projects
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- | ====== Proposed Projects for Fall 2014 ====== | + | ====== Proposed Projects for Fall 2015 ====== |
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- | Supervisor: Katalin Hudak | + | **Supervisor: Katalin Hudak** |
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The Hudak Lab in the Biology Department has an opening for a fourth-year Honours student to assist with a bioinformatics project. We study the pokeweed plant, Phytolacca americana, which displays broad-spectrum virus resistance. To evaluate pokeweed gene expression, we recently sequenced the plant’s mRNA and small RNA transcriptomes under jasmonic acid (JA) treatment. JA is a plant hormone that mediates defence against pathogens and insect herbivores. We are interested in learning how pokeweed gene expression is regulated by miRNAs during biotic stress. | The Hudak Lab in the Biology Department has an opening for a fourth-year Honours student to assist with a bioinformatics project. We study the pokeweed plant, Phytolacca americana, which displays broad-spectrum virus resistance. To evaluate pokeweed gene expression, we recently sequenced the plant’s mRNA and small RNA transcriptomes under jasmonic acid (JA) treatment. JA is a plant hormone that mediates defence against pathogens and insect herbivores. We are interested in learning how pokeweed gene expression is regulated by miRNAs during biotic stress. | ||
Working with the support of a PhD student, your project will involve: | Working with the support of a PhD student, your project will involve: | ||
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1) Prediction of micro RNA (miRNA) targets on the basis of complementary sequence matches | 1) Prediction of micro RNA (miRNA) targets on the basis of complementary sequence matches | ||
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2) Correlation of miRNA and mRNA expression changes to identify genes that are regulated by miRNAs | 2) Correlation of miRNA and mRNA expression changes to identify genes that are regulated by miRNAs | ||
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3) Conducting pathway analysis to determine which biological processes are controlled by miRNAs | 3) Conducting pathway analysis to determine which biological processes are controlled by miRNAs | ||
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4) Construction of a miRNA/ | 4) Construction of a miRNA/ | ||
This work will contribute to a scientific manuscript on miRNA-mediated gene regulation in pokeweed during response to JA. | This work will contribute to a scientific manuscript on miRNA-mediated gene regulation in pokeweed during response to JA. | ||
Requirements: | Requirements: | ||
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1) Pre-requisites as per EECS Calendar | 1) Pre-requisites as per EECS Calendar | ||
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2) Facility with script-writing/ | 2) Facility with script-writing/ | ||
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3) Preference for students with knowledge of statistics and familiarity with R programming | 3) Preference for students with knowledge of statistics and familiarity with R programming | ||
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4) Able to begin in September 2015 | 4) Able to begin in September 2015 | ||
Learning outcomes: | Learning outcomes: | ||
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1) Manipulate and analyze quantitative biological data | 1) Manipulate and analyze quantitative biological data | ||
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2) Develop and test hypotheses by modifying existing software and writing new script | 2) Develop and test hypotheses by modifying existing software and writing new script | ||
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3) Manage a CentOS computer server to store and facilitate ongoing research | 3) Manage a CentOS computer server to store and facilitate ongoing research | ||
No knowledge of biology is required. | No knowledge of biology is required. | ||
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For more information, | For more information, | ||
Hudak Lab website- http:// | Hudak Lab website- http:// | ||
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RNA sequencing- http:// | RNA sequencing- http:// | ||
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miRNAs- http:// | miRNAs- http:// | ||
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projects.txt · Last modified: 2016/01/13 20:05 by stevenc