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dc.contributor.authorBahl, Amit
dc.contributor.authorDavis, Paul H.
dc.contributor.authorBehnke, Michael S.
dc.contributor.authorDzierszinski, Florence
dc.contributor.authorJagalur, Manjunatha
dc.contributor.authorChen, Feng
dc.contributor.authorShanmugam, Dhanasekaran
dc.contributor.authorWhite, Michael W.
dc.contributor.authorKulp, David
dc.contributor.authorRoos, David S.
dc.date.accessioned2019-05-08T16:26:54Z
dc.date.available2019-05-08T16:26:54Z
dc.date.issued2010-10
dc.identifier.citationBahl, Amit, Paul H. Davis, Michael S. Behnke, Florence Dzierszinski, Manjunatha Jagalur, Feng Chen, Dhanasekaran Shanmugam, Michael W. White, David Kulp, and David S. Roos. “A Novel Multifunctional Oligonucleotide Microarray for Toxoplasma Gondii.” BMC Genomics 11, no. 1 (2010): 603. doi:10.1186/1471-2164-11-603.en_US
dc.identifier.issn1471-2164
dc.identifier.urihttps://scholarworks.montana.edu/xmlui/handle/1/15473
dc.description.abstractBackground Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, although the development and use of genome-scale microarrays is often a costly undertaking. Therefore, effective methods for reducing unnecessary probes while maintaining or expanding functionality would be relevant to many investigators. Results Taking advantage of available genome sequences and annotation for Toxoplasma gondii (a pathogenic parasite responsible for illness in immunocompromised individuals) and Plasmodium falciparum (a related parasite responsible for severe human malaria), we designed a single oligonucleotide microarray capable of supporting a wide range of applications at relatively low cost, including genome-wide expression profiling for Toxoplasma, and single-nucleotide polymorphism (SNP)-based genotyping of both T. gondii and P. falciparum. Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome, revealing that ~49% of all annotated genes are expressed in parasite tachyzoites (the acutely lytic stage responsible for pathogenesis) and 26% of genes are differentially expressed among strains. A novel design utilizing few probes provided high confidence genotyping, used here to resolve recombination points in the clonal progeny of sexual crosses. Recent sequencing of additional T. gondii isolates identifies >620 K new SNPs, including ~11 K that intersect with expression profiling probes, yielding additional markers for genotyping studies, and further validating the utility of a combined expression profiling/genotyping array design. Additional applications facilitating SNP and transcript discovery, alternative statistical methods for quantifying gene expression, etc. are also pursued at pilot scale to inform future array designs. Conclusions In addition to providing an initial global view of the T. gondii transcriptome across major lineages and permitting detailed resolution of recombination points in a historical sexual cross, the multifunctional nature of this array also allowed opportunities to exploit probes for purposes beyond their intended use, enhancing analyses. This array is in widespread use by the T. gondii research community, and several aspects of the design strategy are likely to be useful for other pathogens.en_US
dc.rightsCC BY: This license lets you distribute, remix, tweak, and build upon this work, even commercially, as long as you credit the original creator for this work. This is the most accommodating of licenses offered. Recommended for maximum dissemination and use of licensed materials.en_US
dc.rights.uriPublished Articleen_US
dc.titleA novel multifunctional oligonucleotide microarray for Toxoplasma gondiien_US
dc.typeArticleen_US
mus.citation.extentfirstpage603en_US
mus.citation.issue1en_US
mus.citation.journaltitleBMC Genomicsen_US
mus.citation.volume11en_US
mus.identifier.categoryLife Sciences & Earth Sciencesen_US
mus.identifier.doi10.1186/1471-2164-11-603en_US
mus.relation.collegeCollege of Agricultureen_US
mus.relation.collegeCollege of Letters & Scienceen_US
mus.relation.departmentMicrobiology & Immunology.en_US
mus.relation.universityMontana State University - Bozemanen_US
mus.relation.researchgroupMT INBRE Bioinformatics and Biostatistics Core.en_US
mus.data.thumbpage6en_US


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