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Author Topic:   How, and where, does gene expression work?
Ben!
Member (Idle past 147 days)
Posts: 1154
From: San Diego, CA
Joined: 10-14-2004


Message 1 of 12 (167304)
12-12-2004 1:29 AM


How, and where, does gene expression work?
Richard Alex won (1/2 of) the 2004 Nobel Prize in Medicine / Physiology for his (joint) work on the olfactory system. His work is crazy and wonderful; you can listen to a talk on the topic, or read a transcript, from some recent conference at Columbia University.

Here's an article about cloning a mouse based on the DNA of a 'mature' (i.e. non-dividing / replicating) cell, one of the olfactory neurons.

This article brings up some issues about gene expression that I'd like to know more about. It's been puzzling me, and continues to puzzle me.

  1. I know that gene expression can be based on many 'factors'.Here's two that I know.
    • the presence of molecules in the cell that directly trigger gene expression (forgot the technical term)

    • the absence of molecules in the cell that directly inhibit gene expression (forgot the term)
  2. The article says the researchers thought the olfactory sensory neuron 'mature' cells might:
    • choose the single gene (out of a pool of more than 1000) which they express (and thus sense some aspect of smell) due to some re-arrangement of the cell's DNA.

    • fail to replicate because of this suggested rearrangement


    The researchers chose olfactory neurons as the source of genetic material because previous research had suggested that these cells might undergo gene rearrangements during development. Whatever the underlying process involved in generating their spectacular diversity, olfactory neurons are distinguished by their ability to randomly express any one of some 1,500 diverse odor receptor genes. Such genes give rise to the protein receptors on the surface of the neurons that detect specific chemical odorants.

  3. The researchers WERE able to clone using this DNA, suggesting either:
    • The cell's DNA was not re-arranged OR

    • The cell's DNA was re-arranged, BUT it was reversible.


    According to Axel, the cloning achievement eliminates one potential mechanism and narrows the possible ways in which a cell chooses one of thousands of receptor genes. The findings also demonstrate that the developmental changes are reversible.

  4. Finally, Axel suggests at the end of the article that this technique is applicable to discovering these facts about other cells.

    Axel said that the cloning technique should be broadly applicable. gFrom a mechanistic point of view, it's very important to be able to investigate whether irreversible changes in the DNA accompany development, differentiation and maturation,h he said. gThis approach, although technologically demanding, affords an opportunity to detect those changes that are irreversible in virtually all cells.


OK, FINALLY!

My question is, how much do we know about gene expression? What are the ways that gene expression can happen? And what gene expression goes on that we really don't know how it's happening? For example, how does gene expression works such that a cell 'decides' it's going to express this ONE gene out of a pool of more than 1000, even though it is identical to all the other olfactory sensory cells otherwise.

Please, help!!

Ben

P.S. This stuff is so cool!

edited: trying to change non-descript title

This message has been edited by bencip19, 12-12-2004 01:31 AM

ADMIN: can you change the title of the thread to 'How, and where, does gene expression work?' and to remove the subttile? Heck, remove this message too Thanks.

This message has been edited by bencip19, 12-12-2004 01:32 AM


Replies to this message:
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AdminNosy
Administrator
Posts: 4743
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 2 of 12 (167306)
12-12-2004 1:35 AM


Thread moved here from the Proposed New Topics forum.
  
Ben!
Member (Idle past 147 days)
Posts: 1154
From: San Diego, CA
Joined: 10-14-2004


Message 3 of 12 (167823)
12-13-2004 6:40 PM
Reply to: Message 1 by Ben!
12-12-2004 1:29 AM


(bump!)
(sheepishly) .. any takers?

(pacing slowly while looking at my feet, and my hands behind my back)

Ben


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Replies to this message:
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Loudmouth
Inactive Member


Message 4 of 12 (167829)
12-13-2004 7:06 PM
Reply to: Message 1 by Ben!
12-12-2004 1:29 AM


How to Skin a Cat
quote:
My question is, how much do we know about gene expression? What are the ways that gene expression can happen? And what gene expression goes on that we really don't know how it's happening? For example, how does gene expression works such that a cell 'decides' it's going to express this ONE gene out of a pool of more than 1000, even though it is identical to all the other olfactory sensory cells otherwise.

As the title of my post says, there are as many mechanisms for gene expression as there are ways to skin a cat. Just a wild guess, a hypothesis if you will, the olfactory expression may be a "first come, first serve" type of expression. The first gene to be fully expressed may shut down the expression of the other olfactory genes. This would require receptor turnover (ie removal and replacement) because there would be an initial, but limited expression of a number of receptors early on. I could prattle on about this subtopic, so I'll move on.

Gene expression is a very diverse subject. Most gene expression involves something binding to the DNA which initiates trascription or the removal of something from the DNA which initiates transcription. Then there are also invertases. I have only read a couple papers on this, but it is quite interesting. In some bacteria (typhirium IIRC) there is an enzyme that snips the DNA and inverts the whole thing upside down. This actually turns the gene "on" and allows transcription of a whole host of genes. The invertases are thought to have been derived from viral enzymes that perform similar tasks during insertion and infection.

It is very difficult to describe gene expression in over-arching themes because each gene is almost a new case in itself. Also, there are often cascades, or the upregulation of a whole suite of genes by a single regulator. Gene expression is one of those things that "If you can imagine it, it probably happens" sort of phenomena.


This message is a reply to:
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RzL
Inactive Member


Message 5 of 12 (167869)
12-13-2004 9:22 PM
Reply to: Message 4 by Loudmouth
12-13-2004 7:06 PM


Re: How to Skin a Cat
quote:
Gene expression is one of those things that "If you can imagine it, it probably happens" sort of phenomena.

i just wanted to add that i too love gene expression and molecular genetics. I am hoping when i start my undergrad research next semester that i get to study under the professor that i prefer. If so I'll be studying regulation of gene expression of plasmodium falciparum, and promoter identification.

...i'm excited


This message is a reply to:
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Loudmouth
Inactive Member


Message 6 of 12 (168081)
12-14-2004 11:41 AM
Reply to: Message 5 by RzL
12-13-2004 9:22 PM


Re: How to Skin a Cat
quote:
i just wanted to add that i too love gene expression and molecular genetics. I am hoping when i start my undergrad research next semester that i get to study under the professor that i prefer. If so I'll be studying regulation of gene expression of plasmodium falciparum, and promoter identification.

That does sound exciting. My background is in bacterial pathogenesis, but parasitology still interests me quite a bit. Good luck, and handle those vials carefully.


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jjburklo
Inactive Member


Message 7 of 12 (168132)
12-14-2004 2:15 PM
Reply to: Message 5 by RzL
12-13-2004 9:22 PM


Re: How to Skin a Cat
RZL

I just had a friend give a wonderful presentation on Plasmodium falciparum, and I believe she touched on gene expression to some extent. If you're interested I can see about getting her research. Nasty little bug that is!

Just out of curiosity, I'm a biochem undergrad major at the moment, what are you focusing on?

This message has been edited by jjburklo, 12-14-2004 02:16 PM


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RzL
Inactive Member


Message 8 of 12 (168150)
12-14-2004 2:48 PM
Reply to: Message 7 by jjburklo
12-14-2004 2:15 PM


Re: How to Skin a Cat
I'm a biochem & chemistry double major (it was only like 4 classes extra to get the other degree).

I'd be very interested in your friends research if you can get ahold of it.


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Parsimonious_Razor
Inactive Member


Message 9 of 12 (168390)
12-15-2004 2:15 AM
Reply to: Message 1 by Ben!
12-12-2004 1:29 AM


Re: How, and where, does gene expression work?
My primary interest/background is in evolutionary psychology but I have been paying my way through school by research grants to study gene expression and regulation. I work with a researcher, Dr. Stuart Kauffman and several other people in mathematically modeling ideas behind regulation.

20-30 years ago Dr. Kauffman developed the idea that cell types emerged as steady states from random gene regulation interactions. Basically, imagine that every gene can be either "on" or "off" and to make things simple imagine every gene receives two inputs (usually other genes). These inputs are either "on" or "off" then there are a series of Boolean rules that each gene follows to decide if it stays on or off. So if its an 'or' rule the gene stays on or turns off if either input is "on".

You can model these networks, called Random Boolean Networks, using very simple computer programs. What you find is that the genes enter into cycles that repeat. Kauffman proposed that these were actually cell types. And that differentiation took a similar path to what was described above.

This was a long time ago and a lot of research has been done since. For example I am finishing up a paper now that modeled a small 3 gene circuit in a continuous differential equation to test noise. This model does not rely on the discreet states of a Boolean net and we were able to show attractor points were fairly stable to noise. Along with a couple other cool findings.

At the moment I am creating a model known as a medusa network. Where there is a "head" of genes that are regulators and the "tail" genes do not regulate at all. This is viewed as a more accurate model than every gene being a regulator. We are working on applying noise value and scale free aspects as well (scale free is the number of inputs is not defined).

These networks can also be made more accurate by examining cells and how they actually do work. For example, one Boolean network was modeled after a yeast system. Researchers identified the number of regulation genes in the yeast, and which genes they inputted into. This was used as a frame work for a Boolean model. The Boolean rules still had to be randomly generated.

We have recently hooked up with some researchers and are exploring ways of experimentally examining the "rules" behind the networks but are a long ways away from that.


Science Blog: http://www.scienceblog.com/blogs/blog/213
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Wounded King
Member (Idle past 620 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 10 of 12 (170035)
12-20-2004 6:03 AM
Reply to: Message 3 by Ben!
12-13-2004 6:40 PM


Re: (bump!)
Dear Ben,

I'd like to address the specific instance of the SCNT with olfactory cells before addressing the general question of gene expression.

Both the paper by Axel (Eggan, et al., 2004) and a similar paper (Li, et al., 2004) come to the conclusion that there were no genomic rearrangements associated with stable receptor expression. So this is certainly not a case of the SCNT process reversing a rearrangement of the DNA.

As to the general applicability of cloning as a way of testing for irreversible changes to the DNA, this should certainly work in theory but at the moment we don't know enough about the mechanisms involved in 're-setting' nuclei during SCNT to be sure that we arent getting a whole lot of false positives simply because we don't know the right technique to reset that particular change.

A lot of experiments of this type have already been done in otyher systems, some of John Gurdon's very earliest cloning work in amphibians done in the 1960's was on exactly the sort of questions proposed as regards changes during development (Gurdon and Byrne, 2003), as well as a lot of closely related work complementary from the more cloning oriented field as to which cells provide the best source of material and what techniques are best for re-setting them (Gurdon, et al., 2003, Mullins, et al., 2004, Kono, 1997.

As to gene regulation, as has been suggested this is really a very large topic, and we can be pretty certain that we have as yet only a rudimentary grsp of the real complexities involved. As well as the simplest level of regulation, a specific protein binding to a particular DNA site and thereby either promoting or suppressing the expression of the gene by blocking or facilitating the binding of a polymerase there are a host of other possible factors. There are regulatory elements which can function many 100s of Kb upstream of the target gene, some may interact because the DNA conformation brings them into close association but exact mechanisms are still unclear. Factors may alter the DNA structure by the remodelling the histone complement or the methylation or acetylation of histone proteins may lead to a restrictive or permissive environment for gene expression. Changes in the methylation of the DNA can similarly be linked to changes in gene expression, some of which even seem to be heritable cross generationally. The expression of one gene may interfere with another either in the cascading sort of mechanism previously mentioned or in some cases because the transcription of one gene precludes the transcription of another due to their arrangement on the chromosome.

Those are just a few mechanisms related to gene expression that I can think of off the top of my head. As far as your speciifc question of how 1 gene could be stably expressed in preference to 999 others, the most obvious answer is that expression of that one gene acts to supress expression of all the others. It appears that this is probably just a stochastic phenomenon as there seem to some instances where the classes are observed to switch. If you have several million neurons the allowing any cell to find its own class is likely to give you at least some cells expressing each class of receptors, and differences in the proportions of these may well account for different perceptions of smell. I don't know if there is any mechanism for this sort of repression of other receptr genes sadly as I know very little about the organisation of these genes in the genome, if they were all gathered together in one locus then there might be a simpler mechanism than if they were spread all over throughout the genome, a quick check in pubmed tells me that in humans the genes are spread out over 51 loci on 21 chromosomes, so not nicely localised together in that case.

TTFN,

WK


This message is a reply to:
 Message 3 by Ben!, posted 12-13-2004 6:40 PM Ben! has responded

Replies to this message:
 Message 11 by Ben!, posted 12-20-2004 5:24 PM Wounded King has responded

    
Ben!
Member (Idle past 147 days)
Posts: 1154
From: San Diego, CA
Joined: 10-14-2004


Message 11 of 12 (170216)
12-20-2004 5:24 PM
Reply to: Message 10 by Wounded King
12-20-2004 6:03 AM


Re: (bump!)
WK,

Thanks for the post. I read it through yesterday, and I'll go through more thoroughly this week.

My goal is to understand these issues so that, when talking about genetics and especially gene expression and it's role in brain development, I have a better understanding. Kandel gave a talk about long-term memory vs. short-term memory, and labeled it "genetic vs. non-genetic" memory. But of course (given the audience) he glossed over the actual details.

So, just to say thanks and explain the relevance of this for me. Thanks!

Ben


This message is a reply to:
 Message 10 by Wounded King, posted 12-20-2004 6:03 AM Wounded King has responded

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Wounded King
Member (Idle past 620 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 12 of 12 (170549)
12-21-2004 4:54 PM
Reply to: Message 11 by Ben!
12-20-2004 5:24 PM


Genetic memory
Dear Bencip19,

I can't say for sure but, from what I remember of my undergraduate neurobiology, I think that what he meant is that the mechanism by which long term potentiation is established requires de novo gene expression and protein synthesis while short term potentiation does not.

TTFN,

WK


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 Message 11 by Ben!, posted 12-20-2004 5:24 PM Ben! has not yet responded

    
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