, but i know enough of the lore of the machines.)
You completely missed posting the second page of the linked article you provided which contains the following text:
ABC Wrote:Once the synthetic DNA segment reached the desired length the scientists injected it into a Mycoplasma bacterium that had had its own DNA removed earlier. Needless to say, the process of assembling such a lengthy piece of synthetic DNA was complicated.
"I hope the day comes when making genomes is something everyone can do," said Pamela Silver, a systems biologist at Harvard Medical School.
The new, synthetic DNA "booted up" the bacterium, but not without a few problems; several of the synthesized genes didn't work properly. And the genes that did work didn't do anything particularly useful, at least by human standards.
The Mycoplasma bacteria grew and reproduced, but that was about all. Within several years however, Venter, along with dozens of other researchers and companies, hope to create more exciting bacteria that will speed up the production and drive down the costs of biofuels, vaccines and drugs.
Venter has teamed up with a major oil and gas company, and a pharmaceutical company, to help realize these goals.
Venter's work falls into a nascent field of science known as synthetic biology. Synthetic biology builds on the decades-old field of genetic engineering. Unlike genetic engineering, where scientists introduce a handful of new genes into an organism, synthetic biology aims to reprogram entire organisms, including bacteria and viruses.
A Step on the Way to Artificial Life?
The creation and insertion of a synthetic genome more than one million base pairs is a technical landmark, said Frances Arnold, a synthetic biologist at the California Institute of Technology in Pasadena. He says the feat showcases scientists' ability to precisely manipulate long sections of DNA.
But before consumers see any benefit several significant hurdles have to be solved. One of the biggest problems is that scientists are still searching for the specific genetic code to produce cheap drugs, biofuel and other products.
"We can write anything we want," said Arnold. "The problem is that we don't know what to write."
The experiment was successful in the fact that a host genome was taken up by the cell. But the traits encoded by that host were largely not expressed and described to have no large importance in terms of human quantification. In general if they didn't attempt to insert the whole genome, then this experiment would be a failure as the genetic exchange didn't have a benefit for humanity... which is why we use genetic engineering in the first place...
Scientists Create First Cell Controlled by Synthetic Genome - Russt - 2010-05-20
Swerve Wrote:The news always feels that it is necessary to treat it's readers like juvenile school children who haven't grasped the basic fundamentals of biology.
Lowest common denominator.
Scientists Create First Cell Controlled by Synthetic Genome - Swerve - 2010-05-20
Russt Wrote:Lowest common denominator.
That mathematical term is too advanced for use in a news article.
Scientists Create First Cell Controlled by Synthetic Genome - Alloy - 2010-05-20
Swerve Wrote:The experiment was successful in the fact that a host genome was taken up by the cell. But the traits encoded by that host were largely not expressed and described to have no large importance in terms of human quantification. In general if they didn't attempt to insert the whole genome, then this experiment would be a failure as the genetic exchange didn't have a benefit for humanity... which is why we use genetic engineering in the first place...
The thing is not that they inserted the new genome. Heck, viruses already insert their genome into bacteria to reproduce, it has happened before loads of times, everytime you get a cold. The difference is that scientists pulled that genome out of fancy lab bottles. THAT'S where the news is.
Scientists Create First Cell Controlled by Synthetic Genome - Swerve - 2010-05-20
Alloy Wrote:The thing is not that they inserted the new genome. Heck, viruses already insert their genome into bacteria to reproduce, it has happened before loads of times, everytime you get a cold. The difference is that scientists pulled that genome out of fancy lab bottles. THAT'S where the news is.
The following is a scientific journal abstract on the experiment:
[SIZE="5"]
Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides
[/SIZE]We have improved upon the methodology and dramatically shortened the time required for accurate assembly of 5- to 6-kb segments of DNA from synthetic oligonucleotides. As a test of this methodology, we have established conditions for the rapid (14-day) assembly of the complete infectious genome of bacteriophage φX174 (5,386 bp) from a single pool of chemically synthesized oligonucleotides. The procedure involves three key steps: (i) gel purification of pooled oligonucleotides to reduce contamination with molecules of incorrect chain length, (ii) ligation of the oligonucleotides under stringent annealing conditions (55°C) to select against annealing of molecules with incorrect sequences, and (iii) assembly of ligation products into full-length genomes by polymerase cycling assembly, a nonexponential reaction in which each terminal oligonucleotide can be extended only once to produce a full-length molecule. We observed a discrete band of full-length assemblies upon gel analysis of the polymerase cycling assembly product, without any PCR amplification. PCR amplification was then used to obtain larger amounts of pure full-length genomes for circularization and infectivity measurements. The synthetic DNA had a lower infectivity than natural DNA, indicating approximately one lethal error per 500 bp. However, fully infectious φX174 virions were recovered after electroporation into Escherichia coli. Sequence analysis of several infectious isolates verified the accuracy of these synthetic genomes. One such isolate had exactly the intended sequence. We propose to assemble larger genomes by joining separately assembled 5- to 6-kb segments; ≈60 such segments would be required for a minimal cellular genome.
Scientists Create First Cell Controlled by Synthetic Genome - Alloy - 2010-05-20
Swerve Wrote:The following is a scientific journal abstract on the experiment:
[SIZE="5"]Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides[/SIZE]
We have improved upon the methodology and dramatically shortened the time required for accurate assembly of 5- to 6-kb segments of DNA from synthetic oligonucleotides. As a test of this methodology, we have established conditions for the rapid (14-day) assembly of the complete infectious genome of bacteriophage φX174 (5,386 bp) from a single pool of chemically synthesized oligonucleotides. The procedure involves three key steps: (i) gel purification of pooled oligonucleotides to reduce contamination with molecules of incorrect chain length, (ii) ligation of the oligonucleotides under stringent annealing conditions (55°C) to select against annealing of molecules with incorrect sequences, and (iii) assembly of ligation products into full-length genomes by polymerase cycling assembly, a nonexponential reaction in which each terminal oligonucleotide can be extended only once to produce a full-length molecule. We observed a discrete band of full-length assemblies upon gel analysis of the polymerase cycling assembly product, without any PCR amplification. PCR amplification was then used to obtain larger amounts of pure full-length genomes for circularization and infectivity measurements. The synthetic DNA had a lower infectivity than natural DNA, indicating approximately one lethal error per 500 bp. However, fully infectious φX174 virions were recovered after electroporation into Escherichia coli. Sequence analysis of several infectious isolates verified the accuracy of these synthetic genomes. One such isolate had exactly the intended sequence. We propose to assemble larger genomes by joining separately assembled 5- to 6-kb segments; ≈60 such segments would be required for a minimal cellular genome.
If I understood correctly, that is grabbing pieces of DNA and strapping them together, isn't it? Because I know english and all, but I'm not into scientific terms. If that's the case, I believe it seems to grab existing DNA from other organisms, and tape them together to form a new DNA chain with the desired results.
If that's the case, this article talks about CREATING those pieces separately out of chemicals, then taping them together, because they couldn't make long DNA chains in one go. Without a previous organic being. Well, except the clever scientist. Therefore, these guys are a step closer to creating life out of a pool of chemicals.
EDIT: Ok. I have no idea what all that means. I only know the basic stuff, and what I've been told. What do you mean with all that?
Scientists Create First Cell Controlled by Synthetic Genome - Swerve - 2010-05-20
Genomes aren't magically pulled out of lab bottles or mixed together haphazardly in order to form genetically engineered strands. It's like stating that civil engineers magically draw rectangles together in order to make houses or organic chemists draw doodles in order to create final organic products. Computer scientists who press buttons to create programs. You don't simply mix together chemicals in order to create a new nucleotide strand. Bacteria are living organisms that are used as a host cell. They are not synthetic. In addition nucleotides depend on enzymes such as ligase in order to bind it together. It's not all synthesizing chemicals. It's a manipulation of a biological process in order to express desired genes... it's not so much chemical as biological.
I'll describe the Venter paper... when I feel like it.
Scientists Create First Cell Controlled by Synthetic Genome - Alloy - 2010-05-20
Swerve Wrote:Genomes aren't magically pulled out of lab bottles or mixed together haphazardly in order to form genetically engineered strands. It's like stating that civil engineers magically draw rectangles together in order to make houses or organic chemists draw doodles in order to create final organic products. Computer scientists who press buttons to create programs. You don't simply mix together chemicals in order to create a new nucleotide strand. Bacteria are living organisms that are used as a host cell. They are not synthetic. In addition nucleotides depend on enzymes such as ligase in order to bind it together. It's not all synthesizing chemicals. It's a manipulation of a biological process in order to express desired genes... it's not so much chemical as biological.
I'll describe the Venter paper... when I feel like it.
Quote:"This is the first synthetic cell that's been made," said Venter. "We call it synthetic because the cell is totally derived from a synthetic chromosome, made with four bottles of chemicals on a chemical synthesizer, starting with information in a computer."
Seems like they did. They did magically make a rectangle. Oh wait, that didn't make sense. Normal genetic engineering doesn't magically make DNA. This case seems not so normal though, as they used a computer to create the chain from scratch.
And if it's so uninteresting, why did it appear in the news? If they just grabbed pieces of DNA, and pasted it on another, it'd be just tweaking DNA.
EDIT:By the way, that post can't be of this last news thing... The date's from 2003. Sure, things take their time, but 7 years doesn't seem like this one.
Scientists Create First Cell Controlled by Synthetic Genome - Swerve - 2010-05-20
Alloy Wrote:Seems like they did. They did magically make a rectangle. Oh wait, that didn't make sense. Normal genetic engineering doesn't magically make DNA. This case seems not so normal though, as they used a...
a. computer to create the chain from scratch.
b. And if it's so uninteresting, why did it appear in the news? If they just grabbed pieces of DNA, and pasted it on another, it'd be just tweaking DNA.
c. EDIT:By the way, that post can't be of this last news thing... The date's from 2003. Sure, things take their time, but 7 years doesn't seem like this one.
a. Bioinformatics is used to often ascertain genetic information via statistics and computer science. b. Well I tried doing another search through google scholar and I found articles listed to 2008. Unfortunately you aren't able to open full text to look at procedures. But I found one that has full text listed in c. c. I went to google scholar and put in: Venter + synthetic genome. That was the first result I got. Here is another result which is more recent (2008). A quick check on the article indicates that they used restriction endonuclease in order to digest the DNA segments. To be honest, if you want to think of it as chemicals then that's fine. To me, enzymes aren't chemicals and using them in order to prepare the experiment means that it is not exclusively chemical. I was angry at the simplification put forth in the news story. Guanine, Cytosine, Thymine, and Adenine are the four base nucleotides used in order to synthesize genetic information. This does not explain the experimental procedure, but rather just introduces a very basic set of information explained in general Biology. I was annoyed that this article in my opinion is sensationalism. Again, if you think that this is pivotal then I apologize. I overreacted and got really angry over how this issue was presented. I could explain the experiment prep and all about biotechnology but that would take days for me to prepare from the basics. I'm sorry but I don't care about this article to that extent, as I would be spending more time explaining the scientific basis of the article compared to the writer who contributed it. This has been a long time hatred of me with how the news portrays science and it came out on this topic that I have a certain degree of familiarity. I apologize for my conceited and anti-news attitude. But I wrote an explanation in #4 and that really holds the crux of my argument on this issue. In the first experimental procedure I listed, Taq polymerase was used in addition to lysozyme in order to carry out the experiment with the bacteriophage. I apologize but I have nothing more to say on this topic. I'm sorry I acted conceited but it was only because I really hated this article because of it's ignorance of scientific detail. If you disagree then feel free to post it. I will most likely read it. But at this point I am not in the mood to offer another response as this is more or less a restatement of post #4. In general news articles aren't written about a lot of amazing things. For example the development of semi-dwarf resistant rice varieties didn't receive as much coverage as Monsanto releasing it's newly patented soybean resistance crop back in February which has a gene that negates the potent insecticide that the company sells called "Round-Up." It is my impression that the news is biased and subjective, especially in the area of science. Medical discoveries have precedence over discoveries in plants and animal wildlife. Even though consumption of plants and animals are important to preserving the human condition through nutrition and sustenance. The news also tends to pursue politics at the forefront of it's pages rather than endorse ground-breaking research being completed in labs. Again, Russt and I touched upon the fact that the news is written for an audience. An audience that is more likely to understand issues such as politics, abortion, and Sarah Palin rather than concepts such as nucleophile substitution, Higgs mechanis, and Norman Borlaug. Again there is nothing wrong with that. It's just disappointing that the news often misconstrues these issues when they are presented to the public and doesn't explain it very accurately which makes me upset. I already understand that life isn't fair and people aren't interested in a lot of topics governing science. I chose science out of my own volition and a natural consequence as stated before is being ostracized from attempting to raise interest in such a discussion. But understand that when such topics are raised about particular fields that concern me, I get extremely emotional as the only venues I have to discuss such topics are rare and extremely limited. I will not attempt to portray myself as being the expert on molecular genetics, methods of recombinant DNA technology, or nucleotide sequence analysis. But the points I make are familiar to me and are accurate enough for me to convey them without misconstruing scientific fact. My opinions derived from these facts is another story, but please understand that I find no reason to change my subjective opinion on this matter when the objective facts that support that opinion remain unchallenged.
Scientists Create First Cell Controlled by Synthetic Genome - TøbiasBlack - 2010-05-21
Swerve Wrote:-cut-
dude, dont need to apologize so much. o-o
yes the news makes too light/too heavy a lot of things. To me, that they synthesized this and make it work (will use really simple terms because, well, im tired and dont feel like trying to use the appropriate names for things) is a sign of things to come. whether or not theyre good or bad, what the implications that will come, and how they'll affect humanity as a whole, who knows.
but i don't like too much technology myself.
Scientists Create First Cell Controlled by Synthetic Genome - ★★★★★ - 2010-05-21
Science Fight!
I like that the news used the simplest of the simplest ways to try to describe how DNA works...
Scientists Create First Cell Controlled by Synthetic Genome - xLeviathan - 2010-05-21
@Swerve:
EDIT: You're a f`ucking hoot. Everything you said was knowingly and annoyingly wordy. So nvm.
Not everyone knows molecular genetics, so the news simplifies it. This article didn't come from Scientific American, they can't expect 9 out of 10 readers to understand how genetic sequencing works.
Scientists Create First Cell Controlled by Synthetic Genome - Alloy - 2010-05-21
xLeviathan Wrote:Not everyone knows molecular genetics, so the news simplifies it. This article didn't come from Scientific American, they can't expect 9 out of 10 readers to understand how genetic sequencing works.
Exactly. All your walls of text don't give me a slight idea of what you mean. If anything, the news just grabs the information, and delivers it to the mortal population WITHOUT A DEGREE IN BIOCHEMISTRY. Saying you don't like it is like saying how a bunch of photographs can't describe a building fully. Yet it does help approach it to the public.
Scientists Create First Cell Controlled by Synthetic Genome - Rob - 2010-05-21
[color="#000080"]
Alloy Wrote:Exactly. All your walls of text don't give me a slight idea of what you mean. If anything, the news just grabs the information, and delivers it to the mortal population WITHOUT A DEGREE IN BIOCHEMISTRY. Saying you don't like it is like saying how a bunch of photographs can't describe a building fully. Yet it does help approach it to the public.
I kinda agree with Alloy. I don't really get what you're trying to explain Swerve :/ [/color]