T-Rex DNA found in a soft tissue fossil sample...Follow

how the **** did a fragment of soft tissue survive for 65 million years? and where is this article?

This is a rather old news article. The way in which the soft tissue survived was perserved by the fossil around it. Somehow during the fossilization process of this bone it became unsuited for bacteria to grow in and then was sealed off by the natural mineralization that makes fossils. Without bacteria to degrade the tissue it won't rot or break down and just sits there till opened up.

Now the question of DNA, it is probable that some DNA exists there but it is highly unlikely that enough exists to sequence the genome to any significant degree. In every organism there are naturally occuring enzymes called Dnases which chew up DNA makeing one strand into many smaller strands. In addition DNA, while fairly stable, does degrade over time. When you see people talking about isolating DNA from crime scenes many years old its a different kind of technology being used to analyze it. When this happens they are not "sequencing" the DNA in question but rather using the before mentioned enzymes to chew up the DNA makeing what is called a footprint. Every footprint from everyperson is basically unique due to the minor mutations in each of our genetic code that makes us who we are (they are called SNIPs for those interested standing for Single Nucleotide Insertion Point), it is possible theoretically that two unrelated people could have the same footprint but it is highly unlikely (this is one of the things that got OJ off by the way). Anyway back to the T-rex. I am assuming that the T-rex has a genome comperable in size to a large reptile or bird of today. These genomes require a fair amount of DNA to fully sequence the genome, and a lot of money, so I wouldn't expect Jurassic park soon as it would be very difficult to put any sequenced DNA in the proper order genomically. What you might see is the sequencing of short strands of DNA which have been amplified by non-specific primers using a very standerd technology called PCR (polymerase chain reaction). This might yield a full codeing segment (the part of the gene that codes for the protein made by the gene) but in most likelyhood will only get a part of it and depending on the genomic makeup of the organism there is a good chance that any DNA sequenced would contain introns (parts of the gene which are cut out when it is expressed, the parts left in are called exons) or be a part of the large areas on non-codeing regions that make up all our genomes.







oh what the hell, I'll load my T-rex gun on Turok and get ready just in case.

I'm glad to see someone else on FFXI knows a bit about Biology. I completely forget about DNAses which would in fact make it very difficult for a "perfect" strand to be intact. However...

I believe the DNAses target Telomerase (a series of many repeating codons that serve no purpose other than to be sort of a "buffer") first. I was under the assumption that that is what Telomerase was for, to act as a "shield" for DNA from DNAses, as well as other factors that love to nibble on the strands.

Now, my whole point in bringing this up is that:

1.) Dinosaurs may have had a rather long Telmorase at the end of their DNA. They are said to be much longer lived than Human Beings and Telmorase is believed to be one of the keys to Longevity. If this is true, then there is no telling if the DNAses got "through" the telomerase strand. If they haven't, then the original strand of DNA may still be available for cloning.

2.) I was also under the assumption that a segment of DNA codes for a protein which "knows" the DNA's code (the order of Nucleotides). This is used for "proofreading" DNA during replication to assure that there is no frame shift mutation (where the reading frame of DNA is thrown off. Even the slightest frame shift mutation can cause catastrophic events). If I am correct in believing this protein exists, and if I am also correct in its function, then that means we could somehow "use" that protein to "fill in the gaps" and create the DNA we needed.

I am a biology neophyte and it sounds like you have alot more experience than me (first year premed student). Any knowledge you could share would be much appreciated ^^

Ok I wrote a reply but left it on my computer at home so I'm rewriting it at work and hope I remember all that I said:

(Note I don't mean anything I say in a sarcastic or aggressive tone, all the points people brought up are good valid well thought out points and I am simply sharing my views and opinions on them. Remember in science there is always the chance that someone is wrong and what we know today could be disproved at a later date. So don't get upset because it could turn out I am wrong.)

First to Ayazz:



This was what the did in the Jurassic park movie and is a very novel idea that has the potential to work but with the understanding that it will never be a fully genetic dino. The biggest practical problem with this is that it requires you to know 100% all of the genes that make a T-rex different from your comparable creature (believe it or not last I heard parakeets were considered one of the closer to T-rex's). This would work if you have half of a basic gene or housekeeping gene and need to fill in the rest. These genes are genes so fundamental to life, or to a family taxa, that they remain virtually unchanged over evolutionary history. A good example of this are the histone genes. These genes code proteins that are involved in chromatin formation (chromatin makes up chromosomes which are basically a way your body stores its DNA in a compact organized form). Because the chemistry of the interactions with nucleic acids (the A/T/C/G that make up DNA) these remain almost exact copies among multicellular creatures. So you could do it with some genes but the biggest problem is you may not have the genes that really make a t-rex a t-rex and these can't be replaced as there is so much evolutionary distance between t-rex and its modern cousins I doubt many of these genes are still around. Remember t-rex and other dinosaurs died out so there are no evolutionary descendents only evolutionary descendents of the dinosaurs that didn't die out (small ones that became birds in theory) and other distant relatives. So in essence you are trying to figure out something about someone by looking at the descendents of their third or fourth cousin. The short answer to your question is yes and no depending on the situation. In this case it is unlikely in my opinion.

Shaolinz:


A good thought but while telomeres do act as a shield (this is a good analogy but I would be careful in the use of it as the functions of telomeres is still highly debated and you may find yourself the target of unwanted attention by using this in front of the wrong person, as a student your pretty safe using it thought) you have to remember the time involved here is several million years which is a long time for the Dnases to chew on things. Plus while most DNases have a specific sequence they target, this is one of the technologies which makes cloning possible btw, if left alone with DNA long enough they will misfire and cut the wrong sequence. This is a major pain when it happens in the lab btw and is why you usually leave things in a digestion for only a few hours at the most (the time needed depends on the cutting enzyme being used).



You have a few misunderstandings here that I'll try to clear up first of all:
DNA (nucleus) -> mRNA (nucleus and cytoplasm) -> protein (ribosomal complexes in cytoplasm)
So the DNA actually never sees the protein being synthesized by the ribosomes unless it contains a nuclear localization sequence and is in fact a DNA binding protein (most of these are transcription factors). The system that is involved in DNA repair is a bit different because it can not use a protein as a template, remember that most amino acids have multiple codons (tri-nucleotide sequences) that can code for it. So there can not be a literal translation from protein back to DNA in codeing. When DNA is repaired the DNA repair system uses the complementory strand as a template. DNA exists in a double helix with each strand complementary to the other. Recent evidence in humans suggest that infact both strands can be used to code very different protein and out system uses this as a way to sometimes store double the information in the same space. When the repair mechanism comes across damage in one strand it cuts out the damaged part and fills in the complementary nucleotides from the other strand, A=T C=G. This is the most basic form of DNA repair and is the method used with UV damage. Other types of DNA damage have other solutions many less efficient, sometimes the repair mechanism can't figure out which strand is damaged so it simply guesses and fixes one strand giving it a 50/50 shot. Frameshift mutations are a different beast all together. For those wondering a frameshift mutation occurs when there is an insertion or deletion of nucleotides in DNA which severely offsets the codeing. Basically every three nucleotides in a sequence codes a different amino acid so if you insert one you offset all the others afterwards. Example:

For the sequence: ACGGTATAGAAACCC
ACG GTA TAG AAA CCC are the codons that would be coding
If a insertion happened and you had: ACGGGTATAGAAACCC
You would now get:
ACG GGT ATA GAA ACC C so you can see how it can upset a lot of things really fast.

Now I'm sad to say I don't know 100% all the ways in which frame shifts are repaired I want to say a lot of them are just simply tolerated and if it kills the cell another is generated in its place. Remember that if the change isn't in your "seed" it’s not passed on to the next generation. I know one way in which the cell can repair it is by excision and it targets the area basically by finding the "lump" in the DNA that is caused by the addition of this nucleotide. So what it is targeting isn't so much an error in the sequence as an anomaly in the 3D structure of the DNA that is caused by trying to fit in that extra base into the code.

Now to actually answer your question. What you propose is possible but would be very very very very very very difficult and most likely would not give you all the information you need. In any given tissue not all genes are expressed so you can only isolate proteins which are expressed in the tissue that they have. I remember it being a leg bone so you would have none of the proteins that are specific to the heart, brain, liver, ect. Only the ones specific to the tissues present in the sample, I want to say they had a connective tissue like a lignin. It is possible that once isolated you could use protein sequencing (Edmond degradation would probably be the best shot) to identify the amino acids and from that you can guess what the sequence is but remember the amino acids rarely have just one codon that codes for them plus you would get absolutely no information about the promoter or other gene specific aspects that are very important for gene expression.

Yes, every cell has a full copy of DNA but every cell only expresses certain genes this is what makes a liver cell different from brain cell. Lets say a genome has 10 proteins and the organism has two tissues. Genes 1-5 are expressed in tissue 1 while genes 6-10 are expressed in tissue 2. If you extract only proteins and no DNA from tissue 2 you will never see proteins 1-5 becouse they are not expressed in tissue 2.

You can only find out the unexpressed genes from a tissue sample by looking at only the DNA, looking at the proteins present will not tell you anything about the sequence of the genes in the unexpressed sections.

Omg I cant wait to go to Jurasic park! I better loose 100 or 200 pounds so I can at least attempt to run away!