... by its full name: "Bison priscus"

[Jacques Cinq-Mars]

Here is what could be taken as a media “addendum” or complement to the earlier post on the Beringian []Bison[/i].

Not great as far as clear and concise explanations go. We will have to wait for the Geology to be online (see below) to read the actual paper.

DNA Recovered from Ice Age Bison

By Rossella Lorenzi --  Discovery News

Nov. 22 — Fragments of genetic material have been recovered for the first time from an Ice Age bison, British and American researchers report in the December issue of the journal Geology.

The team is hoping that in the future the techniques used to make this discovery may extend our knowledge about the genetic make-up of ancient species, as well as provide answers to long-standing evolutionary puzzles.

Christina Nielsen-Marsh of the University of Newcastle upon Tyne and colleagues from Oxford, Harvard, and Michigan State University analyzed small amounts of two bison priscus fossils, dug out of the permafrost of Siberia and Alaska.

The bones are more than 55,000 years old, although their age, which is beyond the limits of radiocarbon dating, is somewhat imprecise.
In addition to the recovery of mitochondrial DNA, the researchers managed to retrieve the complete sequencing of osteocalcin. This is a small extracellular protein involved in the formation of bone cells, and it is found in all vertebrates' bones.

This discovery is exciting to scientists because calculations suggest that while DNA may only survive for up to 100,000 years, proteins may survive for up to 10 million. That would be long enough to look back to the last common ancestor of humans and chimpanzees.

"For the first time we have a complete amino acid sequence for an ancient protein. Our research finally puts to rest the question of whether indigenous proteins can exist in fossil bones beyond radiocarbon dating age," Nielsen-Marsh told Discovery News.

The groundbreaking research was made possible by an array of hi-tech laboratory tools which included matrix-assisted laser desorption ionization mass spectrometry — a technology that won scientist Koichi Tanaka this year's chemistry Nobel.

The complete sequences of amino acids exactly matched that of the modern bison.

"However, there was one single amino acid difference. This demonstrates that osteocalcin can give genetic information which can help us to investigate evolution of species, though not in the same detail which DNA can provide, if it survives," Nielsen-Marsh said.

Paleolithic cave paintings in Europe and carcasses preserved in frozen ground indicate that bison priscus was quite similar to its modern descendants, though somewhat larger, with long horns and an ornate fur coat. Researchers believe it became extinct around 11,000 years ago.

"The osteocalcin and sequences by themselves do not say much about bison phylogeny or evolution. However, the successful application of these new techniques of protein isolation and sequencing will open the door to exciting new research," Paul Matheus, a researcher with the University of Alaska Fairbanks in the Alaska Quaternary Center and the Institute of Arctic Biology, told Discovery News.

What excites scientists is that proteins are likely to last longer than DNA, which denatures in the presence of water and warm temperatures.

"Now we have the technique which allows to identify, without ambiguity, the presence of protein in ancient bones. We will apply it to older fossils to attempt to determine the survival limit of this protein in the geological record," said Nielsen-Marsh.

Osteocalcin itself may not be able to determine the puzzling lineages of humans over the past six or seven million years, but the method could be applied to other proteins. Nielsen-Marsh warns that "the original accomplishment of sequencing osteocalcin was not easy" — it will take time to establish the method successfully for another protein.

"However, the present technique may be useful for resolving relationships such as that between modern and extinct reptiles and birds — the old dinosaur-bird connection, for instance. But we're a far way from getting complete osteocalcin sequences out of dinosaur bones," said Matheus.

As I said, the December issue of Geology had yet to be online. When it does, it will be accessible HERE.

Jacques Cinq-Mars

[Jacques Cinq-Mars]

All,

The December issue of Geology is now online and the paper mentioned in my earlier post is nowhere to be found. I suppose we can blame Discovery News for this incorrect reference, that is, unless it was to some other geology journal.

Jacques Cinq-Mars

[Daryl Habel]

Apparently Discovery News reported correctly that the article was scheduled to appear in the December issue of Geology (published by the Geological Society of America).  I've found another, slightly more detailed story (which might even be the press release) at:

CLICK HERE

I've cut-and-pasted the story below.  Note at the end it says a copy of the paper is available by request to Ann Cairns at the Geological Society of America (acairns@geosociety.org), although I'd guess this offer probably was intended for media editors and reviewers.

SCIENTISTS DISCOVER ANCIENT PROTEIN AND DNA SEQUENCES IN THE SAME FOSSIL

For the first time in the world, researchers at the University of Newcastle upon Tyne, UK, along with collaborators at the University of Oxford, Harvard University, and Michigan State University have uncovered two genetically informative molecules from a single fossil bone. In addition to the recovery of mitochondrial DNA, the complete sequencing of a bone protein, osteocalcin, makes this a major scientific breakthrough. Extending this work to additional fossils could change perceptions of evolutionary theory. Results of the study are published in the December issue of GEOLOGY, published by the Geological Society of America.

Christina Nielsen-Marsh of the University of Newcastle upon Tyne, along with colleagues at the University of Oxford, Harvard University, and Michigan State University, examined the molecular structure of two fossilized Bison priscus bones, one from Siberia and the other from Alaska. The bones are more than 55,000 years old, although their age is somewhat imprecise because they are beyond the limits of radiocarbon dating. The Siberian fossil ultimately revealed both mitochondrial DNA and a complete sequence of osteocalcin, a protein found in all bones that is involved in bone formation.

The researchers demonstrate, using immunological data, that osteocalcin remains in bones heated to high temperatures (165°C) for several hours and is measurable in bones that are around 120,000 years old, emphasising the survivability of the protein. According to Nielsen-Marsh, "The research has the potential to be applied to much older fossils and extend our knowledge about the genetic make-up of ancient species further back into geological time." The team is hoping that in the future their approach may be able to find the answers to long-standing evolutionary puzzles.

Protein sequencing was carried out at Michigan State University, using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Important steps in the development of this technique are credited to this year's Nobel Prize (Chemistry) winning scientist Koichi Tanaka. Using a variety of approaches, the osteocalcin from the ancient bison bone was fragmented and the information used to construct the amino acid sequence.

Remarkably, the primary sequence of the protein was recovered intact, including the relatively unstable carboxylated glutamic acid (gamma-carboxy glutamic acid) residues. As a consequence of this study, the team has a new optimism regarding the potential for protein sequencing and extending molecular records farther back in time.

Protein sequences can be directly related to the genetic code of DNA. The sequence of amino acids (the building blocks of proteins) record genetic information transferred from DNA. According to Nielsen-Marsh this is important because mutations in DNA over long periods of time result in changes in proteins that contribute to the evolution of life. Calculations suggest, however, that DNA may only survive for up to 100,000 years, whereas proteins may survive for up to10 million.

The traditional way of comparing ancient and modern species to determine how they have changed over time is morphology, where bones are compared for shape and size. This may involve a large margin of error, however, as it can be subjective and bones such as skulls are malleable and prone to changing shape.

According to Nielsen-Marsh, "By extracting biochemical information from fossils, scientists utilize tools that avoid these difficulties and offer more objective comparisons between ancient and modern species." This approach could possibly unearth new knowledge about evolutionary relationships.

"This research is groundbreaking," continues Nielsen-Marsh, "because it finally puts to rest the question of whether indigenous proteins can exist in fossil bones beyond radiocarbon dating age. Moreover, intriguing data from our laboratories suggest that extending protein sequencing well beyond 55,000 years is a realistic possibility."

###

Funding for the study was provided by the Wellcome Trust and the National Science Foundation.

To obtain a copy of the paper "Sequence preservation of osteocalcin protein and mitochondrial DNA in bison bones older than 55 ka" contact Ann Cairns at the Geological Society of America (acairns@geosociety.org).

Author contact information:

Christina M. Nielsen-March
c/o Dept. of Geological Sciences
Michigan State University
517-355-8307
nielse42@msu.edu

Joint Release:
Geological Society of America
University of Newcastle upon Tyne

GSA Release No. 02-54
Contact: Ann Cairns
303-357-1056
acairns@geosociety.org

University of Newcastle upon Tyne
Contact: Claire Jordan
+44-0-191-222-6067
Claire.Jordan@ncl.ac.uk

Source of the given news and the copyrights belong to a Geological Society of America

Publishing date: November 19, 2002

The question remains about why it did not appear in the December issue of Geology

Dar

[Jacques Cinq-Mars]

Apparently Discovery News reported correctly that the article was scheduled to appear in the December issue of Geology (published by the Geological Society of America).  I've found another, slightly more detailed story (which might even be the press release) at:
<snip>

Dar,

Thanks for this added bit of information and clarification. I guess the next step is to try to obtain a copy of this mysterious paper which sounds promising in terms of proteomic studies. Whether or not it will add much to our understanding of the importance of Bison priscus in the larger palaeoanthropological scheme of things is another story altogether.

Jacques

[Jacques Cinq-Mars]

All,

Coincidentally, here is a paper (current issue of JAS) that specifically deals with the question of the preservation and retrieval of the protein “osteocalcin”, in bone. From the abstract alone, it seems that the reported research was not carried out on bone samples obtained from high latitude deposits (i.e., cold/permafrost environments). It does fit, however, what has already been said, here and elsewhere, regarding the obvious latitudinal variability exhibited in the case of (relative) bone collagen preservation when using it for other types  of assays, including C14 dating.

Jacques Cinq-Mars

Smith, C.I., O.E. Craig, R.V. Prigodich, C.M. Nielsen-Marsh, M.M.E. Jans, C. Vermeer, and M.J. Collins. 2005. Diagenesis and survival of osteocalcin in archaeological bone. Journal of Archaeological Science 32(1): 105-113.

Abstract:

It has been demonstrated that the protein osteocalcin can survive in bone in the archaeological record, and postulated that it has the potential to survive over geological time periods. The precise mechanism for this longevity of survival is not yet fully understood, and has not been extensively studied in comparison to other diagenetic aspects of archaeological bone. We report a comparison between osteocalcin survival and the state of preservation of more than 60 bones from 14 archaeological sites. The amount of osteocalcin, assayed immunologically, was compared with diagenetic parameters that measure: the amount of ‘collagen’ in the bone, the mineral changes, the porosity, and the histological preservation of the material. The findings indicate that microbial taphonomy and mineral alteration of bone have a profoundly damaging effect on the preservation of osteocalcin.

Keywords:

Osteocalcin; Archaeological bone; Bone diagenesis; ELISA; Histological index; Infrared splitting factor; Collagen

Copyright © 2004 Elsevier Ltd All rights reserved.

For access to the full paper, click HERE

[Daryl Habel]

All,

Coincidentally, here is a paper (current issue of JAS) that specifically deals with the question of the preservation and retrieval of the protein “osteocalcin”, in bone. From the abstract alone, it seems that the reported research was not carried out on bone samples obtained from high latitude deposits (i.e., cold/permafrost environments). It does fit, however, what has already been said, here and elsewhere, regarding the obvious latitudinal variability exhibited in the case of (relative) bone collagen preservation when using it for other types  of assays, including C14 dating.

Jacques Cinq-Mars

For access to the full paper, click HERE

I might add that the January 2005 issue of Journal of Archaeological Science has become a free available download from Science Direct as a complementary issue (announced yesterday by e-mail to registered members), so this 'osteocalcin' paper can be read beyond the abstract.

It seems the samples from the JAS paper originated from Britain, Netherlands, Sweden and Italy (200-6000 yrs old), as well as 3 samples of Bison priscus from the Yukon area of the USA (well, that's what table 1 says)!!!! and the 3 Yukon USA samples are (from section 2.1 of the text) somewhere between 800 and 53000 years old.

Science Direct announced yesterday that Quaternary Science Reviews (QSR) January 2005 issue also has been rendered free complementary download.  It's that time of year when the complementary issues from Science Direct are changed.

Dar