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2025-03-19

This is Simon's COMMONS Lab daily Open Notebook.

Today is 2025.03.19

Todo today

Have a look at the COMMONS research discussion forum

- https://github.com/orgs/commons-research/discussions

Doing

Some reading about bark extraction This article seems nice: https://pmc.ncbi.nlm.nih.gov/articles/PMC5905184/ 10.1186/s13020-018-0177-x

  • What kind of method do we use to extract ? liquid chromatography-mass spectrometry, is it talked about in the document ? Not sure. Is it simply maceration or sublimation ?
  • Maybe the method of extraction is sublimation/maceration, and the LC is the method of separation. If this is the case, another article should be found, for this one doesn't include sublimation.

https://www.researchgate.net/publication/232089322_Isolation_identification_and_purification_of_cinnamaldehyde_from_Cinnamomum_zeylanicum_bark_oil_An_antibacterial_study

  • Extraction of a very specific bark component in the tree Cinnamomum zelyanicum
  • Use of steam distillation in a Clevenger-type apparatus for 8h to extract the essential oils. Maybe this is a method proper to essential oils extraction, but unfit for all bark components ? Would it be mass-spec friendly ?

Richard, B., Bénard, A., Dumarçay, S. et al. Wood, knots and bark extractives for oak, beech and Douglas fir: a dataset based on a review of the scientific literature. Annals of Forest Science 81, 9 (2024). https://doi.org/10.1186/s13595-024-01223-0

  • Have a very similar project of mapping the metabolome of a few species (Quercus robur L., Quercus petraea Liebl., Fagus sylvatica L. and Pseudotsuga menziesii ) in France, and in the whole organism.
  • Wood_db-chemistry database, EXTRAFOR_EST scientific project
  • Database is available
  • Used 12 different extraction techniques, are note described in the paper cuz it is a metaanalysis
  • Many links to papers and their method of extraction (https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.57745/QZYPUA) => need to take a look later

https://www.researchgate.net/publication/230771042_Handbook_Of_Wood_Chemistry_And_Wood_Composites. https://doi.org/10.1201/b12487

  • Introduction book on wood/bark chemistry, and their extractives
  • chemical constituents of bark can be classified into four major groups: polysaccharides (cellulose, hemicellulose, and pectic materials); lignin and polyphenols; hydroxy acid complexes (suberin); and extractives (fats, oils, phytosterols, resin acids, waxes, tannins, terpenes, phlobaphenes, and flavonoids).
  • The analysis methods developed for wood cannot be used for bark directly. - There are many compounds in bark that are not found in wood that interfere with these analysis methods. Because of the interference of the extractives in polysaccharide and lignin analysis, procedures for elucidation of the chemical composition of bark begin with an extraction protocol that consists of sequential extraction solvents of increasing polarity. A common protocol begins with a diethyl ether extraction step that yields waxes, fatty acids, fats, resin acids, phytosterols, and terpenes. This is followed by an ethyl alcohol extraction step that yields condensed tannins, flavonoids, and phenolics. The third step uses hot water, and yields condensed tannins and water-soluble carbohydrates. To release phenolic acids, hemicelluloses, and suberin monomers from the residue from the third step, 1% aqueous sodium hydroxide is used (Holloway and Deas 1973, Kolattukudy 1984). The extract fractions from the above-mentioned steps are then subjected to further workup to separate each into easy-to-analyze mixtures of compounds. For example, partitioning the diethyl ether fraction against aqueous sodium bicarbonate separates the fatty acids and resin acids from the neutral components, tannins, terpenes, and flavonoids. The neutral fraction is then saponified to give the alcohols and salts of fatty acids, dicarboxylic, hydroxy-fatty, and ferulic acids. Ethanol extraction followed by hot water extraction of the insoluble ether fraction yields soluble simple sugars and condensed tannins. Sodium hydroxide extraction of the insoluble residue gives soluble suberin monomers, phenolic acids, and hemicelluloses. Sulfuric acid treatment of the insoluble fraction yields lignin (Chang and Mitchell 1955, Hemingway 1981, Laks 1991).
  • Why no use of MS ? Is it a very recent tech ?
  • Procedure for extraction varies between labs. No comparison between data is thus possible.

Tanase C, Coșarcă S, Muntean D-L. A Critical Review of Phenolic Compounds Extracted from the Bark of Woody Vascular Plants and Their Potential Biological Activity. Molecules. 2019; 24(6):1182. https://doi.org/10.3390/molecules24061182

  • Extraction of phenolic compounds only
  • Description of many different methods (ultrasounds, microwaves, ...) with their pros and cons

Zidorn, C. Seasonal variation of natural products in European trees. Phytochem Rev 17, 923–935 (2018). https://doi.org/10.1007/s11101-018-9570-4

  • Interesting in the case of variability of the metabolome through the year
  • Big bias towards study of leaves and phenolics. Other compounds are understudied.

Paused

Done

Notes

Todo tomorrow, one day ... or never

Take a look at many wood extraction methods (https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.57745/QZYPUA)

Today I learned that