Functional phenomics
Functional phenomics is an emerging transdisciplinary field in biological sciences that evolved mainly by investigating the relationship between plant phenotypes and their function in an ecosystem. The whole approach combines high-throughput phenotyping, physiology, data science, and computational bioengineering to fill various aspects of the knowledge gap to gain a holistic understanding of plant functioning [2]. In other words, functional phenomics is a roadmap that interconnects gene, phene, function, and how it influences the environment or vice versa.
Current advances in high-throughput and high-dimensional genotyping, phenotyping, transcriptomics, proteomics, and metabolomic technologies enable researchers to gain in-depth understanding of molecular mechanisms at different levels. By combining these networks, researchers can uncover a complete picture of various functional phenotypes.[3]
Another approach that aims to elucidate how different components of a biological system orchestrate together to produce a typical phenotype is functional genomics. Functional genomics is a branch that integrates cell biology and molecular biology high-throughput techniques to investigate complete structures, regulations, and functions of genes in contrast to the old classical gene-by-gene approach [4]. The Human Genome Project is an integral component of functional genomics.
Application of functional phenomics
Plant research
In plant sciences, researchers aim to apply functional phenomics to fight prime global challenges such as crop improvement, food insecurity, functional food design, biofuel development, mitigating climate change, environmental degradation, or medicinal discovery [5][6][7]. The list of applications of functional phenomics keeps growing.
For example, in this study [8] researchers established high-throughput technologies to investigate multiple traits within root economics space. A phenotypic analysis of diverse 276 genotypes for root respiration and architectural traits was performed, unmasking significant variations involved in specific root respiration and specific root length, the main indicators of root metabolic and structural costs. Thus, the utility of functional phenomics could be harnessed to improve crop breeding for the development of sustainable agroecosystem. Another example, where researchers have overcome challenges in traditional methods and applied novel modern technologies, is the investigation of the connection between plant size and water use in the model C4 grass Setaria [5].
Other research areas
Scientists are also applying high-throughput technologies to gain in-depth understanding of the function of genes, proteins, and their interactions that are playing a role in animal and human health and diseases (such as cancer, neurological disorders, infectious diseases, etc.). This review [9] sheds light on functional genomics and its power to map genetic and molecular pathways involved in different cancer phenotypes by manipulating the cell's function at the genetic level (RNAi, CRISPR-Cas9). The major challenge for these pooled screenings applied in functional genomics is that they fail to identify particular genotypes associated with specific cellular phenotypes [10]
Many recent advances in single-cell high-throughput technologies (single-cell RNA-Seq, single-cell transcriptomics) are emerging as key players in gaining in-depth understanding of responsible genes, proteins, and interaction partners regulating cellular function. The research field is still lacking a way to directly connect single-cell functional phenotypes with the underlying genetic and transcriptional landscape. The massive amount of data produced by the multi-omics technologies on biologically relevant genes and proteins could only be fully understood by elucidating their localization, activation state, and interactions in living cells, either in vitro or in vivo models. The whole field of functional phenomics is growing with an aim to uncover pathways regulating cellular and molecular mechanisms at different levels of biological complexity. A German biotech company, evorion biotechnologies GmbH, claims to apply functional phenomics to parallelly link numerous single cells' functional phenotypes with various multi-omics data (single-cell transcriptional analysis, secretion profiles) by applying single-cell microfluidic technology.[11][12]
See also
References
- ↑ Peyraud, Rémi; Dubiella, Ullrich; Barbacci, Adelin; Genin, Stéphane; Raffaele, Sylvain; Roby, Dominique (May 2017). "Advances on plant-pathogen interactions from molecular toward systems biology perspectives". The Plant Journal. 90 (4): 720–737. doi:10.1111/tpj.13429. PMC 5516170. PMID 27870294.
- ↑ York, Larry M (2018-10-31). "Functional phenomics: an emerging field integrating high-throughput phenotyping, physiology, and bioinformatics". Journal of Experimental Botany. 70 (2): 379–386. doi:10.1093/jxb/ery379. ISSN 0022-0957. PMID 30380107.
- ↑ Peyraud, Rémi; Dubiella, Ullrich; Barbacci, Adelin; Genin, Stéphane; Raffaele, Sylvain; Roby, Dominique (2017). "Advances on plant–pathogen interactions from molecular toward systems biology perspectives". The Plant Journal. 90 (4): 720–737. doi:10.1111/tpj.13429. ISSN 1365-313X. PMC 5516170. PMID 27870294.
- ↑ Saraswathy, Nachimuthu; Ramalingam, Ponnusamy (2011-01-01). "Functional genomics". Concepts and Techniques in Genomics and Proteomics. Woodhead Publishing. pp. 123–145. doi:10.1533/9781908818058.123. ISBN 978-1-907568-10-7. Search this book on
- ↑ 5.0 5.1 Feldman, Max J.; Ellsworth, Patrick Z.; Fahlgren, Noah; Gehan, Malia A.; Cousins, Asaph B.; Baxter, Ivan (2018-01-30). "Trait components of whole plant water use efficiency are defined by unique, environmentally responsive genetic signatures in the model C4 grass Setaria". bioRxiv: 234708. doi:10.1101/234708. Unknown parameter
|s2cid=ignored (help) - ↑ Mittler, Ron; Shulaev, Vladimir (2013). "Functional genomics, challenges and perspectives for the future". Physiologia Plantarum. 148 (3): 317–321. doi:10.1111/ppl.12060. ISSN 1399-3054. PMID 23582101.
- ↑ York, Larry Matthew; Nord, Eric; Lynch, Jonathan (2013). "Integration of root phenes for soil resource acquisition". Frontiers in Plant Science. 4: 355. doi:10.3389/fpls.2013.00355. ISSN 1664-462X. PMC 3771073. PMID 24062755.
- ↑ Guo, Haichao; Ayalew, Habtamu; Seethepalli, Anand; Dhakal, Kundan; Griffiths, Marcus; Ma, Xue-Feng; York, Larry M. (2021). "Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture". New Phytologist. 232 (1): 98–112. doi:10.1111/nph.17329. ISSN 1469-8137. PMID 33683730 Check
|pmid=value (help). Unknown parameter|s2cid=ignored (help) - ↑ O'Loughlin, Thomas A.; Gilbert, Luke A. (2019-03-04). "Functional Genomics for Cancer Research: Applications In Vivo and In Vitro". Annual Review of Cancer Biology. 3 (1): 345–363. doi:10.1146/annurev-cancerbio-030518-055742. ISSN 2472-3428.
- ↑ Lee, Jun-Seok; Kim, Yun Kyung; Kim, Han Jo; Hajar, Siti; Tan, Yee Ling; Kang, Nam-Young; Ng, Shin Hui; Yoon, Chang No; Chang, Young-Tae (2012-02-23). Karamanos, Nikos K., ed. "Identification of Cancer Cell-Line Origins Using Fluorescence Image-Based Phenomic Screening". PLOS ONE. 7 (2): e32096. doi:10.1371/journal.pone.0032096. ISSN 1932-6203. PMC 3285665. PMID 22384151.
- ↑ Kleine-Brüggeney, Hans; Vliet, Liisa D. van; Mulas, Carla; Gielen, Fabrice; Agley, Chibeza C.; Silva, José C. R.; Smith, Austin; Chalut, Kevin; Hollfelder, Florian (2019). "Long-Term Perfusion Culture of Monoclonal Embryonic Stem Cells in 3D Hydrogel Beads for Continuous Optical Analysis of Differentiation". Small. 15 (5): 1804576. doi:10.1002/smll.201804576. ISSN 1613-6829. PMID 30570812.
- ↑ Mulas, Carla; Hodgson, Andrew C.; Kohler, Timo N.; Agley, Chibeza C.; Humphreys, Peter; Kleine-Brüggeney, Hans; Hollfelder, Florian; Smith, Austin; Chalut, Kevin J. (2020). "Microfluidic platform for 3D cell culture with live imaging and clone retrieval". Lab on a Chip. 20 (14): 2580–2591. doi:10.1039/D0LC00165A. ISSN 1473-0197. PMID 32573646 Check
|pmid=value (help).
External links
- evorion biotechnologies GmbH
- https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032096
Category:Plant sciences, Category:Microbiology, Category:Omics, Category:Biological engineering, Category:Cell culture, Category:Cell biology, Category:Cancer immunotherapy
This article "Functional phenomics" is from Wikipedia. The list of its authors can be seen in its historical and/or the page Edithistory:Functional phenomics. Articles copied from Draft Namespace on Wikipedia could be seen on the Draft Namespace of Wikipedia and not main one.
