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Synthetic Biology Inquiry - What?!

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Kurtron
#1
Mar14-13, 07:06 PM
P: 2
Hey everyone,

I wonder if there are any geneticists out there. I am quite uneducated pertaining to biology. So please bear with me. As I understand it, GMOs are living beings that have had traits inserted into their DNA, ie, arctic fish genes inserted into tomatoes to enable them to withstand and survive cold snaps. This is the genetic expression of the "Chimera" from greek mythology of different beasts fused together. Taking a trait from an animal and giving it to a plant. This in itself is mind blowing. And then I read a book called Regenesis, George Church's book on synthetic biology, wherein it was described how they used a virus containing the DNA of one bacteria to infect a different, similar species of bacteria with the former's DNA, and effectively "converted" the latter into the former organism. It was a simple enough cellular system that the whole works could replace itself. Here's what the WSJ said they did:

To begin, they wrote out the creature's entire genetic code as a digital computer file, documenting more than one million base pairs of DNA in a biochemical alphabet of adenine, cytosine, guanine and thymine. They edited that file, adding new code, and then sent that electronic data to a DNA sequencing company called Blue Heron Bio in Bothell, Wash., where it was transformed into hundreds of small pieces of chemical DNA, they reported.

To assemble the strips of DNA, the researchers said they took advantage of the natural capacities of yeast and other bacteria to meld genes and chromosomes in order to stitch those short sequences into ever-longer fragments until they had assembled the complete genome, as the entire set of an organism's genetic instructions is called.


They transplanted that master set of genes into an emptied cell, where it converted the cell into a different species.

WHAAAAT.

I cannot fathom the full implications of this. I have some questions....

1. To what extent could this synthetic DNA be implanted into an already living/functioning cell that hasn't yet been emptied and morph it?

2. Could you alter a complex system of living/functioning cells that have differentiated tasks that are already living--Say, fixing a part of an internal organ or even replacing the whole thing without surgery?

3. Would the cellular system need to be suspended or die in order to alter it? Is an empty cell "dead" in the first place?

4. Could it devised to look into an individual's DNA and see their specific liver, and create a DNA sequence that produces only the tissue that needs healing, and functions in replacing only the sick parts, killing and creating a new, up to the healthy parts?

5. Does it matter where the energy comes from in order for a cell to function as long as it is received in ATP?


Hopefully y'all can shed some light on this. The old adage comes to mind: "If you don't stand for something, you'll fall for anything"

We'll see.

THank you,

~Kurtis
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mazinse
#2
Mar14-13, 08:50 PM
P: 190
1. To what extent could this synthetic DNA be implanted into an already living/functioning cell that hasn't yet been emptied and morph it?

Yes, but not very well. The problem is a technological limit not theorectical limit. You cant accurate control where the new DNA goes. This is true when you use bacteria plasmids or viral vectors, they have their own places they want to go

2. Could you alter a complex system of living/functioning cells that have differentiated tasks that are already living--Say, fixing a part of an internal organ or even replacing the whole thing without surgery?

This is hard. You want to turn off the genes already there and on the other genes resetting the tissues back to its stem cell stage. This is why a lot of stuff in science fiction will remain fiction. You are doing more damage to the existing system when you are dedifferentiating a component.
3. Would the cellular system need to be suspended or die in order to alter it? Is an empty cell "dead" in the first place?

If you empty out a cell, it will die because the membrane structures will fall apart without the DNA to direct new proteins to hold things together. Although the proteins have a half life / turn over rate, it will take a while for things to die.

4. Could it devised to look into an individual's DNA and see their specific liver, and create a DNA sequence that produces only the tissue that needs healing, and functions in replacing only the sick parts, killing and creating a new, up to the healthy parts?

Again this goes back to question 1. Most cells have a stages of differentiation starting from the embryo stage when exposed various growth factors. If you inject an adult with these growth factors that arent around anymore you could get disastrous effects. Maybe you are thinking of doing this a lab. Grow it then transplant? That sounds more likely though.


5. Does it matter where the energy comes from in order for a cell to function as long as it is received in ATP?

Whereever the cells used to get energy from, even if you mess with the genes it will still use those energy.
Kurtron
#3
Mar15-13, 12:07 PM
P: 2
Thank you Mazinse.

Yes, but not very well. The problem is a technological limit not theorectical limit. You cant accurate control where the new DNA goes. This is true when you use bacteria plasmids or viral vectors, they have their own places they want to go
Let's assume that there is a nanotechnology that is sufficiently advanced to account for that chaos. Could you implant the DNA directly where it needed to go and have the cell morph into something else? And isn't this how viruses work anyways?

This is hard. You want to turn off the genes already there and on the other genes resetting the tissues back to its stem cell stage. This is why a lot of stuff in science fiction will remain fiction. You are doing more damage to the existing system when you are dedifferentiating a component.
What if you modified the DNA of the progenitor cells that are responsible for maintaining the tissues? Over a long enough time couldn't you succeed in replacing the established systems cell by cell, so long as they kept the essential tissue function viable? (I read once that all the cells of our body die and are replaced over a period of 7 years).



And again thank you for your input. I am uneducated in biology so what can and cannot be done is something I speculate upon without a true scientific understanding.

Ryan_m_b
#4
Mar16-13, 09:22 AM
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Synthetic Biology Inquiry - What?!

Quote Quote by Kurtron View Post
Hey everyone,
Welcome to the forums
Quote Quote by Kurtron View Post
This is the genetic expression of the "Chimera" from greek mythology of different beasts fused together.
That's one way to analogise it but don't get carried away by it. This kind of analogy IMO misinformed the public by playing onto concerns of "unnatural" and "Frankenstein" science.
Quote Quote by Kurtron View Post
Taking a trait from an animal and giving it to a plant. This in itself is mind blowing.
Whilst it is impressive bear in mind that animals share a lot of DNA with plants anyway. IIRC some fruits are 40% genetically identical to humans.
Quote Quote by Kurtron View Post
I cannot fathom the full implications of this. I have some questions....

1. To what extent could this synthetic DNA be implanted into an already living/functioning cell that hasn't yet been emptied and morph it?
If it hasn't been emptied of genetic material then anything could happen from non-viability to novel features.
Quote Quote by Kurtron View Post
2. Could you alter a complex system of living/functioning cells that have differentiated tasks that are already living--Say, fixing a part of an internal organ or even replacing the whole thing without surgery?
This is sort of the basis of gene therapy that has been experimented with for decades. However there is a difference between fixing a genetic defect (I.e. inserting a working copy of CFTR gene to a cystic fibrosis patient) and controlling cell/ behaviour in a manner that provides regeneration. The latter is investigated in the field of regenerative medicine and gene therapy like this is of limited use because most of the time the problem isn't genetic.
Quote Quote by Kurtron View Post
3. Would the cellular system need to be suspended or die in order to alter it? Is an empty cell "dead" in the first place?
A dead cell has no metabolic activity and so could not be used in this way.
Quote Quote by Kurtron View Post
4. Could it devised to look into an individual's DNA and see their specific liver, and create a DNA sequence that produces only the tissue that needs healing, and functions in replacing only the sick parts, killing and creating a new, up to the healthy parts?
DNA doesn't work like this. There are no blue prints in DNA, there's no collection of genes that map out how to build a liver. This is very complicated to explain without studying biology but ill give it a go. Firstly it's important to understand what genes are. Genes are portions of DNA that code for proteins. When expressed these genes are "read" and a specific protein is produced. Read up on the central dogma of biology to learn more about this.

Proteins then interact with each other and other molecules to form metabolic pathways. These pathways determine cell characteristics and behaviours. They act like complex switches that sense the environmental conditions and adapt the cells behaviour. For example: when oxygen is present in a cell some of it will be used by proteins in oxygen dependent reaction to interfere with another pathway that controls low-oxygen response. When there isn't enough oxygen these reactions cease and the low-oxygen response pathway can do its job because it is no longer being interfered with. This involves switching on genes that will produce proteins to stimulate things like blood vessel growth. To learn more I suggest you also read up on metabolic pathways, this one I've used as an example is the hypoxia pathway.

I've simplified this as much as possible but I hope I've given you enough to read up on and get your head around the idea that genes don't code for body parts, but the interaction between genes and the environment will result in the phenotype (physical characteristics) of an organisms.

On a separate note with regard to regenerating organs I suggest you look not regenerative medicine, specifically tissue engineering. One method of trying to regenerate organs is to grow them in-vitro by creating 3d scaffolds with specific material and chemical properties that will nudge cell behaviour to grow into the desired tissue. These cells would come from the patient so no rejection.
Quote Quote by Kurtron View Post
5. Does it matter where the energy comes from in order for a cell to function as long as it is received in ATP?
I'm not really sure I understand the question?
Quote Quote by Kurtron View Post
Let's assume that there is a nanotechnology that is sufficiently advanced to account for that chaos.
This is a poorly formed premise. Nanotechnology is not a monolithic field, it is huge in scope and the pop sci perception of what it is is drastically different from what it actually is. Be wary about invoking it in discussions without clarification else the thread risks spiralling off into science fiction.
Quote Quote by Kurtron View Post
Could you implant the DNA directly where it needed to go and have the cell morph into something else? And isn't this how viruses work anyways?
You could certainly change it's behaviour. But whether or not that was useful really depends on if the problem was one which different genetics could solve best. In reality the best way to alter cell behaviour is to interfere with metabolic pathways which most of the time will involve altering gene expression but not the genome.

Viruses replicate by co-opting the "manufacturing components" of the cell (ribosomes) to produce more viruses until the cell bursts. Whilst they can insert their DNA into the genome this process is significantly different than the synthetic biology example at the start of this feared.
Quote Quote by Kurtron View Post
What if you modified the DNA of the progenitor cells that are responsible for maintaining the tissues? Over a long enough time couldn't you succeed in replacing the established systems cell by cell, so long as they kept the essential tissue function viable? (I read once that all the cells of our body die and are replaced over a period of 7 years).
The problems with gene therapy are many. Other than the fact that it isn't always appropriate getting the DNA into the right cells and into the right part of the genome are big problems to be overcome. We could wave them away but that doesn't really tell us anything.
Quote Quote by Kurtron View Post
And again thank you for your input. I am uneducated in biology so what can and cannot be done is something I speculate upon without a true scientific understanding.
No problem, just be conscious of wandering too far into over speculation. This forum exists to teach established science, not speculate on future science. If the thread does head down that path it will have to be locked (so note for future contributors lets keep it within the realms of current science. With topics like this it's easy to wander off into over speculative future applications).
Ygggdrasil
#5
Mar16-13, 01:17 PM
Other Sci
Sci Advisor
P: 1,389
We are already capable of introducing synthetic DNAs into living human cell in order to reprogram the fates of those cells. In 2006, researchers discovered that , by introducing a set of four genes, they could transform an adult human cell back into a stem cell (Takahashi and Yamanaka, 2006). Subsequent studies have shown that these reprogrammed cells (called induced pleuripotent stem cells or iPS cells) can then be turned into any type of human cell by growing them in the proper environment. Shinya Yamanaka was awarded the 2012 Nobel Prize in Medicine for this discovery.

Many scientists hope that technologies like this can form the basis for a new field which has been termed "regenerative medicine." We envision being able to take cells from a patient, transform these cells into stem cells (along with performing additional manipulations to fix defective genes or coax them to differentiate into a specific tissue type), then introduce the stem cells back into the patient where they can help fix malfunctioning tissues. One could imagine using this approach to grow functional pancreatic islet cells to cure type I diabetes or grow nerve cells to replace those lost in diseases like Parkinsons or Alzheimers.

We are currently very far away from these goals and have many potential problems to work out. For example, we need much more research into the best ways to coax these cells to develop into the tissue types we want and ways to avoid having these iPS cells develop in unwanted ways (for example, into cancer cells). Indeed, we currently do not know whether these approaches to curing disease will be safe enough to use on patients. There are, however, clinical trials underway testing some of these ideas. For example, Advanced Cell Technology is attempting to use embryonic stem cells (not reprogrammed cells in this case) to regrow retinal cells in the eyes of blind patients who suffer from macular degeneration.

These cellular reprogramming techniques work because all human cells, whether they are liver cells or skin cells or neurons, have the same DNA (there are a few exceptions here). What differentiates the various cell types in our bodies is not the underlying DNA that they contain, but the regulation of the DNA -- that is, which genes are turned on and which genes are turned off. Cellular reprogramming techniques rely on temporarily turning on a few powerful genes that essentially reset the regulation of the DNA and turn on the regulatory programs that tell the cells to act like stem cells.

Transform cells from one species into cells from another species, however, actually requires making changes to the underlying DNA sequence (likely in addition to resetting the regulation of the DNA), so the problem is much more difficult and I think we would be unlikely to be able to do this in a living organism. There may be ways to introduce simple traits into a living organism through gene therapy approaches (but again these techniques are in their infancy and have a long way to go before they are actually useful). However, large scale changes would be very difficult.

The following site seems to have some good resources related to this topic of stem cells and regenerative medicine: http://www.stemcellschool.org/index.html

Also, you may find the following PF thread, which discusses Venter's synthetic bacterium experiment, to be a useful read: http://www.physicsforums.com/showthread.php?t=404603
Darwin123
#6
Mar25-13, 10:05 AM
P: 741
Quote Quote by mazinse View Post
2. Could you alter a complex system of living/functioning cells that have differentiated tasks that are already living--Say, fixing a part of an internal organ or even replacing the whole thing without surgery?
One could do all that with "simple" systems because you can correlate the function with the system. An example of a simple system would be a single hormone. Biologists have correlated single hormones with single functions, often without knowing the physics of reactions involved. There may not be any known correlation between the effect and the specific gene sequence with a complex system. Unless you know what a gene sequence would do in terms of the complex system, you don't know what gene sequence will work.

One would have to know a lot more about development in complex systems before one were able to reliably control a complex system. Being able to insert any gene sequence into a cell is not enough. Even know the complete genome in the human body is not enough. One would have to know what parts of the genome control which complex systems, and how they control the complex system.

Pituitary extract causes growth. A hormone in the pituitary extract has been correlated with growth, using clinical trials. So some diseases causing dwarf syndrome have been cured using injections of this hormone. I conjecture that one can place a gene coded for this hormone directly into the cells of a person and then turned on. This could cure dwarf syndrome, maybe better than the standard injection method. So maybe gene therapy may be a useful preventative for dwarf syndrome.

This case is particularly simple since the hormone had already be studies by "traditional" methods. The problem is that the trial and error experiments were necessary to identify what sequence of genes could be useful. There was no way that the function of the hormone could have been determined merely by knowing the structure of the hormone. The standard experiments on organisms were necessary to even know the genetic sequence which could be useful in some forms of dwarfism.

The growth of an organ involves hundreds of enzymes being generated at specific times. Many of the enzymes remain unknown. The timing of the gene expression is often unknown. Genetic manipulation would involve inserting the right genetic sequence for each enzyme, and making the gene express itself at the right time. Each heart, lung, nerve ganglion, etc. involved dozens of gene sequences being expressed in a specific order at specific times. Even knowing the gene sequences, the order and timing are difficult.

Natural selection has had four billion years of trial and error to get the sequences right for complex systems. Starting from simple systems, sequences have been modified in small increments for four billion years. The vast majority of the trials have resulted in the immediate death of the organism. This is what happens when one doesn't know the physics of the system one is experimenting with. The FDA wouldn't approve natural selection.
mazinse
#7
Mar30-13, 02:37 AM
P: 190
This is why scifi is just so misleading. You cant alter someone's DNA the way you are hoping by injecting them with something without risking killing them 99% of the time .
Apophenia
#8
Jun5-13, 05:08 AM
P: 61
Along the OP's lines:

1) Does synthetic biology typically constitute and addition to the host cell's genome, i.e., when a string of synthetic DNA (or any DNA) is inserted, the host cell just acquires the sequence into its own?

2) If so, are there any methods to replace parts of the host's genome with "additive DNA"? or would this be harmful to the host cell? Is it theoretically possible to replace portions of the host's genome?

I am relatively illiterate in biology so forgive the generality or misinformation.
Ygggdrasil
#9
Jun8-13, 03:55 PM
Other Sci
Sci Advisor
P: 1,389
Quote Quote by Apophenia View Post
1) Does synthetic biology typically constitute and addition to the host cell's genome, i.e., when a string of synthetic DNA (or any DNA) is inserted, the host cell just acquires the sequence into its own?
No, if you introduce synthetic DNA into a cell, most cells will not incorporate the foreign DNA into the host cell's genome. The DNA can traffic to the nucleus and be transcribed into mRNA, but eventually the DNA will be degraded. Such introduction of foreign DNA into a cell is called transient transfection, since the DNA does not stay around indefinitely.

On rare occasions, a cell transfected with synthetic DNA will integrate the DNA into its genome at a random location. If this synthetic DNA contains a selectable marker (such as an antibiotic resistance gene that allows the cell to survive in the presence of a drug that would kill normal cells), you can isolate this population of cells that has been stably transfected with the synthetic DNA.

For more information about transfection see the wikipedia article: https://en.wikipedia.org/wiki/Transfection

Note that the above information is primarily relevant for transfection of mammalian cells. The situation is a bit different in bacteria and yeast, however, as you can engineer synthetic DNAs that will replicate themselves in the host cell.

2) If so, are there any methods to replace parts of the host's genome with "additive DNA"? or would this be harmful to the host cell? Is it theoretically possible to replace portions of the host's genome?
Yes. Although the stable transfection methods above are one method to introduce foreign DNA into cells, they present many problems because the DNA inserts randomly into the genome. Luckily, biologists have developed a new generation of genome engineering tools that allow us to more precisely insert synthetic DNAs at defined positions. These techniques rely on programmable DNA binding proteins (examples include zinc-finger nucleases, TAL effector nucleases, and the CRISPR/cas system) that can be engineered to bind a specific sequence in the genome and cut that sequence to facilitate the insertion of a synthetic DNA.

See the following wikipedia article for more information https://en.wikipedia.org/wiki/Genome...ered_nucleases


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