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Rewriting history through proteins
Andrew S. Wiecek
BioTechniques, Vol. 54, No. 1, January 2013, pp. 19–21
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Today, researchers interested in exploring ancient samples and remains at the molecular level mainly rely on DNA. But proteins might tell us even more about history. Andrew Wiecek examines how protein analysis techniques are shedding new light on Inca history.

At age 15, she was determined to be a rare example of physical and spiritual perfection, and therefore chosen for sacrifice. Preparations began a year beforehand during which time she was confined to a closed house within the Inca capital of Cusco and fed a rich diet of maize and llama meat. She then traveled more than 1200 miles to the snowy summit of the volcanic Mount Llullaillaco. Consuming an intoxifying meal of caco leaves washed down with maize beer, she quickly fell asleep only to be covered with volcanic ash and left to die.

Well, at least, that's the story according to Spanish explorers. However, forensic anthropologist Angelique Corthals, an assistant professor at the Stony Brook University School of Medicine and director of Stony Brook's BioBank, isn't quite so sure. But to piece together what was really happening during those final days, Corthals and her team would have to travel back in time, using the latest in proteomics technology to analyze proteins from the young girl's mummified remains. Corthals’ efforts would provide a surprising molecular snapshot into the world of this doomed child.

500 years later

In 1996, a group of archaeologists uncovered the remains of what appeared to be the 15-year old Inca girl along with two younger children, a boy and a girl, on Mount Llullaillaco. The cold temperatures and volcanic ash had actually protected their bodies from decomposition. Nicknamed “the maiden,” the archaeologists performed radiocarbon dating and genomic analysis to learn more about who this teenage girl was and whether or not she might have been sacrifice victim from the explorer's stories (1).

The research team's carbon dating data indicated that “the maiden” died around 500 years ago, in agreement with the stories, while dietary isotopic data detected a sudden shift in diet during her final year of life, moving toward rich animal protein. Analysis of mitochondrial DNA samples also defined her haplogroup, further confirming the carbon dating data, and strongly indicating that this mummy was, in fact, the sacrifice victim.

But Corthals, who is also part archeologist and part biomedical researcher, knew this genomic analysis was only scratching the surface of the potential molecular information these samples held. While sequencing ancient DNA can be used to get a list of genes and specific mutations for a given individual, it says nothing at all about how or when those genes are expressed in cells. In contrast, if one were to analyze the proteome, a cell's protein composition, this could actually provide a clearer window into what was physiologically happening when “the maiden” died.

“That's the beauty of proteins, they basically indicate what the individual is expressing at the time of sampling,” says Corthals. This means that if you sample a person's proteome today and then resample in a month, the profiles would be different, the result of changes in gene expression in response to external conditions such as disease or diet or something else.

A clearer example of this can be seen when researchers discover pathogen DNA in an ancient sample. They can compare the ancient and the modern versions of the pathogen at the nucleotide level to determine the “age” of the pathogen, or the specific subtype of pathogen in the sample. But the presence of that pathogen DNA, even if it is determined by sequence analysis to not be contamination, doesn't necessarily mean the individual was infected by the pathogen or that their death was a result of the pathogen.

In order to figure those things out, researchers would need to analyze the immune response of the host at the time of death; experiments that require specialized tools and methods capable of analyzing the abundance of proteins involved with, and regulated by, the immune response – from limited samples that are hundreds to thousands of years old.

Further back in time

At the Natural History Museum of Denmark, postdoctoral fellow Enrico Cappellini studies both ancient DNA and ancient proteins. Like Corthals, he believes ancient proteomics is a strong complement to ancient DNA studies.

From a technical standpoint, there is an advantage to working with ancient proteins: some proteins don't degrade as quickly as DNA. While it is currently difficult to recover DNA from samples that are more than 500,000 years old, collagen—an abundant protein that makesup connective tissue in vertebrates—has been recovered from samples that are up to 1 million years old.

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