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Bioinformatics, Genomics, Proteomics
Bioinformatics and computational biology use of techniques from applied mathematics, informatics, statistics, and computer science to solve biological problems. The terms bioinformatics and computational biology are often used interchangeably, although the former typically focuses on algorithm development and specific computational methods, while the latter focuses more on hypothesis testing and discovery in the biological domain. In general, this type of research includes the development and testing of software tools to generate new knowledge from primary source information deposited in databases and the literature.
Genomics is the large-scale investigation of the structure and function of genes. Understanding the structure and function of genomes aids in drug discovery and development, agricultural research, and other fields.
Proteomics is the genome-wide analysis of protein regulation, expression, structure, post-translational modification, interactions, and function. This term was coined to make an analogy with genomics, yet proteomics is much more complicated than genomics. The genome is a rather constant entity, while the proteome differs between cell types and fluctuates in response to interactions with the environment.
The interdisciplinary MSU faculty in Bioinformatics, Genomics, and Proteomics developed teaching and training programs that responds to current and future needs of the field.
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Molecular BIOSciences |> Bioinformatics, Genomics, Proteomics
|> Faculty |> Christa Merzdorf, Ph. D
Developmental Neurobiology
Current Research
We study the molecular mechanisms that underlie patterning of the vertebrate nervous system during embryonic development. Our lab focuses on how the early neural plate is subdivided into the different regions of the brain. We use the frog Xenopus and the chick as model organisms.
A critical step in CNS development is formation of the boundary between the midbrain (future optic tectum) and the anterior hindbrain (future cerebellum). The gene interactions that we study at the midbrain/hindbrain boundary (MHB) include how the transcription factor zic1 contributes to formation of the MHB and later to the delay in nerve cell differentiation that is characteristic for the MHB. In addition to experiments in whole embryos, we are using tissue explant assays to recreate artificial MHBs in vitro that allow the study and manipulation of gene expression in a more controlled environment.
Several of the genes that are important for early neural tube formation are also important for neural crest formation and somite development. We are studying some of the similarities and differences between the activities that the same genes perform in these different contexts and the differences in how they are regulated.
The zic1 transcription factor plays multiple roles during development. It is one of the first genes expressed in response to neural induction and plays later roles in the development of the dorsal neural tube, the neural crest, and somites. Thus, it is of great interest to identify genes that are regulated by this transcription factor. We have conducted a microarray screen designed to identify genes that are direct targets of zic1. Several of the genes we identified participate in early neural crest formation. One of the novel genes, Xfeb, appears to participate in maintaining the anterior boundary of the hindbrain. Another gene, aqp-3b, may play a role in neural fold formation and neural tube closure.
Finally, developmental genes often occur as gene families. The Zic gene family comprises five members. These genes are highly homologous and are expressed in overlapping and also distinct areas during embryonic development. We are studying these different family members to gain an understanding of the overlapping and individual contributions that each Zic family member makes to early neural development.
Recent Publications
Li, S, Y. Shin, K. Cho, and C.S. Merzdorf (2006). The Xfeb gene is directly upregulated by Zic1 during early neural development. Dev. Dyn. 235:2817-2827
Merzdorf, C.S. and H. Sive (2006). The zic1 gene is an activator of Wnt signaling. Int. J. Dev. Biol 50:611-617
Sun Rhodes, L.S. and C.S. Merzdorf (2006). The zic1 gene is expressed in chick somites but not in migratory neural crest. Gene Expr. Patterns 6:539-545
Merzdorf, C.S. (2007). Emerging roles for zic genes in early development. Dev. Dyn. 236:922-940.
Cornish, E.J., S.M. Hassan, J.D. Martin, S. Li, and C.S. Merzdorf (2009). A microarray screen for direct targets of Zic1 identifies an aquaporin gene, aqp-3b, expressed in the neural folds. Dev. Dyn. 238:1179-1194
McMahon, A.R. and C.S. Merzdorf (2010). The Expression of the zic1, zic2, zic3, and zic4 Genes in Early Chick Embryos. BMC Research Notes 3:167
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