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Author Topic:   Genetics Review Article
JustinC
Member (Idle past 4844 days)
Posts: 624
From: Pittsburgh, PA, USA
Joined: 07-21-2003


Message 1 of 8 (282920)
01-31-2006 3:28 PM


I'm writing a review article (for a student journal at the University of Pittsburgh) about how comparisons of the genomes of species, alone, is not necessarily a good indicator of how similar the organisms are (it is good for constructing phylogenies, though).
The idea is that portions of the genomes which are different can affect how the similar portions are used. So for instance, we know that chimpanzees and humans share approximately 98.8% of our DNA. Well the 1.2% we don't share may affect the portions we do share in substantial ways. For instance, they may cause alternative-splicing of the primary mRNA transcript from the similar portions.
This is also consistent with our new discoveries about genetics, which show that increased complexity does not necessarily mean an increased number of genes.
So basically I'm looking for mechanisms which may cause similar portions of genomes to perform different functions in different species.
So far, my list includes:
1. alternative splicing
2. transcriptional initiation
3. transciptional regulation patterns
I would also like to include the following:
1. DNA rearrangement
2. post-translational modifications
First off, I really don't know what DNA rearrangement is. I've only seen it referred to briefly. Just guessing, I think it is when parts of genes are switched and swapped to produce variation (like how various antibodies are produced). Is this correct?
Second, I would like to know if anyone knows of any post-translational modifications that may be species-specific. Even if it may not be species-specific, I would like to know if there are any research articles. I've only found one which is from 1981, which is way too old.
Also, any thoughts on the subject or other ideas are welcome.
Thanks

Replies to this message:
 Message 3 by Brad McFall, posted 01-31-2006 5:57 PM JustinC has replied
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 Message 8 by 666_DBz, posted 02-23-2006 7:12 PM JustinC has not replied

  
AdminJar
Inactive Member


Message 2 of 8 (282926)
01-31-2006 3:50 PM


Thread moved here from the Proposed New Topics forum.

  
Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 3 of 8 (282952)
01-31-2006 5:57 PM
Reply to: Message 1 by JustinC
01-31-2006 3:28 PM


link to ornithology
DO DNA DISTANCES REVEAL AVIAN PHYLOGENY?
L. J. Gibson
Geoscience Research Institute
Geoscience Research Institute | I think we need more research on that...
This article discusses the "classic" case, or so it appeared to me. After reading some of
quote:
Sibley, C.G. and J.E. Ahlquist. 1986. Reconstructing bird phylogeny by comparing DNA's. Scientific American 254(2):82-92. Sibley, C.G. and J.E. Ahlquist. 1987. DNA hybridization evidence of hominoid phylogeny: results from an expanded data set. Journal of Molecular Evolution 26:99-121. Sibley, C.G., J.E, Ahlquist, and F.H. Sheldon. 1987. DNA hybridization and phylogenetics. Reply to Cracraft. Evolutionary Biology 21:97-125.
and listening to Judge Ito discuss DNA in the Simpson Trial, I could not believe I lived in the same country any more.
I know you are looking for things that might indicate differences rather than similarities but you probably should give this literature at least a brief glance. Perhaps I am just naively confused with the transition from your first to second paragraphs but if genome comparisons are good at reconstructing species phylogenies then are they not good indicators of how similar the component organisms are ipso facto. If you meant simply to introduce the particular molecular kinematic units that might be operative for you to report on “that portions of the genomes which are different can affect how the similar portions are used” then disregard my question please.

This message is a reply to:
 Message 1 by JustinC, posted 01-31-2006 3:28 PM JustinC has replied

Replies to this message:
 Message 4 by JustinC, posted 02-01-2006 12:03 AM Brad McFall has replied

  
JustinC
Member (Idle past 4844 days)
Posts: 624
From: Pittsburgh, PA, USA
Joined: 07-21-2003


Message 4 of 8 (283031)
02-01-2006 12:03 AM
Reply to: Message 3 by Brad McFall
01-31-2006 5:57 PM


Re: link to ornithology
Thanks for the response, I always enjoy your posts.
quote:
Perhaps I am just naively confused with the transition from your first to second paragraphs but if genome comparisons are good at reconstructing species phylogenies then are they not good indicators of how similar the component organisms are ipso facto.
The transition is a bit awkward. I'm supposed to discuss the naive position that "if species share 98.8% of their DNA then the species are 98.8% similar."
While DNA similarity is a good indication of how closely related species are, the DNA similarity alone is not a good indicator how similar the species are (so the argument goes). The reason why is that the differing portions of the genome can effect the similar portions.
In other words, just because we share 98.8% of our DNA with chimpanzees doesn't mean our gene products or the physiological effects caused by those genes are 98.8% the same. There are alot of papers which show that species diversification can result from species-specific alternative splicing of very similar DNA portions. So, while the nucleotide sequence of an open reading frame may be the same for two species, it does not mean that the products are the same.
Similarly, even if we share a lot of the same gene products with a chimpanzee, these gene products can be coordinated through transcriptional regulation to produce a myriad of physiological affects. So in one species they may be coordinated differently than in another species. (maybe coordinated isn't the right word, i'm referring to simultaneous transcripton of particular genes). There is evidence that the increased complexity we see in vertebrates compared to invertebrates is the result of the complex coordination of our genes, and not necessarily an increase in gene products (we do have about double their genes, but most seem to be duplications).
Does this make sense?

This message is a reply to:
 Message 3 by Brad McFall, posted 01-31-2006 5:57 PM Brad McFall has replied

Replies to this message:
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 5 of 8 (283055)
02-01-2006 5:38 AM
Reply to: Message 4 by JustinC
02-01-2006 12:03 AM


Vertebrate innovation
One interesting feature of vertebrate genomes is the presence of quite large stretches of highly conserved non-coding DNA. Not only are these regions non-coding but there is no evidence that they are transcribed as might be the case if they contained microRNA operons.
Exactly how these stretches act to regulate gene expression is unclear but they provide a fertile substrate for the generation of distinct expression patterns by very small changes in the genome.
TTFN,
WK

This message is a reply to:
 Message 4 by JustinC, posted 02-01-2006 12:03 AM JustinC has not replied

  
Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 6 of 8 (283072)
02-01-2006 7:25 AM
Reply to: Message 4 by JustinC
02-01-2006 12:03 AM


Re:coordination of physiological affect
Yes it does make a worthy amount of sense.
I used to think that protein folding patterns might be independent of transcription physics and Gladyshev's ideas I have spoken of here on EVC suggest that lipids play a role not well appreciated.
Part of the problem is our subjective view of different creatures. I have a large belly from some recent depression, a bad back with a limp and glasses. I *look* very different to passersby these days than I did passing the same streets 20 years ago and yet my genes probably have not changed one iota. The difficulty is figuring out how the internal interactions effect the external formations. Good luck. If you find some phenomenon that seems generalizable beyond a particular lineage or clade I would be interested to learn about that. What I realized in the early 90s was that sheep are different than mice than cows etc(than man) when it comes to congressing of chromosomes during cell division and metaphase plate formation and that diversity rather than identity is the rule in general. Identifying the structure of the increased "coordination" however would be a great career possibility, even more than a simple demonstration paper.

This message is a reply to:
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666_DBz
Inactive Junior Member


Message 7 of 8 (289878)
02-23-2006 7:12 PM
Reply to: Message 1 by JustinC
01-31-2006 3:28 PM


Homeotic Genes or Drosophila, of Mice and Men
Primate "indels" or single "string" in sequencing
_____________________________________________________
Huh????
> I'll take a moment of your time We can come off a thread debating an issue
without a bit of trouble I'm not sure if this independent of transcription physics directly relates (in any way) to Genetic Engineering but I just have to get a better understanding
Q. -- Has anyone of you (in your research for a paper) noticed a questioning of phylogenetic relations in texts cited about...Primate "indels" (insertions/deletions) phylogenetic arrangements or lines Two sets of numbers must mean there are "two types" of transcription in the sequence of the chimpanzee genome as compared with the human genome I don't understand the differentiation in (Molecular) biology, & phylogenetics can you
clear that up, too ???
P.S.-- Heads-up I'm looking for any papers research on phylogenetic arrangements or mechanisms [within] Homeotic Gene expression in Humans beings.Something Creationists haven't looked into or study; I'm so there
This message has been edited by 666_DBz, 02-23-2006 09:44 PM

Interests are : Philosophy, Archaeology, UFOs, Science and the Life Sciences

This message is a reply to:
 Message 1 by JustinC, posted 01-31-2006 3:28 PM JustinC has not replied

  
666_DBz
Inactive Junior Member


Message 8 of 8 (289879)
02-23-2006 7:12 PM
Reply to: Message 1 by JustinC
01-31-2006 3:28 PM


??? Homeotic Genes or Drosophila, of Mice and Men
>We are consistent with evolutionary theory "approximately 98.8% of our DNA" is shared by lower Apes ?
..................................................................
Q. -- What's that big missed something ? A certain cohesion factor unifies and explains evidence and phenomena across many scientific disciplines. In particular, the fact that the very recent science of Genetics, which Darwin and well over 100 years more study of evolution did not have the advantage of knowing anything about, remains amazingly consistent with evolutionary theory That said. Why do I notice a distancing of Man from Higher Apes from some Creationist's literature
>
Remember My P.S. -- Has anybody information about phylogenetic arrangements or mechanisms [within] Homeotic Gene expression in Humans. Something Creationists haven't looked into or study; so I'm there
_____________________________________________
For some belief is "the" cohesion factor; for some Hard Science is "the" cohesion factor
This message has been edited by 666_DBz, 02-23-2006 09:31 PM

This message is a reply to:
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