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Author Topic:   Introduction to Genetics
Taq
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Posts: 7971
Joined: 03-06-2009
Member Rating: 4.5


Message 46 of 236 (680860)
11-21-2012 2:24 PM
Reply to: Message 45 by crashfrog
11-21-2012 2:12 PM


Re: QUESTION 9: "Junk DNA"
And by "purifying selection", you mean "natural selection against mutations"?

Negative selection is probably the easiest to detect, but my population genetics is not the greatest so feel free to correct me on that one.


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Dr Adequate
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Posts: 16097
Joined: 07-20-2006


Message 47 of 236 (681009)
11-22-2012 1:14 AM
Reply to: Message 44 by crashfrog
11-21-2012 2:11 PM


Re: QUESTION 9: "Junk DNA"
Well, if you pack each gene with introns, and every base has an equal chance of being an indel, then you increase the chance that a frameshift mutation will be canceled out by another one, downstream.

I still don't follow that. Yes, if you make the gene longer, than there's more likely to be two indels in it, but there's also more likely to be one, or three which are not all of the same kind, or four, or ... etc. The ideal number is zero.

Also, how would it help if you got a compensating indel in an intron? This intron is taken out before the translation. If it was translated and then the amino acid sequence corresponding to the intron was taken out after the translation, then an indel in the intron would compensate for an opposite indel in an exon, but it isn't ...

... I don't really see what you're getting at, or if I do, it isn't right. One or the other.

Edited by Dr Adequate, : No reason given.


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Dr Jack
Member (Idle past 300 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 48 of 236 (681020)
11-22-2012 4:45 AM
Reply to: Message 44 by crashfrog
11-21-2012 2:11 PM


Re: QUESTION 9: "Junk DNA"
Well, if you pack each gene with introns, and every base has an equal chance of being an indel, then you increase the chance that a frameshift mutation will be canceled out by another one, downstream.

I don't follow; introns are excised by the gene machinery - indels in them make no odds corrected or not - it's only indels in exons that are relevant and the chance for them to occur remains constant regardless of how many introns you insert or how widely spaced genes are on the genome.


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Dr Jack
Member (Idle past 300 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 49 of 236 (681022)
11-22-2012 4:53 AM
Reply to: Message 45 by crashfrog
11-21-2012 2:12 PM


Re: QUESTION 9: "Junk DNA"
And by "purifying selection", you mean "natural selection against mutations"?

Not quite, purifying selection is the removal of harmful alleles from the population, not simply the removal of mutations. Neutral and positive mutations will persist.


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PaulK
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Posts: 15212
Joined: 01-10-2003
Member Rating: 3.4


Message 50 of 236 (681025)
11-22-2012 5:23 AM
Reply to: Message 48 by Dr Jack
11-22-2012 4:45 AM


Re: QUESTION 9: "Junk DNA"
I'm pretty sure that Crashfrog is wrong, because if it worked that way an indel IN the intron would affect the gene, so overall the risk of frameshift mutations would go up. The statistics don't work out in a way that favours his view, either.

If, on the other hand introns reset the reading frame, then the effect of indels would be limited to the start of the next intron - assuming that the frameshift doesn't mess that up. I'm speculating here, but it sounds like something that might be true....


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Dr Jack
Member (Idle past 300 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 51 of 236 (681040)
11-22-2012 7:56 AM
Reply to: Message 50 by PaulK
11-22-2012 5:23 AM


Re: QUESTION 9: "Junk DNA"
Introns don't reset the frame; you can get codons split between two exons.
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crashfrog
Inactive Member


Message 52 of 236 (681041)
11-22-2012 8:02 AM
Reply to: Message 47 by Dr Adequate
11-22-2012 1:14 AM


Re: QUESTION 9: "Junk DNA"
Look, you guys can be as skeptical as you like, but this is straight out of Leninger Principles of Biochemistry, Inferring Phylogenies, and for that matter Wikipedia:

quote:
Noncoding DNA separate genes from each other with long gaps, so mutation in one gene or part of a chromosome, for example deletion or insertion, does not have the "frameshift mutation" on the whole chromosome. When genome complexity is relatively high, like in the case of human genome, not only different genes, but also inside one gene there are gaps of introns to protect the entire coding segment to minimise the changes caused by mutation.

Probably not the clearest way to put it - this doesn't seem like it was written by a native English speaker, actually - but I'm hardly running off the edge of the science, here.

Edited by crashfrog, : No reason given.


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PaulK
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Posts: 15212
Joined: 01-10-2003
Member Rating: 3.4


Message 53 of 236 (681046)
11-22-2012 8:32 AM
Reply to: Message 52 by crashfrog
11-22-2012 8:02 AM


Re: QUESTION 9: "Junk DNA"
quote:

Look, you guys can be as skeptical as you like, but this is straight out of Leninger Principles of Biochemistry, Inferring Phylogenies, and for that matter Wikipedia:

Crash, that quote doesn't say anything about the non-coding regions being an advantage because they might get extra mutations putting things right. That idea is still very implausible just from statistical principles.

The question I'm really interested in is how this protection works, and your quote doesn't address that at all.


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Dr Jack
Member (Idle past 300 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 54 of 236 (681051)
11-22-2012 8:45 AM
Reply to: Message 53 by PaulK
11-22-2012 8:32 AM


Re: QUESTION 9: "Junk DNA"
It seems to be referring to something like this (unfortunately the paper's in Russian which I can't read). I can see that against chemical mutagens non-coding DNA could be protective (although I doubt it would be against radiation) but I don't see how it's particularly relevant to indels (thought to occur primarily through slippage during replication).
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crashfrog
Inactive Member


Message 55 of 236 (681053)
11-22-2012 8:48 AM
Reply to: Message 53 by PaulK
11-22-2012 8:32 AM


Re: QUESTION 9: "Junk DNA"
Crash, that quote doesn't say anything about the non-coding regions being an advantage because they might get extra mutations putting things right. That idea is still very implausible just from statistical principles.

Hrm, then maybe I misunderstood. I'll see if I can dig up a better reference. I know I've gone back and forth on this over the years, so in the meantime I'm happy to have people consider the claim withdrawn. I'll see if I can find some support for it. This is a good thread, I think the potential for informing Faith is pretty high, and I like to not drag it off-topic towards confusion.

Edited by crashfrog, : No reason given.


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Faith
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Posts: 32157
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 56 of 236 (719178)
02-12-2014 12:34 AM


The Specific Genetics of a Specific Species
I just skimmed this thread starting with my original questions. A lot of them did get answered although the thread took a much too technical turn for me.

The question that brought me back to this thread is really a wish to know what differentiates the genome of one species from another. Like they say there is only about 5% difference between the human genome and the chimp genome. That 5% of the human genome then must contain the coding for what is specifically human and not ape, and same with the ape genome. But is that particular 5% even recognizable, is it clear in the genome where it is located and what it codes for? In other words I'd really like to know the specifics about that part of every genome for every creature that differentiates it from all the others. What makes a cat genome a cat genome, a dog genome a dog genome etc?

Edited by Faith, : No reason given.


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AZPaul3
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Posts: 4263
From: Phoenix
Joined: 11-06-2006
Member Rating: 3.7


(1)
Message 57 of 236 (719209)
02-12-2014 7:14 AM
Reply to: Message 56 by Faith
02-12-2014 12:34 AM


Re: The Specific Genetics of a Specific Species
This might help explain a bit. It's not technical and will not answer all your questions but it does give you an idea of the problems in trying to give these answers.

In short, we may know enough to look at two specific genomes and say in general this is probably a bonobo and this a human, but we do not yet know how some of these differences work. For instance, humans and bonobos have some genes that are identical but, for reasons we do not yet understand, work in different ways. The proteins created are identical but under the influence of the full score of proteins in the system these identical proteins do different things in different places within the different species. This, of course, will lead to differences in phenotype just as well as a gene difference. Differences in DNA structure are but a beginning point in determining what creature is being made.

The study of proteomics is the study of the interrelationships of the proteins produced by the genome. As you can imagine this is highly complex and we have just barely begun. To fully determine what makes such a different animal, a bonobo, from a nearly identical genome as a human will be decades in the future.

here


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ramoss
Member
Posts: 3111
Joined: 08-11-2004


(1)
Message 58 of 236 (719249)
02-12-2014 1:40 PM
Reply to: Message 20 by Percy
11-10-2012 6:37 PM


Re: QUESTION ONE: Species ID / CHROMOSOMES
There IS a case in China where a man has 44 chromosomes, because he got a fusion event.

http://genetics.thetech.org/original_news/news124

This seems very rare, but possible.


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Taq
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Posts: 7971
Joined: 03-06-2009
Member Rating: 4.5


(1)
Message 59 of 236 (719273)
02-12-2014 5:45 PM
Reply to: Message 56 by Faith
02-12-2014 12:34 AM


Re: The Specific Genetics of a Specific Species
The question that brought me back to this thread is really a wish to know what differentiates the genome of one species from another.

The answer is the order of nucleotides on the DNA strands.

Like they say there is only about 5% difference between the human genome and the chimp genome.

That means that when you compare 2 homologous strands of DNA there will be the same base 19 out of 20 times when comparing the two genomes.

That 5% of the human genome then must contain the coding for what is specifically human and not ape, and same with the ape genome.

The 5% difference between chimps and humans also contains the chimp specific mutations that differentiate them from the other apes. It is also worth mentioning that we are the chimps closest relative. Chimps share more DNA with us than they do with the other apes, such as gorillas and orangutans. If chimp DNA is ape DNA, then we are apes, too.

But is that particular 5% even recognizable, is it clear in the genome where it is located and what it codes for?

It is easily recognizable once the sequencing and assembly is done. It is as simple as doing a BLAST search using nucleotide sequence from one species to query the genome of another species.

http://blast.ncbi.nlm.nih.gov/Blast.cgi

In other words I'd really like to know the specifics about that part of every genome for every creature that differentiates it from all the others. What makes a cat genome a cat genome, a dog genome a dog genome etc?

The differences are going to be found throuhgout the billions of bases in the genome.

Perhaps it would help if I show a specific example. What I did was copy a smaller chunk of DNA sequence from human chromosome 1. You can find the entire sequence of chromosome 1 here:

http://www.ncbi.nlm.nih.gov/nuccore/NC_000001.11?report=f...

Next, I went to the BLAST page for the chimp genome, which can be found here:

http://www.ncbi.nlm.nih.gov//blast/Blast.cgi?PAGE_TYPE=Bl...

I pasted the copied portion of the human genome into the query sequence box at the top of the page, then clicked on the BLAST button towards the bottom of the page. I got one hit back, and here is a screen cap of the alignment between human (query) and chimp (subject) genomic DNA:

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


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Taq
Member
Posts: 7971
Joined: 03-06-2009
Member Rating: 4.5


Message 60 of 236 (719289)
02-12-2014 7:22 PM
Reply to: Message 57 by AZPaul3
02-12-2014 7:14 AM


Re: The Specific Genetics of a Specific Species
In short, we may know enough to look at two specific genomes and say in general this is probably a bonobo and this a human, but we do not yet know how some of these differences work.

I think it is also important to point out that there are differences between one human genome and another. The HapMap project is trying to catalogue human genetic variation, and other projects are looking at the variation in different species.

https://www.genome.gov/10001688

You can even zoom in to the actual sequence and find where humans differ at a given base, and the percentages of people with those variants among the pools they have tested.


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