Spatial biology
Spatial biology is how biological molecules and cells are organized, interact, and function in their native 2 and 3 dimensional environment.[1] Many fields within biology are studied for their individual contribution to spatial biology.
Spatial biochemistry
[edit]Spatial biochemistry refers to the study of biochemical processes in their 3 dimensional cellular state. Biochemical reactions require molecular interactions for a process to proceed. Spatial biochemistry determines the spatial distribution that dictates these biochemical processes in the cell.
For example, enzymes require access to their substrate for a biochemical reaction to proceed.[2] In a cellular environment an enzyme can be compartmentalized or sequestered away from its substrate and then activated by substrate presentation. Enzymes activated by this type of spatial biochemistry include phospholipase D and gamma secretase.[3]
Within the membrane, the spatial distribution is controlled by clusters of lipids including PI(4,5)P2 and saturated lipids that bind palmitate.
Spatial proteomics
[edit]Spatial proteomics is the localizations of proteins and their dynamic expression at the sub-cellular level.[4] A spatial map of proteins and their modifications in 3-D space generates a spatial proteome. Both how much of a protein is present and the types of modification to the protein are important.
Spatial genomics
[edit]Spatial genomics utilizes the spatial readout of gene transcripts to determine the 3-dimensional biological function of a cell.[5] The technique spatial transcriptomics was introduced in 2016 [6]
References
[edit]- ^ Nussinov, Ruth; Yavuz, Bengi Ruken; Jang, Hyunbum (September 2024). "Single cell spatial biology over developmental time can decipher pediatric brain pathologies". Neurobiology of Disease. 199: 106597. doi:10.1016/j.nbd.2024.106597. PMC 11286356. PMID 38992777.
- ^ Petersen, E. Nicholas; Chung, Hae-Won; Nayebosadri, Arman; Hansen, Scott B. (15 December 2016). "Kinetic disruption of lipid rafts is a mechanosensor for phospholipase D". Nature Communications. 7 (1): 13873. Bibcode:2016NatCo...713873P. doi:10.1038/ncomms13873. PMC 5171650. PMID 27976674.
- ^ Wang, Hao; Kulas, Joshua A.; Wang, Chao; Holtzman, David M.; Ferris, Heather A.; Hansen, Scott B. (17 August 2021). "Regulation of beta-amyloid production in neurons by astrocyte-derived cholesterol". Proceedings of the National Academy of Sciences. 118 (33). Bibcode:2021PNAS..11802191W. doi:10.1073/pnas.2102191118. PMC 8379952. PMID 34385305.
- ^ Lundberg, Emma; Borner, Georg H. H. (May 2019). "Spatial proteomics: a powerful discovery tool for cell biology". Nature Reviews Molecular Cell Biology. 20 (5): 285–302. doi:10.1038/s41580-018-0094-y. PMID 30659282.
- ^ Jena, Siddhartha G.; Verma, Archit; Engelhardt, Barbara E. (4 September 2024). "Answering open questions in biology using spatial genomics and structured methods". BMC Bioinformatics. 25 (1): 291. doi:10.1186/s12859-024-05912-5. PMC 11375982. PMID 39232666.
- ^ Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J (July 2016). "Visualization and analysis of gene expression in tissue sections by spatial transcriptomics". Science. 353 (6294): 78–82. Bibcode:2016Sci...353...78S. doi:10.1126/science.aaf2403. PMID 27365449. S2CID 30942685.