Proteomics of the Book: Difference between revisions
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Biocodicology is an extension of [https://en.wikipedia.org/wiki/Codicology#:~:text=Codicology%20(from%20Latin%20codex%2C%20genitive,or%20paper)%20as%20physical%20objects.| codicology.] Both fields seek to answer questions about the book beyond its literary content. While codicology makes use of aspects of the book that we can see such as its [http://digitalbookhistory.com/culturesofthebook/Category:Materiality material], [[Decorative Bindings|binding style]], or other physical aspects, biocodicology delves into remnants of the book that can't be seen with the naked eye. Biocodicology relies on the analysis of [https://en.wikipedia.org/wiki/Nucleic_acid nucleic acids] and [https://en.wikipedia.org/wiki/Amino_acid amino acids] that can be extracted from a books surface. [https://en.wikipedia.org/wiki/Genomics Genomics] is the study of [https://en.wikipedia.org/wiki/DNA DNA] and [https://en.wikipedia.org/wiki/RNA RNA], molecules that have nucleic acid subunits. [https://en.wikipedia.org/wiki/Proteomics#:~:text=Proteomics%20is%20the%20large%2Dscale,ever%20increasing%20numbers%20of%20protein. Proteomics] is the study of [https://en.wikipedia.org/wiki/Protein proteins], molecules that have amino acid subunits. | |||
==The Field of Proteomics== | ==The Field of Proteomics== | ||
Proteomics involves identifying all the proteins present in a given sample.<ref name = "One"> Fiddyment, S., Teasdale, M.D., Vnouček, J. et al. So you want to do biocodicology? A field guide to the biological analysis of parchment. Herit Sci 7, 35 (2019). https://doi.org/10.1186/s40494-019-0278-6</ref> Samples could range from [https://en.wikipedia.org/wiki/Organism organisms], biological [https://en.wikipedia.org/wiki/Assay assays], or physical objects (like books). Once the proteins have been identified, researchers can use that information to make inferences about the sample. For an organism this can take the form of its current state of health (during a check up when your doctor asks you to pee in a cup one of the things checked are your protein levels). Identifying proteins is only half of the endeavor, it is also equally important to analyze the quantity of the proteins in a sample. Both the types and quantity of protein present are necessary for one to make an important inference.<ref name = "Two"> “Why Proteins.” Somalogic, https://somalogic.com/technology/why-proteins/</ref> | |||
==Proteins== | |||
[[File:27368227421 e4f2f84cb1 w.jpg|thumb|Sticky Proteins Carry Vaccines by National Institutes of Health (NIH)]] | |||
Proteins have a [https://en.wikipedia.org/wiki/Protein_primary_structure primary structure], which consist of a string of its amino acids in the order that they were placed. This primary structure more or less determines how a protein folds/forms, leading to its shape, which then determines its function.<ref name = "Three"> James Morris et al. How Life Works. W. H. Freeman and Company, 2019.</ref> Slight changes in the primary sequence of the same protein can help people using proteomic techniques to discriminate between different [https://en.wikipedia.org/wiki/Species species] and allow for specific species identification. | |||
Unlike DNA, which remains the same regardless of [https://en.wikipedia.org/wiki/Cell_(biology) cell] type within an organism, proteins have [https://en.wikipedia.org/wiki/Tissue_(biology) tissue] specificity. Protein levels are are also susceptible to environmental factors.<ref name = "Three"> James Morris et al. How Life Works. W. H. Freeman and Company, 2019.</ref> This means that one can not only identify the species but also the specific biological tissue. | |||
==Proteomics in Biocodicology== | ==Proteomics in Biocodicology== | ||
[[File:3379709212 eb70385442 w.jpg|thumb|left|370px|Parchment Paper That Could Be Analyzed With Proteomics]] | |||
Because the information gathered from proteomic techniques that determines the specific tissues on the sample, proteomics can be used to help determine certain stains on a book and also provide insight on how the physical document could have been used in the past.<ref name = "One"> Fiddyment, S., Teasdale, M.D., Vnouček, J. et al. So you want to do biocodicology? A field guide to the biological analysis of parchment. Herit Sci 7, 35 (2019). https://doi.org/10.1186/s40494-019-0278-6</ref> | |||
Parchment analysis plays a major role in biocodicology because parchment paper is almost entirely made from [https://en.wikipedia.org/wiki/Organic_compound organic compounds,] mainly skin from a [https://en.wikipedia.org/wiki/Domestication_of_animals domesticated animal],<ref name = "Five"> Amarth Borsuk. The Book. The MIT Press, 2018</ref> as compared to other writing substrates where other [https://en.wikipedia.org/wiki/Inorganic_compound inorganic compounds] are central to its role of development. With this logic, clay tables would be expected to have the least amount of cellular markers that could be extracted for analysis. Cheap and fast proteomic methods (i.e. eZooMS)<ref name = "Four"> “eZooMS.” BookSilkRoads.Library.UToronto, https://booksilkroads.library.utoronto.ca/ezooms</ref> are being used to identify the animal species that a specific parchment paper was made out of. Using the PQI (Parchment Quality Index), these techniques can also shed light on the production quality of parchment samples.<ref name = "One"> Fiddyment, S., Teasdale, M.D., Vnouček, J. et al. So you want to do biocodicology? A field guide to the biological analysis of parchment. Herit Sci 7, 35 (2019). https://doi.org/10.1186/s40494-019-0278-6</ref> | |||
Usually proteomic analysis is combined with genomic analysis to get a complete picture of the [https://en.wikipedia.org/wiki/Microorganism microbial] environment of a sample. While the two often overlap there are differences between the two that when taken together tell the whole story about the sample(s). For example, genomic analysis is able to detect if the parchment used in one book came from the same animal or if not then if the animals involved were related in any way (genomic analysis can also determine the gender of the animal used to make the substrate). With proteomic analysis one could determine the health of the animal(s) and in some cases see if a disease had spread through the population for a period of time. | |||
Proteomic analysis, especially for use in biocodicology, is an emerging field where there are plenty more areas waiting to be discovered. | |||
==Current Challenges Within This Subfield of Biocodicology== | |||
Any analysis of a book can only go so far as to not damage the substrate. This immediately presents a problem for someone wanting to obtain a sample from a book. However, many techniques have been invented and are continually being evolved so that only a very small sample size is used to obtain a big picture. Because proteomics technologies and developments have more or less only been made for biological advances, where there isn't as much emphasis on preservation, there are challenges when selecting a proteomic analysis technique to use for a given book. This problem, though, is not as significant as one might expect because given the nature of the size of proteins, most technologies in isolating a sample leave the book preserved and unarmed. Still, it would be better from a biocodicology standpoint if the already new and small field of proteomics gave birth to a new field of study that seeks to make proteomic sample gathering techniques as friendly to the book as possible. | |||
==References== | ==References== | ||
<references/> | |||
Latest revision as of 19:20, 9 December 2020
Biocodicology is an extension of codicology. Both fields seek to answer questions about the book beyond its literary content. While codicology makes use of aspects of the book that we can see such as its material, binding style, or other physical aspects, biocodicology delves into remnants of the book that can't be seen with the naked eye. Biocodicology relies on the analysis of nucleic acids and amino acids that can be extracted from a books surface. Genomics is the study of DNA and RNA, molecules that have nucleic acid subunits. Proteomics is the study of proteins, molecules that have amino acid subunits.
The Field of Proteomics
Proteomics involves identifying all the proteins present in a given sample.[1] Samples could range from organisms, biological assays, or physical objects (like books). Once the proteins have been identified, researchers can use that information to make inferences about the sample. For an organism this can take the form of its current state of health (during a check up when your doctor asks you to pee in a cup one of the things checked are your protein levels). Identifying proteins is only half of the endeavor, it is also equally important to analyze the quantity of the proteins in a sample. Both the types and quantity of protein present are necessary for one to make an important inference.[2]
Proteins
Proteins have a primary structure, which consist of a string of its amino acids in the order that they were placed. This primary structure more or less determines how a protein folds/forms, leading to its shape, which then determines its function.[3] Slight changes in the primary sequence of the same protein can help people using proteomic techniques to discriminate between different species and allow for specific species identification.
Unlike DNA, which remains the same regardless of cell type within an organism, proteins have tissue specificity. Protein levels are are also susceptible to environmental factors.[3] This means that one can not only identify the species but also the specific biological tissue.
Proteomics in Biocodicology
Because the information gathered from proteomic techniques that determines the specific tissues on the sample, proteomics can be used to help determine certain stains on a book and also provide insight on how the physical document could have been used in the past.[1]
Parchment analysis plays a major role in biocodicology because parchment paper is almost entirely made from organic compounds, mainly skin from a domesticated animal,[4] as compared to other writing substrates where other inorganic compounds are central to its role of development. With this logic, clay tables would be expected to have the least amount of cellular markers that could be extracted for analysis. Cheap and fast proteomic methods (i.e. eZooMS)[5] are being used to identify the animal species that a specific parchment paper was made out of. Using the PQI (Parchment Quality Index), these techniques can also shed light on the production quality of parchment samples.[1]
Usually proteomic analysis is combined with genomic analysis to get a complete picture of the microbial environment of a sample. While the two often overlap there are differences between the two that when taken together tell the whole story about the sample(s). For example, genomic analysis is able to detect if the parchment used in one book came from the same animal or if not then if the animals involved were related in any way (genomic analysis can also determine the gender of the animal used to make the substrate). With proteomic analysis one could determine the health of the animal(s) and in some cases see if a disease had spread through the population for a period of time.
Proteomic analysis, especially for use in biocodicology, is an emerging field where there are plenty more areas waiting to be discovered.
Current Challenges Within This Subfield of Biocodicology
Any analysis of a book can only go so far as to not damage the substrate. This immediately presents a problem for someone wanting to obtain a sample from a book. However, many techniques have been invented and are continually being evolved so that only a very small sample size is used to obtain a big picture. Because proteomics technologies and developments have more or less only been made for biological advances, where there isn't as much emphasis on preservation, there are challenges when selecting a proteomic analysis technique to use for a given book. This problem, though, is not as significant as one might expect because given the nature of the size of proteins, most technologies in isolating a sample leave the book preserved and unarmed. Still, it would be better from a biocodicology standpoint if the already new and small field of proteomics gave birth to a new field of study that seeks to make proteomic sample gathering techniques as friendly to the book as possible.
References
- ↑ 1.0 1.1 1.2 Fiddyment, S., Teasdale, M.D., Vnouček, J. et al. So you want to do biocodicology? A field guide to the biological analysis of parchment. Herit Sci 7, 35 (2019). https://doi.org/10.1186/s40494-019-0278-6
- ↑ “Why Proteins.” Somalogic, https://somalogic.com/technology/why-proteins/
- ↑ 3.0 3.1 James Morris et al. How Life Works. W. H. Freeman and Company, 2019.
- ↑ Amarth Borsuk. The Book. The MIT Press, 2018
- ↑ “eZooMS.” BookSilkRoads.Library.UToronto, https://booksilkroads.library.utoronto.ca/ezooms