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Author Topic:   Introduction to Genetics
Faith
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Message 5 of 236 (678629)
11-09-2012 2:28 PM
Reply to: Message 2 by Taq
11-05-2012 3:44 PM


QUESTION ONE: Species ID from DNA
Thanks, TAQ, for your thoughtful replies.

(Took me so long to answer because I didn't see the "request password" link when I tried to log in)

I wrote out one long reply to both your posts and was driven to the conclusion that there’s just too much here to try to respond to all of it at once and maintain any kind of order, so I decided to try to limit things by focusing on one question at a time.

If you have some cells of some creature but don't know what creature it is, is it always easy to identify it from its DNA?

At one time the answer would have been "No". In order to identify a species by their DNA you need DNA from a known source. Not too long ago (i.e. 20 years ago) there simply wasn't a lot of DNA sequence known. Luckily, methodologies and technologies have greatly increased our ability to sequence DNA akin to Moore's Law and computer chips. If you are trying to work on identifying the species then a larger BAC clone would be the way to go. In this methodology you use an enzyme to break up the DNA into large chunks (or physical shearing), and then randomly insert those chunks into the BAC plasmid. You then use Sanger sequencing from the known plasmid sequences that flank the insert of interest. This usually gives 300 to 700 bases of good read from both ends of the insert. In the olden days we used radioactive terminators and autoradiography from big gels to run these sequencing reactions. Now it is all automated on capillary gels that use fluorescent dyes instead. The results of the run will look something like this: [chart]

Once you have your sequence you then dump it into BLAST. If it is not able to find a perfect match for your sequence it will give a phylogeny of the closest related sequences so you will at least be able to see what kind of critter you are working with. With some luck, you may even be able to identify not only the species, but where in the genome that DNA chunk came from.

So you are apparently giving a “yes” to this question because now it is possible, by the various means you mention (that are technically rather over my head), to find out “at least…what kind of critter you are working with.” I gather it’s not “easy” at all since it does require quite a bit of technical work to arrive at the conclusion but that you CAN indeed find out the species.

So I'd sum up:

ANSWER: YES, WE CAN IDENTIFY THE SPECIES, BUT IT’S NOT EXACTLY “EASY.”

Fair enough?

I am a bit surprised because I did assume that the number of chromosomes would be the major indicator, which I also assumed wouldn’t be hard to determine, but you didn’t address that part of the question. (“What are the defining factors: the number of chromosomes only?” )

If my paraphrase of your answer is correct enough I’m happy with it, but I don’t want to move on until any further thoughts on the subject that might occur to anyone are considered.

P.S. I did look up some unfamiliar terminology but think I'll leave the technical parts of the answers to later. Right now they could get to be a long rabbit trail.


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 Message 2 by Taq, posted 11-05-2012 3:44 PM Taq has responded

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Faith
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Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 6 of 236 (678631)
11-09-2012 2:32 PM
Reply to: Message 3 by Dr Adequate
11-05-2012 4:26 PM


Dr. A. Proposal Genetics Course
Dr. A: Thanks and I may need your help with getting some answers in more accessible English at least, so I may well ask some questions of you.

I’m glad to hear you’ve been thinking of doing a course on genetics for beginners as I very much appreciate your course on geology.

What I told Percy is that I would like to see such a course done but expected it would rapidly get over my head, so I didn’t really think of this thread along those lines, but as a way of learning more about some particular questions I’ve had in mind for some time.


This message is a reply to:
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Faith
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Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


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Message 12 of 236 (678639)
11-09-2012 3:48 PM
Reply to: Message 2 by Taq
11-05-2012 3:44 PM


QUESTION TWO: ID of Breeds from DNA
Thanks for all the answers about chromosome number.

I'm going to get lost if we don't stick more or less to the order of the questions. Although that's an artificial order it IS an order.

It looks like Question One is finished so on to Question Two.

If you have DNA from strikingly different breeds of, say, dogs, say a greyhound, a chihuahua, a black lab, a Bichon Frise, a Dalmation, or take your pick of what are the least similar -- are you able to tell which is which from just looking at the DNA and what exactly do you look for?

Not without a lot of background work. You would first need to find breed specific sequences from each of those breeds which takes a lot of work. At best, you could determine if another dog is the parent/sibling of another dog assuming you had the STR data needed for such an analysis.

ANSWER: NO.

OK?

You may want to read about human DNA fingerprinting to get a better idea of how this would work:
http://en.wikipedia.org/wiki/DNA_profiling

From the article on DNA profiling:

Although 99.9% of human DNA sequences are the same in every person, enough of the DNA is different to distinguish one individual from another, unless they are monozygotic twins.[2] DNA profiling uses repetitive ("repeat") sequences that are highly variable,[2] called variable number tandem repeats (VNTRs), particularly short tandem repeats (STRs). VNTR loci are very similar between closely related humans, but so variable that unrelated individuals are extremely unlikely to have the same VNTRs.

My thoughts on this would probably lead down too many rabbit trails but I’ll mention this much anyway: I think I “knew” that a great percentage of DNA merely identifies us as human so that what identifies us as individuals involves a very small percentage but it helps to have it repeated. I would suppose then that a breed or a “race” of a Species might eventually be identifiable by certain characteristics within the smaller percentage and that this may be established some time in the future. Or make that a question.

Again, I’ll wait for thoughts about this one before going on to No. 3.


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Faith
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Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 13 of 236 (678640)
11-09-2012 3:50 PM
Reply to: Message 11 by crashfrog
11-09-2012 3:18 PM


Question for later
Hi Crash.
This answer from you is going to be useful when that question comes up but please let's wait. I should have realized all those questions could drown a thread, but some of them will probably be answered fairly quickly.
This message is a reply to:
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Faith
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Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


(1)
Message 17 of 236 (678806)
11-10-2012 4:57 PM
Reply to: Message 14 by Percy
11-09-2012 4:31 PM


Re: QUESTION ONE: Species ID / CHROMOSOMES
Hello Percy. I think I'm getting it about chromosomes, that numbers are shared between different species so can't be used to identify a species without further investigation. Apparently I had a very oversimplified notion about that.

You are saying that all individuals of a species have the same number of chromosomes, but didn't someone here say that even within a species some individuals may have a different number? Ignore this if I got that wrong. I didn't review the whole thread.

PaulK's link gives the biggest number to a fern called "adders tongue" at a staggering 1440 chromosomes.

Now I'm getting more curious about chromosomes.

Coded within the DNA are the genes. A specific gene always resides on the same chromosome, though it can move around somewhat on that chromosome during reproduction.

What on earth IS a chromosome anyway? It SEEMS like it's just arbitrary segments of DNA that COULD have been simply one long string instead. Is there any point to its being broken up into separate chromosomes? Do the different chromosomes have some identifiers that give them particular functions? Not sure what I'm asking, it's hard to get the questions clear.

it's very interesting that a particular gene is always located on a particular chromosome. Is this true across species in some overall general way, that genes for particular traits that are shared among different species show up on the same chromosome sort of more or less? Meaning for instance eye color which is always the one that comes to mind for some reason, is that gene or set of genes always located on a chromosome that is the same in all species where variations in eye color are a factor?

Are my questions making any sense?


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Faith
Member
Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 18 of 236 (678808)
11-10-2012 4:59 PM
Reply to: Message 15 by nwr
11-09-2012 4:44 PM


Re: QUESTION TWO: ID of Breeds from DNA
Hi NWR,
Yes, I think it's becoming clear that breeds COULD be identifed by DNA but that it would take the building up of a library or database of the identifying sequences for each. It's more a technical problem than a conceptual probleml, as you say.
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Faith
Member
Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 21 of 236 (678835)
11-10-2012 7:30 PM
Reply to: Message 20 by Percy
11-10-2012 6:37 PM


Re: QUESTION ONE: Species ID / CHROMOSOMES
Percy writes:

It is genes that code for the proteins that produce different functions. Each gene is comprised of a part of the length of the DNA strand that makes up a chromosome. Usually the coiled DNA strand that is a chromosome contains many genes.

Maybe you answered it and I didn't recognize it, but the question I had in mind was whether the chromosomes might be identified by the particular genes that reside there? They are numbered so that you run across such statements as "such and such a gene on Chromosome 15," so the question is whether this sort of locatability perhaps gives a chromosome its peculiar identity, even a raison d'etre.


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Replies to this message:
 Message 22 by Percy, posted 11-10-2012 8:04 PM Faith has responded
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 Message 24 by sfs, posted 11-10-2012 9:30 PM Faith has responded

    
Faith
Member
Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 25 of 236 (678862)
11-10-2012 10:36 PM
Reply to: Message 22 by Percy
11-10-2012 8:04 PM


Re: QUESTION ONE: Species ID / CHROMOSOMES
Percy writes:

If you're asking how you look at a set of chromosomes and tell that this one is #12 and that one is #17, I don't know.

Yes, I think that is the question I'm trying to ask. Maybe someone else will have the answer.


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Faith
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Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 26 of 236 (678865)
11-10-2012 10:42 PM
Reply to: Message 24 by sfs
11-10-2012 9:30 PM


Re: QUESTION ONE: Species ID / CHROMOSOMES
sfs writes:

The particular set of genes on a chromosome give it its identity, but there (mostly) isn't anything special about which genes are where. Big chunks of genes can be swapped between chromosomes without it having any real effect on the organism, or example.

This is the sort of frustrating information I've thought might be the case. So you are saying that genes on say Chromosome 12 can trade places with genes on Chromosome 8, I assume during meiosis -- I also assume it would be a comparable chunk size-wise? -- so that pretty much does in any idea that the chromosome can be definitively identified by its set of genes. Or is there nevertheless some rule to this sort of event, rather than the randomness it sounds like?

But let me ask: Is this swapping a rare occurrence or fairly common?

{ABE} Also, I'm assuming the DNA strand doesn't break for this exchange to take place, break apart and come together again, so it isn't exactly right to say that a whole GENE is being moved, is it? Is it right to say that whatever alleles are getting paired for particular genes are getting placed on the opposite chromosome or something like that?

Edited by Faith, : No reason given.


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Faith
Member
Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 28 of 236 (678867)
11-10-2012 10:51 PM
Reply to: Message 23 by anglagard
11-10-2012 8:36 PM


Re: QUESTION ONE: Species ID / CHROMOSOMES
Hello Adversary Anglagard. Perhaps you'll be able to find time for a zinger or two between your courses.

Thanks for the recommendation but I've got such a long list of books I'd like to read and never will, that one doesn''t stand a chance. The point of this thread is to raise some particular questions I've had about DNA for some time now, about DNA in general and not particularly about human DNA if at all.

I think the thread really should be titled something like "Questions About DNA" rather than "Introduction to Genetics" which would better describe what Dr. A has in mind for a future project.


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Faith
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Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 29 of 236 (678868)
11-10-2012 11:01 PM
Reply to: Message 27 by crashfrog
11-10-2012 10:50 PM


Re: QUESTION ONE: Species ID / CHROMOSOMES
Aha, "numbered in order of length." Thanks, Crash, a nice simple direct practical answer.

I actually have some questions about this occasional occurrence of a different number of chromosomes in some individuals, but the questions are pretty blurry at the moment, will probably get back to them later.

Edited by Faith, : No reason given.


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Faith
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Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 33 of 236 (678946)
11-11-2012 7:37 PM
Reply to: Message 30 by Percy
11-11-2012 8:08 AM


Re: QUESTION ONE: Species ID / CHROMOSOMES
Thanks for everybody's input on chromosomes. I'll never get all of this straight I'm sure but some of it is sinking in.

I did go look up meiosis and mitosis and watched some animations, more than once. Thought I knew about cell division all the way back in high school already, but I'm finding that it's hard to retain the details in mind after watching even many times. Just getting old I guess.

But watching them did make me aware that chromosomes aren't just arbitrary bits of DNA, they have a structure, even down to the "centromere" and the cell division process acts upon them rather strikingly.

Could get bogged in detail if I pursue any of this further so I'm going to go on to another question.


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Faith
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Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 34 of 236 (678947)
11-11-2012 7:51 PM
Reply to: Message 11 by crashfrog
11-09-2012 3:18 PM


QUESTION FOUR: Reading the DNA
OK, we can think about the question you answered, Crash. I'm skipping over #3 for now just because it doesn't interest me at the moment.

[qs]

Do you ever actually look at the DNA itself or are you looking at some sort of indicator, model, or whatever you call it that you somehow derive from the cell? I know a DNA portrait as it were is often represented by some sort of bars that to me are indecipherable. Do I have to learn what those mean in order to get answers to the sort of questions I'm asking?

You post a picture of a test tube with some white filaments at the top. That's the DNA out of the peas?

Crashfrog writes:

In this form, it doesn't tell anybody much at all. It's just a slimy fiber. Learning to read this - for that matter, learning what it did - was the central task in biology and biochemistry for about 50 years. As a field, we're largely moving away from "black bars"-type techniques in molecular biology and more into direct sequencing. Actually I'd say that we already have. So, no, you won't have to learn how to read one of those.

But what IS direct sequencing? You look at the DNA strand under a microscope and count off the chemicals?

Taq seems to be saying something somewhat different:

Taq writes:

Most sequencing uses Sanger sequencing (as cited above). DNA profiling uses PCR to amplify short tandem repeats (STR's), and the gel then separates these short sequences by size. Those will produce the bands you see on some of those gels, such as this one:

[he inserts a link here that I can't get to work]

There is also RFLP techniques that look at larger chunks of DNA and how they are chopped up by different enzymes:

[and another unfunctioning link]

IOW, there are many ways of doing DNA fingerprints, and not all of them require direct sequencing. PCR and endonucleases are two indispensible tools used in this type of work, so if you want to understand what is going on you should really learn what those tools are and how they are used.

I doubt I'm going to get very far into learning much about the secondary techniques involved in reading DNA. My questions come more from wanting to be able to visualize the DNA strand and what's going on there more than anything else. There are plenty of Wikipedia articles that do give diagrams that demonstrate various DNA events, such as different kinds of mutations.

Maybe I don't know what I'm asking.

But again: In direct sequencing are you actually looking at an actual DNA strand and what does it look like? I'm sure the diagrams are accurate enough but the reality must be a lot messier.


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Faith
Member
Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 36 of 236 (679044)
11-12-2012 2:44 AM
Reply to: Message 35 by crashfrog
11-11-2012 8:24 PM


Re: QUESTION FOUR: Reading the DNA
That's all really helpful, sorts a bunch of stuff out for me. Thanks. Now I can see I'm going to have some questions about the actual sequences, the CAGT sequences and what they tell you.

For starters let me guess, you don't sequence an entire gene, which is too huge, but there are parts of the sequence that give you useful information about it?


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Faith
Member
Posts: 32726
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 38 of 236 (680563)
11-20-2012 3:53 AM
Reply to: Message 37 by crashfrog
11-12-2012 9:39 AM


QUESTION 9: "Junk DNA"
Hello Crash,
Sorry I've been so neglectful of this thread. Hope I can get back to it with more concentration soon.

Didn't want to let things get out of order here but maybe it's OK as long as the subtitles identify the topic. I really would like to know about "Junk DNA" and was going to skip to that question anyway when I saw Dr. A's post with the diagram of the Human Genome here: http://www.evcforum.net/dm.php?control=msg&m=680560

It doesn't even mention Junk DNA. Can you explain?

Thanks

ABE: The Wikipedia article on Noncoding DNA seems to suggest that the term Junk DNA applies to all DNA that does not produce protein.

http://en.wikipedia.org/wiki/Noncoding_DNA#Junk_DNA

Reading through this site I see a description of Pseudogenes that fits my understanding of Junk DNA:

PseudogenesPseudogenes are DNA sequences, related to known genes, that have lost their protein-coding ability or are otherwise no longer expressed in the cell. Pseudogenes arise from retrotransposition or genomic duplication of functional genes, and become "genomic fossils" that are nonfunctional due to mutations that prevent the transcription of the gene, such as within the gene promoter region, or fatally alter the translation of the gene, such as premature stop codons or frameshifts.[11] Pseudogenes resulting from the retrotransposition of an RNA intermediate are known as processed pseudogenes; pseudogenes that arise from the genomic remains of duplicated genes or residues of inactivated genes are nonprocessed pseudogenes.[11]

I don't see an indication of what percentage of the Genome is pseudogenes.

Then there is a discussion of Junk DNA farther down which also fits my understanding, that is, formerly functioning DNA that was killed by deleterious mutations:

"Junk DNA" is a term that was introduced in 1972 by Susumu Ohno,[30] who noted that the mutational load from deleterious mutations placed an upper limit on the number of functional loci that could be expected given a typical mutation rate. Ohno predicted that mammal genomes could not have more than 30,000 loci under selection before the "cost" from the mutational load would cause an inescapable decline in fitness, and eventually extinction. This prediction remains robust, with the human genome containing approximately 20,000 genes.

Junk DNA remains a label for the portions of a genome sequence for which no discernible function had been identified.

Obviously I could think a lot more carefully about all of this than I have and hope I can eventually. Meanwhile it looks like a starting point.

P.S. I'm counting on you to be able to reduce this to a practical, manageable, digestible summary for the nonscientist.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : Add P.S.


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