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Author Topic:   Quick Questions, Short Answers - No Debate
14174dm
Member
Posts: 128
Joined: 10-12-2015


Message 391 of 467 (785423)
06-04-2016 3:09 PM
Reply to: Message 387 by AZPaul3
05-05-2016 5:00 PM


Re: A song........
Maybe not these songs, but some old songs are used in games like Guitar Hero. My teenage son & friends actually like my music since they hear it on their video games.

(geezer mode) Or it could be that the old stuff that is still around is good music and most new stuff is terrible. Survival of the fittest in action.


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Dr Adequate
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Posts: 15972
Joined: 07-20-2006
Member Rating: 4.2


Message 392 of 467 (785435)
06-05-2016 2:57 AM
Reply to: Message 390 by caffeine
06-04-2016 1:47 PM


Re: Mitochondrial haplotypes
I stumbled across a conceptual problem when caused me to abandon a reply to Faith, and was hoping someone with more genetics knowledge would be able to help.
How is it that people can be said to have a specific haplotype at any locus for a mitochondrial gene. You don't only inherit one mitochondrion from your mother, but several. These will presumably accumulate mutations as they go, causing the mitochondria within a single cell to diversify. I can understand a selective sweep homogenising the cell's mitochondria again, but does this happen often enough that there's never time for diversity to establish itself?

There are about 100 mitochondria in a human cell. Suppose they were all different (they won't be, that's what we're trying to explain, but suppose they were). They (approximately) double in number and then the cell divides. But there's no reason why each daughter cell should get one copy of each distinct mitochondrion. (Unlike chromosomes, where there's a mechanism for this.) Instead, there's a sort of founder effect every time a cell division takes place.

The graph below shows the average behavior of the diversity if we started with 100 mitochondria all different. As you can see even given this starting point we expect the diversity to be completely eliminated after about 400 cell divisions.


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herebedragons
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Posts: 1413
From: Michigan
Joined: 11-22-2009
Member Rating: 2.6


(1)
Message 393 of 467 (785440)
06-05-2016 7:59 AM
Reply to: Message 390 by caffeine
06-04-2016 1:47 PM


Re: Mitochondrial haplotypes
How is it that people can be said to have a specific haplotype at any locus for a mitochondrial gene. You don't only inherit one mitochondrion from your mother, but several. These will presumably accumulate mutations as they go, causing the mitochondria within a single cell to diversify.

In addition to what Dr. A said, the replication of mtDNA is severely down regulated during embryogenesis which reduces the per cell copy number creating a mitochondrial bottleneck.This also serves to restrict the mitochondrial haplotypes that are eventually put into oocytes.

Another thing to keep in mind is that the human mitochondrial genome is only about 17k bases as opposed to nuclear DNA which is about 3 billion bases. If the expected mutation rate for nuclear DNA is about 300 bases per generation, the expected mutation rate for mtDNA would be 0.0017 mutation per generation or 1 mutation every 588 generations. Of course, mtDNA mutation rates are higher than that for nDNA due to the less precise replication machinery and less redundancy in DNA repair mechanisms (some estimates are that the rate is 10x higher).

This study empirically determined the mutation rate to be 3 mutation in 705 mtDNA transmissions:

quote:
we sequenced the mtDNA control region in 272 individuals, who were related by a total of 705 mtDNA transmission events, from 26 large Icelandic pedigrees. Three base substitutions were observed, and the mutation rate across the two hypervariable regions was estimated to be 3/705 = .0043 per generation (95% confidence interval [CI] .00088.013), or .32/site/1 million years (95% CI .065.97).

The Mutation Rate in the Human mtDNA Control Region

So we would expect that most of the time the offspring would inherit the exact same mtDNA as the parent had.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


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Replies to this message:
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RAZD
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Posts: 19220
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.4


Message 394 of 467 (785451)
06-05-2016 10:23 AM
Reply to: Message 366 by Lammy
04-12-2016 5:57 PM


Re: FYI, I've shamelessly stolen EvC technology
So did you put a counter on it to see how much activity it got?


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

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RAZD
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From: the other end of the sidewalk
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(1)
Message 395 of 467 (785452)
06-05-2016 10:36 AM
Reply to: Message 385 by Percy
05-05-2016 8:27 AM


Re: A song........
that always takes me back to university daze lying on the quad grass with that playing out someone's window ... when I wasn't playing frisbee ...
Enjoy

we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

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NosyNed
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Posts: 8800
From: Canada
Joined: 04-04-2003
Member Rating: 10.0


Message 396 of 467 (785457)
06-05-2016 1:04 PM
Reply to: Message 393 by herebedragons
06-05-2016 7:59 AM


H. e. l. p. !
Ok, now I will sound like Faith. There is kinda a lot of jargon in there but I would like to wrap my head around it.

In addition to what Dr. A said, the replication of mtDNA is severely down regulated during embryogenesis which reduces the per cell copy number creating a mitochondrial bottleneck.This also serves to restrict the mitochondrial haplotypes that are eventually put into oocytes.

Means? When the mtDNA is reproducing it is restricted. Like only a very small number of mitrochondria contibute to the final embryo? I don't get "down regulated" in here though.

Now to put this in the context of this discussion (which I haven't been working hard enough on). This means that the "slate is wiped clean" or almost so regularly. Thus changes we see have to be due to new mutations?


This message is a reply to:
 Message 393 by herebedragons, posted 06-05-2016 7:59 AM herebedragons has responded

Replies to this message:
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herebedragons
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Posts: 1413
From: Michigan
Joined: 11-22-2009
Member Rating: 2.6


Message 397 of 467 (785483)
06-05-2016 9:55 PM
Reply to: Message 396 by NosyNed
06-05-2016 1:04 PM


Re: H. e. l. p. !
Ok, now I will sound like Faith. There is kinda a lot of jargon in there but I would like to wrap my head around it.

Oh, no problem Ned. I'll admit I can use "jargon" at times, the reason is that it is not "jargon" to me. To me the meaning of "down regulated" is just as obvious as "mutation" and neither term seems like "jargon" to me. So it can sometimes be difficult to know when a commonly used genetic term needs more explanation.

When I read some of the physics threads, especially stuff on quantum physics and string theory, it is completely meaningless to me, gooblygook is the correct term I believe. But then again, I don't claim to have any knowledge about the subject matter nor am I especially inclined to try and understand the physics "jargon."

ABE:

I was going to respond in a different thread, but decided it was easier to just do it here. If the conversation needs to continue, we can move it then.

The ovum, or egg, has a large number of mitochondria. But during embryogenesis, the replication of mitochondria is down regulated, meaning simply that they replicate very slowly rather than at a normal pace. As the blastocyst forms, the mitochondria are partitioned into the dividing cells. Because they are not replicating, the number of mitochondria in each cell is greatly reduced compared to the original ovum. Normally, the mitochondria would be replicating so that the number of mitochondria in each cell would remain constant (of course different cell types have differing numbers of mitochondria - some have higher energy requirements than others).

The mitochondria don't begin replicating at a normal rate until I think gastrulation, when cells begin differentiating into different tissue types. By this time, the cell line that will develop into new oocytes will have a limited number of mitochondrial haplotypes. So even if there many haplotypes in the original egg, they have now been segregated into many cell lines and there will very few haplotypes (possibly only 1) that are passed on to the next generation.

Now to put this in the context of this discussion (which I haven't been working hard enough on). This means that the "slate is wiped clean" or almost so regularly. Thus changes we see have to be due to new mutations?

I'm not sure "wiped clean" would be accurate, instead just a relatively small number of mitochondria are funneled to new oocytes and so the number of different haplotypes being passed on to the next generation is limited. Also the mutations that will accumulate in the mitochondria that will be passed on to the next generation are only those that occur in the cell line leading to the reproductive cells. So we don't expect large numbers of mutations in each generation nor do expect to see significant numbers of haplotypes being passed on. More like it is a very reliable method of inheritance.

HBD

Edited by herebedragons, : No reason given.


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 396 by NosyNed, posted 06-05-2016 1:04 PM NosyNed has responded

Replies to this message:
 Message 398 by NosyNed, posted 06-06-2016 9:01 PM herebedragons has not yet responded

  
NosyNed
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Posts: 8800
From: Canada
Joined: 04-04-2003
Member Rating: 10.0


Message 398 of 467 (785550)
06-06-2016 9:01 PM
Reply to: Message 397 by herebedragons
06-05-2016 9:55 PM


Example
Ok let me try to see if I got it. And I'll make up some example numbers that you can correct.

Let's say that an ovum has 30 mitochondria. As it starts to develop for the first while they don't multiply. So let's say that they end up with 10 cells lines before the normal multiplication starts. Each of these has 3 mitochondria.

That sort of makes 10 bottlenecked subpopulations out of them One of these goes into the germ line with many fewer mutations than the female parent appeared to pass on.


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Dr Adequate
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Posts: 15972
Joined: 07-20-2006
Member Rating: 4.2


Message 399 of 467 (785574)
06-07-2016 9:40 AM


What Is This Flower?
Does it have a name? Thanks.


Replies to this message:
 Message 400 by kjsimons, posted 06-07-2016 10:03 AM Dr Adequate has responded

  
kjsimons
Member
Posts: 648
From: Orlando,FL
Joined: 06-17-2003


Message 400 of 467 (785576)
06-07-2016 10:03 AM
Reply to: Message 399 by Dr Adequate
06-07-2016 9:40 AM


Re: What Is This Flower?
It reminds me of Lantana but the leaves are wrong. Perhaps it is Iberis/Candytuft ?
This message is a reply to:
 Message 399 by Dr Adequate, posted 06-07-2016 9:40 AM Dr Adequate has responded

Replies to this message:
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Dr Adequate
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Posts: 15972
Joined: 07-20-2006
Member Rating: 4.2


Message 401 of 467 (785577)
06-07-2016 10:11 AM
Reply to: Message 400 by kjsimons
06-07-2016 10:03 AM


Re: What Is This Flower?
So it is, thank you.
This message is a reply to:
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Emotive
Junior Member (Idle past 156 days)
Posts: 11
Joined: 01-30-2015


Message 402 of 467 (786714)
06-25-2016 1:23 PM


PM notifications?
A quick question: Is there a notification system for private messages? I just sent one and it occurred to me this is the first time I bothered to go to the Messaging tab in many hours I've been here reading the forums. If other are like me, it could go unseen for many moons.
Replies to this message:
 Message 403 by jar, posted 06-25-2016 1:58 PM Emotive has not yet responded
 Message 404 by RAZD, posted 06-25-2016 2:00 PM Emotive has responded

    
jar
Member
Posts: 29613
From: Texas!!
Joined: 04-20-2004
Member Rating: 1.9


(1)
Message 403 of 467 (786715)
06-25-2016 1:58 PM
Reply to: Message 402 by Emotive
06-25-2016 1:23 PM


Re: PM notifications?
If you are logged in any new email or PMs will show at the Message button.

I just sent you a test PM.


Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
 Message 402 by Emotive, posted 06-25-2016 1:23 PM Emotive has not yet responded

  
RAZD
Member
Posts: 19220
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.4


(1)
Message 404 of 467 (786716)
06-25-2016 2:00 PM
Reply to: Message 402 by Emotive
06-25-2016 1:23 PM


Re: PM notifications?
Yes. the tab button Messaging blinks.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

This message is a reply to:
 Message 402 by Emotive, posted 06-25-2016 1:23 PM Emotive has responded

Replies to this message:
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Emotive
Junior Member (Idle past 156 days)
Posts: 11
Joined: 01-30-2015


Message 405 of 467 (786717)
06-25-2016 2:18 PM
Reply to: Message 404 by RAZD
06-25-2016 2:00 PM


Re: PM notifications?
Thanks, RAZD and jar. I got the idea.
This message is a reply to:
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