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Dinosaur-Bird Link: Ancient Proteins Preserved In Soft Tissue From 80 
Million-Year-Old Hadrosaur

Samples of ancient protein dating back 80 million years preserved in bone 
fragments and soft tissues of a hadrosaur. (Credit: Courtesy of NCSU)

ScienceDaily (May 1, 2009) — Ancient protein dating back 80 million years to 
the Cretaceous geologic period has been preserved in bone fragments and soft 
tissues of a hadrosaur, or duck-billed dinosaur, according to a study in the 
May 1 issue of Science.

Led by scientists at Beth Israel Deaconess Medical Center (BIDMC) and North 
Carolina State University (NCSU), the research support earlier results from 
analyses suggesting that collagen protein survived in the bones of a well 
preserved Tyrannosaurus rex, and offer robust new evidence supporting previous 
conclusions that birds and dinosaurs are evolutionarily related.

In April 2007 John Asara, PhD, Director of the Mass Spectrometry Core at BIDMC, 
together with NCSU paleontologist Mary Schweitzer, PhD, published two papers in 
Science describing their discovery that collagen extracted from bone fragments 
of a 68-million-year-old T. rex closely matched the amino acid sequences of 
modern day chickens. Not surprisingly, the widely publicized findings created a 
great deal of controversy.

"With this new paper, we hoped to show that our T. rex discovery was not a 
unique occurrence," notes Asara, who is also an Instructor in Pathology at 
Harvard Medical School. "This is the second dinosaur species we've examined and 
helps verify that our first discovery was not just a one-hit wonder. Our 
current study was the collaborative effort of a number of independent 
laboratories, whose findings collectively add up to a robust conclusion."

At the heart of the controversy is the idea that ancient protein can exist at 
all. When an animal dies, protein immediately begins to degrade and, in the 
case of fossils, is slowly replaced by mineral, a substitution process assumed 
to be complete by 1 million years. But with this latest evidence, it appears 
that some proteins do indeed have real staying power.

"We wound up identifying nearly double the number of amino acids we recovered 
in the T. rex study," says Asara. "The sequences displayed high spectral 
quality and the interpretations were of high confidence."

The two scientists had decided to collaborate again after Schweitzer and 
paleontologist Jack Horner of Montana State University's Museum of the Rockies 
recovered the 80-million-year-old Brachylophosaurus canadensis femur bone in 
the summer of 2007 and observed that it appeared to be even better preserved 
than the original T. rex fossil.

Schweitzer's initial laboratory analyses confirmed this observation: After 
being subjected to demineralization, the B. canadensis bone fragments showed 
marked preservation of original tissues and molecules, with microstructures 
resembling soft, transparent vessels, cells and fibrous matrix – even though 
the fossil was much older than the T. rex sample.

"Deep burial in sandstone seems to favor exceptional preservation," notes 
Schweitzer, explaining that this fossil was found under approximately seven 
meters of sandstone in the Judith River Formation, in parts of what is now 
Eastern Montana.

Chemical extractions of bone and vessel were subsequently sent to the 
laboratories of BIDMC scientists Lewis Cantley, PhD, and Raghu Kalluri, PhD, 
where immunoblots and immunochemistry analyses were conducted to determine the 
presence of collagen protein in the samples.

"Having been a part of the T. rex study, I was curious to be part of this 
investigation as well," explains Cantley, Chief of the Division of Signal 
Transduction at BIDMC. "In view of the skepticism about the original findings, 
it was important to demonstrate that our findings in T. rex could be verified 
in another dinosaur and in other laboratories."

The results confirmed the existence of protein. "Because I am a collagen 
biochemist, our lab was contacted to perform an independent analysis of this 
new bone find," explains Kalluri, who is Chief of the Division of Matrix 
Biology at BIDMC. "We isolated the proteins – collagen, laminin and elastin – 
from the bone, and also extracted bone cells and blood vessels from this 
sample. Our findings demonstrated that it did contain basement membrane matrix."

In addition, In situ mass spectrometry studies conducted at Montana State 
University by Recep Avci and Zhiyong Suo independently verified amino acids in 
dinosaur tissues, including the collagen signature amino acid, hydroxylated 

>From there, using a combination of two mass spectrometry technologies – linear 
>ion trap and hybrid linear ion trap/orbitrap – Asara was able to improve upon 
>the techniques he had used in analyzing both the T. rex specimen and specimens 
>from bones of other prehistoric animals including a 300,000-year-old mammoth 
>and mastodon.

At the beginning of the study, Asara explains, his lab used an ion trap mass 
spectrometer, which captures and holds peptides through time so that after the 
collected peptides are measured for mass they are isolated and fragmented to 
reveal their amino acid sequence. Then, while the study was in progress, his 
lab acquired a high-resolution and highly mass-accurate Orbitrap XL mass 
spectrometer, which was used during the second half of the analysis.

"Because it is capable of sub 2 ppm mass accuracy, the Orbitrap allowed us to 
make more confident sequence calls than we did in the T. rex study," Asara 
explains. "For example, the mass difference between a hydroxyproline amino acid 
residue [which is plentiful in collagen] and a leucine or isoleucine residue is 
only 0.0364 Da. Although this very small measurement proved to be an obstacle 
for the ion trap, it was not a problem for the Orbitrap." Material for mass 
spectrometry sequence analysis was also sent to the lab of William Lane at 
Harvard University and mass spectrometry sequence data were independently 
verified by John Cottrell, PhD, at Matrix Science in London, UK.

The end result was a total of eight collagen peptides and 149 amino acids from 
four different samples, sequences that held up when multiple validation steps 
were performed, including comparisons with synthetic peptides using a spectral 
comparison algorithm and statistical evaluation.

In the final portion of the study, coauthor Chris Organ, PhD, a Postdoctoral 
Fellow in the Department of Organismic and Evolutionary Biology at Harvard 
University, conducted a rigorous phylogenetic analysis of the identified 
sequences to determine B. canadensis' place within the evolutionary tree of 
animals. The B. canadensis collagen sequence data were compared to a database 
of collagen sequence data from 21 species of living animals and sequences from 
two other fossils, mastodon and T. rex. The results placed B. canadensis on the 
same family-tree branch with T. rex, in the same group as chicken and ostrich, 
and more distantly, to alligator and lizard.

"The phylogenetic analysis yielded clear results, but the placement of the 
extinct dinosaurs still rests on a limited amount of sequence data," notes 
Organ. "There is not enough sequence data to correctly parse out the 
relationships within Dinosauria [the group containing B. canadensis, T. rex and 
the two birds] but the group as a whole is well supported by the analysis, 
which is consistent with studies based on morphology."

Ultimately, notes Asara, "We were able to achieve these results, in part, 
because the mass spectrometry systems that our lab has set up for cancer 
research are capable of a similar concentration range – low to sub femtomole -- 
needed for ancient fossil protein sequencing. We hope to meet with similar 
success when it comes to identifying novel signaling proteins from cancerous 

This study was funded, in part, through grants from the National Science 
Foundation, the David and Lucile Packard Foundation, the Merck Postdoctoral 
Science Research Fellowship, the National Institutes of Health and the Taplin 
Funds for Discovery, Harvard Medical School.

In addition to Asara and Schweitzer, coauthors include BIDMC investigators 
Lewis Cantley, Raghu Kalluri, Lisa Freimark, Valerie Lebleu, and Michael Duncan 
II; Wenxia Zheng of North Carolina State University; Chris Organ, John Neveu 
and William Lane of Harvard University; Recep Avci, and Zhiyong Suo of Montana 
State University; John Horner of the Museum of the Rockies (MT); Matthew Vander 
Heiden of the Dana-Farber Cancer Institute; and John Cottrell of Matrix 
Science, London, UK.

Journal reference:

   1. Mary H. Schweitzer, Wenxia Zheng, Chris L. Organ, Recep Avci, Zhiyong 
Suo, Lisa M. Freimark, Valerie S. Lebleu, Michael B. Duncan, Matthew G. Vander 
Heiden, John M. Neveu, William S. Lane, John S. Cottrell, John R. Horner, Lewis 
C. Cantley, Raghu Kalluri, and John M. Asara. Biomolecular Characterization and 
Protein Sequences of the Campanian Hadrosaur B. canadensis. Science, 2009; 324 
(5927): 626 DOI: 10.1126/science.1165069

Adapted from materials provided by Beth Israel Deaconess Medical Center.
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Proteins Preserved In Soft Tissue From 80 Million-Year-Old Hadrosaur. 
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