Protein power
Ancient DNA may be entering its golden age, but some researchers have their eyes on another molecule that may offer new view of the past: protein, which has some advantages over its more famous cousin. Tissues are full of protein, making analysis easier. Proteins also resist the ravages of time far better than fragile DNA and so have the potential to look further back in time—researchers have identified 300 million year old proteins in fish fossils. Ancient proteins have already illuminated a few far-flung corners of past life, including identifying the family tree of strange, extinct South American mammals that flummoxed even Charles Darwin. The method appears particularly promising in archaeology, where it can reveal the diets and lifestyles of past cultures. Still, the technique has a long way to go before it reaches the maturity of paleogenetics, chiefly because methods to sequence amino acids lag behind DNA sequencing.http://news.sciencemag.org/paleontology/2015/07/protein-power
Ancient human microbiomes
Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.
Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.
Detecting the Immune System Response of a 500 Year-Old Inca Mummy
Corthals A, et al. PLoS ONE7(7): e41244. doi:10.1371/journal.pone.0041244.Disease detection in historical samples currently relies on DNA extraction and amplification, or immunoassays. These techniques only establish pathogen presence rather than active disease. We report the first use of shotgun proteomics to detect the protein expression profile of buccal swabs and cloth samples from two 500-year-old Andean mummies. The profile of one of the mummies is consistent with immune system response to severe pulmonary bacterial infection at the time of death. Presence of a probably pathogenicMycobacterium sp. in one buccal swab was confirmed by DNA amplification, sequencing, and phylogenetic analyses. Our study provides positive evidence of active pathogenic infection in an ancient sample for the first time. The protocol introduced here is less susceptible to contamination than DNA-based or immunoassay-based studies. In scarce forensic samples, shotgun proteomics narrows the range of pathogens to detect using DNA assays, reducing cost. This analytical technique can be broadly applied for detecting infection in ancient samples to answer questions on the historical ecology of specific pathogens, as well as in medico-legal cases when active pathogenic infection is suspected.Rewriting history trough proteins.
Wiecek. A.S. BioTecniques 54:19-21. doi: 10.2144/000113975.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.
The Silk Road, Marco Polo, a bible and its proteome: A detective story.
Lucia Toniolo, et al. Journal of Proteomics. 2012, 75 (11), 3365–3373. http://dx.doi.org/10.1016/j.jprot.2012.03.051
Around the end of XIII century (at the time of young Marco Polo's first trip to China at the court of Khubilai Khan in Khan Baliq) a pocket Bible was delivered by a Franciscan friar to the Mogul Emperor, in the framework of the evangelization program of the Far East. Four centuries later, in 1685, this Bible was rediscovered by the Jesuit Philippe Couplet in the house of a rich Chinese in Nanchin and donated to Cosimo III, Grand Duke of Tuscany. This Bible was recently “unearthed” in the Biblioteca Medicea Laurenziana in Florence, wrapped up in a precious yellow silk cloth, in a rather ruined state. After two years of restoration, the Bible will return to China in 2012 for a celebration of its > 700 years of life and of its remarkable return trip on the Silk Road. On account of the thinness of the parchment (barely 80 μm thickness, the size of each foil being 16.5 × 11 cm) it was widely held that the pages were produced from foetal lambskins. On tiny fragments of the margins of a foil, after several unsuccessful attempts at digesting the vellum, we were able to obtain a tryptic peptide mixture, which, upon mass spectrometry analysis, yielded the identity of 8 unique proteins, belonging to the genus Bos taurus, thus confirming the origin of the vellum from calfskins rather than from foetal lambskins. Our results prove that it is possible to obtain reliable protein extraction and IDs from ancient parchment documents.
Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins.
Enrico Cappellini, et al. J. Proteome Res. 2012, 11, 917–926http://pubs.acs.org.pbidi.unam.mx:8080/doi/pdf/10.1021/pr200721u
We used high-sensitivity, high-resolution tandem mass spectrometry to shotgun sequence ancient protein remains extracted from a 43 000 year old woolly mammoth (Mammuthus primigenius) bone preserved in the Siberian permafrost. For the first time, 126 unique protein accessions, mostly low-abundance extracellular matrix and plasma proteins, were confidently identified by solid molecular evidence. Among the best characterized was the carrier protein serum albumin, presenting two single amino acid substitutions compared to extant African (Loxodonta africana) and Indian (Elephas aximus) elephants. Strong evidence was observed of amino acid modifications due to postmortem hydrolytic and oxidative damage. A consistent subset of this permafrost bone proteome was also identified in more recent Columbian mammoth (Mammuthus columbi) samples from temperate latitudes, extending the potential of the approach described beyond subpolar environments. Mass spectrometry-based ancient protein sequencing offers new perspectives for future molecular phylogenetic inference and physiological studies on samples not amenable to ancient DNA investigation. This approach therefore represents a further step into the ongoing integration of different high-throughput technologies for identification of ancient biomolecules, unleashing the field of paleoproteomics.
Paleoproteomic study of the Iceman’s brain tissue.
Maixner et al.
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New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing |
Cell Mol Life Sci. 2013 Jun 6. [Epub ahead of print]
http://link.springer.com/article/10.1007%2Fs00018-013-1360-y
http://link.springer.com/article/10.1007%2Fs00018-013-1360-y
The Tyrolean Iceman, a Copper-age ice mummy, is one of the best-studied human individuals. While the genome of the Iceman has largely been decoded, tissue-specific proteomes have not yet been investigated. We studied the proteome of two distinct brain samples using gel-based and liquid chromatography-mass spectrometry-based proteomics technologies together with a multiple-databases and -search algorithms-driven data-analysis approach. Thereby, we identified a total of 502 different proteins. Of these, 41 proteins are known to be highly abundant in brain tissue and 9 are even specifically expressed in the brain. Furthermore, we found 10 proteins related to blood and coagulation. An enrichment analysis revealed a significant accumulation of proteins related to stress response and wound healing. Together with atomic force microscope scans, indicating clustered blood cells, our data reopens former discussions about a possible injury of the Iceman's head near the site where the tissue samples have been extracted.
2D gels still have a niche in proteomics
Adelina Rogowska-Wrzesinska,http://dx.doi.org/10.1016/j.jprot.2013.01.010.
With the rapid advance of MS-based proteomics one might think that 2D gel-based proteomics is dead. This is far from the truth. Current research has shown that there are still a number of places in the field of protein and molecular biology where 2D gels still play a leading role. The aim of this review is to highlight some of these applications. Examples from our own research as well as from other published works are used to illustrate the 2D gel driven research in the areas of: 1) de novo sequencing and protein identification from organisms with no or incomplete genome sequences available; 2) alternative detection methods for modification specific proteomics; 3) identification of protein isoforms and modified proteins. With an example of the glycoprotein TIMP-1 protein we illustrate the unique properties of 2D gels for the separation and characterisation of multiply modified proteins. We also show that careful analysis of experimental and theoretical protein mass and pI can lead to the identification of unanticipated protein variants modified by for example proteolytic cleavage. Together this shows that there is an important niche for 2D gel-based proteomics, which compliments traditional LC-MS techniques for specific protein research purposes.
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