Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment

Abstract Background The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in ske...

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Bibliographic Details
Published in:BMC Systems Biology
Main Authors: Ptitsyn, Andrey, Schlater, Amber, Kanatous, Shane
Format: Article in Journal/Newspaper
Language:English
Published: Springer Science and Business Media LLC 2010
Subjects:
Applied Mathematics
Computer Science Applications
Molecular Biology
Modeling and Simulation
Structural Biology
Antarctic
Weddell
Antarc*
Weddell Seal
Weddell Seals
Online Access:http://dx.doi.org/10.1186/1752-0509-4-133
https://link.springer.com/content/pdf/10.1186/1752-0509-4-133.pdf
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Summary:Abstract Background The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal ( Leptonychotes weddellii ) genes. Results Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable signal from at least 7000 probe sets present in all samples and replicates. Relative expression levels for these genes was used for further analysis of the biological pathways implicated in the metabolism transformation which occurs in the transition from newborn, to juvenile, to adult seals. Cytoskeletal remodeling, WNT signaling, FAK signaling, hypoxia-induced HIF1 activation, and insulin regulation were identified as being among the most important biological pathways involved in transformation. Conclusion In spite of certain losses in specificity and sensitivity, the cross-species application of gene expression microarrays is capable of solving challenging puzzles in biology. A Systems Biology approach based on gene interaction patterns can compensate adequately for the lack of species-specific genomics information.

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