Martina V. Stromvik, PhD (Illinois)
Associate Professor
Phone: 514-398-8627
Fax: 514-398-7897
martina [dot] stromvik [at] mcgill [dot] ca (E-mail)
Research interests
Dr. Stromvik combines her bioinformatics and molecular biology/genomics expertise to research functional anatomy as a result of cell or tissue specific gene expression in crop and forest plants.
Each plant species is considered to have between 20,000 and 60,000 genes. Expression of each gene at the correct time and in the correct cells is made possible by the composition of the associated gene cis-acting regulatory sequences, the promoters. Diversity in plant promoters and regulatory elements is the primary basis for the development of functional organisms. Promoters are also recognized as an incredible source of tools for correctly expressing genes in crop improvement and metabolic engineering such as for the development of new bio products (medicines, vaccines, industrial oils, paints, lubricants, adhesives, plastics, alternative energy sources, and plants for industrial decontamination). However, to date little is known about promoters, and especially about plant promoters.
Dr. Stromvik's research program elucidates plant gene expression and promoters on a global scale, using bioinformatics and microgenomics methods in the important crop plant soybean (Glycine max (L.) Merr.), but also in other species such as Oxytropis spp., and Arabidopsis thaliana.
We also develop databases and bioinformatics tools:
SoyXpress: A soybean transcriptome database.
Seeder: Discriminative seeding DNA motif discovery.
DDOPM: A database of dicotyledonous orthologous promoter motifs.
Additional projects in the group include:
Cell specific gene expression studies using Laser Capture Microdissection
Discovery of tissue specific regulatory elements in promoter sequences
Discovery of co-regulation in metabolic pathways and gene families
Promoter studies using transgenics
Large scale data mining and integration
Plant virus sequence data analysis
M.Sc./Ph.D. student positions are currently available in the group for self-funded students only. Projects are either in bioinformatics, micro-genomics or a mix of both. Contact Dr. Stromvik for more details.
See also the website for the McGill Centre for Bioinformatics and my bioinformatics courses Bioinformatics for Genomics BINF 511 and Bioinformatics: Molecular Biology BINF 621.
Current lab members
Annie Archambault (Ph.D. student - Molecular Biology)
Muhammad Chragh (M.Sc. student - Molecular Biology)
Nadia Chaidir (M.Sc. student - Bioinformatics)
Haritika Majithia (M.Sc. student - Bioinformatics)
Yevgen Zolotarov (M.Sc. student - Bioinformatics)
Caroline Treynor (undergraduate student)
Maxym Malynowsky (undergraduate student)
André Lessard (Sys Admin)
Graduates
Francois Fauteux (Ph.D. 2010 - Bioinformatics)
Julie Livingstone (M.Sc. 2009 - Bioinformatics)
Hanaa Saeed (M.Sc. 2008 - Molecular Biology)
Kei Chin Cheng (M.Sc. 2007 - Bioinformatics)
Recent publications
Archambault, A. and Strömvik, M.V. (2011) “The Y-segment of novel cold dehydrin genes is conserved and codons in the PR-10 genes are under positive selection in Oxytropis (Fabaceae) from contrasting climates” Molecular Genetics and Genomics (Online first).
Hunt, M., Kaur, N., Stromvik, M., and Vodkin, L. (2011). "Transcript Profiling Reveals Expression Differences In Wild-Type and Glabrous Soybean Lines". BMC Plant Biology 11: 145.
Livingstone, J.M., Zolotarov, Y., and Strömvik, M.V. (2011). "Transcripts of soybean isoflavone 7-O-glucosyltransferase and hydroxyisoflavanone dehydratase gene homologues are at least as abundant as transcripts of their well known counterparts". Plant Physiology and Biochemistry 49: 1071-1075.
Archambault, A. and Strömvik, M.V. (2011) "PR-10, defensin and cold dehydrin genes are among those over expressed in Oxytropis (Fabaceae) species adapted to the arctic". Functional and Integrative Genomics 11: 497-505 (Online First).
Livingstone, J.M., Seguin, P., and Strömvik, M.V. (2010) "An in silico study of the genes for the isoflavonoid pathway enzymes in soybean reveals novel expressed homologues" Can. J. of Plant Science 90: 453-469.
Livingstone, J.M., Cheng, K.C., and Strömvik, M.V. (2010) Chapter 12: "Bioinformatics as a Tool" in Genetics, Genomics and Breeding in Soybean" Eds. K. Bilyeu, M.B. Ratnaparkhe, C. Kole, CRC Press, Science Publishers Enfield, New Hampshire (Bookchapter).
Fauteux, F., and Strömvik, M.V. (2009) “Seed storage protein gene promoters contain conserved composite DNA motifs in Brassicaceae, Fabaceae and Poaceae.” BMC Plant Biology 9:126.
Hakimov, H.A., Verschoor, C.P., Wright, T., Walters, S., Gadish, M., Chiu, D.K.Y., Forsberg, C.W., Strömvik, M.V., Golovan, S.P. (2009) “Application of iTRAQ to catalogue the skeletal muscle proteome in pigs and assessment of effects of gender and diet dephytinization.” Proteomics 9: 4000-4016.
Viel, C., Ide, C., Cui, X., Farsi, M., Wang, A., Michelutti, R and Stromvik M.V. (2009) “Isolation, partial sequencing and phylogenetic analyses of Soybean mosaic virus (SMV) in Ontario and Québec.” Canadian Journal of Plant Pathology 30: 108-113.
Gagarinova, A., Babu, M., Stromvik, M., and Wang, A. (2008). "Recombination analysis of Soybean Mosaic virus full-length genome sequences reveals evidence of RNA recombination between distinct pathotypes." Virology Journal 5:143.
Fauteux, F., Blanchette, M., and Stromvik, M.V. (2008) "Seeder: Discriminative Seeding DNA Motif Discovery" Bioinformatics 24: 2303-2307 doi: 10.1093/bioinformatics/btn444.
Cheng, K.C. and Stromvik, M.V. (2008) "SoyXpress: a database for exploring the soybean transcriptome". BMC Genomics 9:368.
Saeed, H., Vodkin, L.O., and Stromvik, M.V. (2008) "Promoters of the soybean seed lectin homologues Le2 and Le3 regulate gene expression in vegetative tissues in Arabidopsis." Plant Science 175: 868-876 doi:10.1016/j.plantsci.2008.08.013.
Cheng, K.C., Beaulieu, J., Iquira, E., Belzile, F.J., Fortin, M.G. and Stromvik, M.V. (2008). "Effect of transgenes on global gene expression in soybean is within the natural range of variation of their conventional counterparts." Journal of Agricultural and Food Chemistry 56: 3057-3067.
Dauch, A.L., Morissette, D., Brousseau, R., Masson, L., Stromvik, M.V. and Jabaji-Hare, S.H. (2008). "Analysis of enriched transcripts induced during velvetleaf-Colletotrichum coccodes interaction." Canadian Journal of Plant Pathology, vol 30(1).