Promote Intracellular Symbionts!

[greenprogrammin]

Can anyone here think of a good prokaryotic microorganism that would benefit a eukaryotic organism from an intracellular symbiotic relationship?

 

I'm thinking of halophiles, thermophiles, etc...

 

What do you think?

[georgeskohler]

how about mitochondria in humans? okay, so that does not help, sorry!

[Mr Skeptic]

Well there's mitochondria and chloroplasts, which provide ATP synthesis and photosynthesis to cells. I'm not sure what you are looking for though. The extremophiles may be able to survive in harsh environments, but their resistance is intrinsic to them, they cannot share it. To survive in the conditions they do, we'd have to fundamentally alter our proteins, which would be pretty much impossible to do while remaining human.

 

Regardless, we are already the best extremophiles, being able to survive in tough environments such as space as well as hot and cold, land, air, and sea, radiation, salt, acid environment, whatever. We are the only creatures on earth that can survive in all of those.

[greenprogrammin]

I wish I had the genomic material for metamorph functionality.

 

Say the hox gene set for worm to fly metamorphism.

 

If I could figure out some of the genomic characteristics of mitosis and meiosis chromosomal rearrangement down to the histone remodeling.

 

I think it would be fun to experiment in interspecies chromosomal rearrangement in culture. Think about it... it is a symbiosis but typically only possible through horizontal gene transfer.

 

It seems that sexual reproduction is great for the vertical, but, I believe we have lost our touch with our horizontal symbionts naturally found in nature.

 

Any thoughts?

Edited November 15, 2009 by greenprogrammin

[georgeskohler]

I wish I could form a pili and transfer chromosomes to bacteria and see what happens.

 

I think homologous recombination is cool...like mitotic recombination is relatively rare, right? I guess there is recombinational repair. And meiotic recombination can generate cool combinations of alleles for the next generation.

[greenprogrammin]

Agrobacterium can transfer genes pretty good. It's not like you have to worry about a pili.

 

But, if you can work on a genomic level in a tissue culture medium you could probably find some interesting ways to allow crossover and other meiotic rearrangement.

Edited November 15, 2009 by greenprogrammin

[georgeskohler]

oh yeah, agrobacterium...that's the one that forms that makes trees look all funky?

[greenprogrammin]

yeah... I don't know the limitations on the DNA transfer but I think it would be fun to have the ability to design a set of chromosomes and understand the entire genome.

 

But, I'm sure there are so many maintainance genes and much activity that would prove to kick start into functioning.

 

I believe I would need to have a functional eukaryotic cell (preferably an animal or even a protist at first) and try to add chromosomes/ plasmids to the point of replacing the original chromosome, finally to remove the original chromosome.

 

I guess I could try to find a model organism, the karyotype, chromosome stain/banding patterns, inheritance patterns of various loci/ linkages, metabolome, genome, etc...

 

The only problem is all the supposed junk DNA. There are the Introns,Exons, tandom repeats, etc...

 

I don't know how many generations a cell could procede through before the missing Genomic material is missed.

 

If we could completely remove the nulcear DNA and replace it with custom chromosomes and get all the orgnelle functioning again, we would be able to do some real research...

 

I think understanding Stem Cell Biology, differentiation, etc... would be interesting starting points.

 

A project such as this would require huge computing resources and database integration.

 

In the end, I think we could set a good stage for the primary metabolism and then develop the secondary metabolism.

 

From a book I have just picked up it seems to be within reach. This book is called "The Regulatory Genome".

 

As I read more I will post info to promote a little thought.

Edited November 15, 2009 by greenprogrammin

[CharonY]

Uhm, horizontal gene transfer and symbioses are quite different things. Unless one wants to go down and discuss quasi-symbiotic relationships of mobile genetic elements (like viruses) with their hosts. And just btw. Agrobacteria hijack plant tissues and lets them produce opines.

[greenprogrammin]

I'm more interested in the control and deeper understanding versus the method.

 

If I am unable to develop chromosomes from scratch in my lifetime, I would be satisfied with integrating genomes and determine sustainability of the organism.

 

There is just too many applications that could justify such research, experimentation and development.

 

Someday, NASA may produce a cream / culture that could provide protection from space allowing us to explore with little more than modified scuba gear.

 

And to think about innoculating living organisms into space to colonize objects in efforts to prepare for higher tropic levels.

 

This is merely a brain storm thread with intent to bring others into the subject and provoke thought.

 

BTW.... What are opines good for? I seen a list of them but have little detail as to their use.

Edited November 15, 2009 by greenprogrammin

[CharonY]

Unfortunately much of it is based on some misconception as to what the mechanisms may be involved in, say horizontal gene transfer or symbioses. I have the feeling that the basic assumption of this thread is to create GMOs capable of the feats described above which, as it is, is still in the realms of science fiction.

The understanding of cellular processes still only allows us a limited prediction as to what certain genetic changes will result in overall phenotype of a cell, much less of a whole organism with the exception of a limited number of well known pathways. For instance, using reverse genetics to create a microorganism that produces a higher amount of certain substances (as e.g. amino acids or vitamins) is generally rewarded with limited success (as e.g. compared to screening for organisms that do it naturally). Is it possible to dream of a chromosome sequence and stitch together a DNA molecule? Yes it is, but dreaming of a some complicated phenotypes and then create such an organism is still far from possible.

[greenprogrammin]

I think we are not too far from the possibility.

 

I have been looking into the biobricks and NEB.com and think there is some good resources. Yet, I have sooo much more to read in various areas of bio.

 

Organizing these resources and referencing material in various threads will possibly bring us on the same page.

 

Have you worked with agrobacterium, tissue cultures, palsmid vectors, etc?

What kind of work do you currently do and specialize in?

 

I'm currently preparing for plant tissue cultures and then later hopefully animal tissue cultures.

I would like to culture various non/cancerous tissues and understand it more by growing.

 

A focus on culturing various cells/tissues will help me understand the nutritional needs of the cells/tissues.

 

It seems in plant tissue cultures there is various mediums for the need.

First you need a callus medium to dedifferentiate the plant cells

Second you need a rooting medium

last you neet a shoot developing medium.

 

The difference between the mediums seem to be primarily hormonal.

I'm wondering if there is much of a difference for animal cells/tissue.?.

 

I'm guessing there is not much known on dedifferentiating animal cells.

 

Here's what I foundd so far:

://www.hhmi.org/research/investigators/keating.html

in Laymens terms:

://www.wired.com/medtech/genetics/news/2005/04/67155

Edited November 15, 2009 by greenprogrammin

[Mr Skeptic]

Greenprogramming, for now the most you can probably do is to donate your spare computing cycles to Folding@Home -- we still cannot quickly nor reliably determine how a given protein (from its DNA sequence) will fold, and without knowing that cannot possibly hope to create our own artificial chromosomes, unless you meant to do it by trial and error.

 

Anyhow, before creating our own artificial chromosomes, we need to know how to modify a few individual proteins with good results. What is probably confusing you is the talk of synthesizing a known chromosome, which some people are trying to do just to show they can. However the result of that, though you could call it an "artificial chromosome" would just be the same as the chromosome they were copying, really a mostly pointless project.

[georgeskohler]

in terms of dedifferentiating cells, we have turned adult somatic cells to induced pluripotent stem cells, and can differentiate these cells to many different cell types.

 

Also, I think there is some value in showing we can synthesize a known chromosome--maybe down the road it will contribute to our understanding of chromatin structure...

[CharonY]

NEB? As in the company new england biolabs? No offense, but if you are really interested in it I would really recommend some basic cell biology books first rather than trying to piece together information from various websites, manufacturers of enzymes etc.

I assume that your major interest in in the field of bioengineering. A major roadblock, however, is the lack of our understanding of how even basic processes interact within a cell (an much less between cells). The field tends to be super-specialized due to the complexity of even apparently trivial interactions.

 

Cell cultivation is one field on its own and while often being a prerequisite of genetic works, it tends to harbor different questions. If you are really interested again, I would refer you to the basics and then build up specific questions from there. At this point your questions are not focused enough to be able to guide you in any direction. If you have specific questions regarding a given technique (molecular biological or cultivation technique), it may be more useful to start a separate thread for each.

Edited November 15, 2009 by CharonY

[greenprogrammin]

I think there is much we can do now that has not been a focus before.

 

Mr. Skeptic: I understand what your talking about. Lots of thought to go deeper into interspecies genomic integration. This is just something that peaks my interest and I will consider continuously throughout time.

 

George: Yes the wired article has discussed the proteins seperated from Newts and application to mouse muscle with the result of stem cell development. I'm sure there are many other experiments to include humans. It would be nice to have a good collection of journals related to the subject.

 

CahryonY: NEB, VWR, and various lab suppliers are essential for developing a price range for lab development. I have plenty of books on the various general to specialized subjects/protocols.

 

I am just pumping thought out to gather reactions form others in the similar frame of mind. This is just my little think tank. I will be considering various other threads for the need. Right now I'm just kinda getting to know you all.

 

Thanks!

Edited November 16, 2009 by greenprogrammin