February 7, 2017

Undergraduate summer research at UTM

If you are an undergraduate enrolled at the University of Toronto and are interested in summer or fall research, I am offering several undergraduate research projects through the Research Opportunity Program.

Note: The ROP application deadline has been extended to Friday, March 3, 2017.

Here are the summer projects I will supervise:


Project 1: Transcriptomics and metabolomics data pipeline development for medicinal plants
Background and objectives
Bioinformatics increasingly plays a central role in organizing and processing data derived from omics type technologies in biological research. Management of large data sets is particularly relevant to accelerating the pace of discovery when working with non-model organisms for which online resources are not available. Several essential oil producing plants under investigation in my laboratory, including rose geranium and cilantro, have not yet been characterized at the molecular level. The objective of this project is to perform transcriptome assemblies using existing RNA sequencing data for BLAST searches and identification of essential oil biosynthetic genes for cloning. Metabolomics data from these same plants are highly complementary to sequencing data, but simple scripts and semi-automated analysis pipelines are needed to facilitate their routine analysis.

Student participation
This student will perform bioinformatics based transcriptome assemblies using publicly available software and the departmental computer cluster. RNA sequencing data previously obtained from glandular trichomes of medicinal plants will be used for this purpose. The student will use the assembled transcriptome to search for genes related to essential oil biosynthesis. Design of cloning primers and identification of full length open reading frames of target genes may form part of this effort. These efforts will be complemented by the establishment of data processing scripts to facilitate the analysis of metabolomics data obtained from these same plants.

Project 2: Deciphering plant responses to environmental stress with metabolomics analysis
Background and objectives
Metabolomics analysis has become a central tool in understanding plants’ adaptive responses to environmental stress. Hundreds of metabolites representing dozens of metabolic pathways can be analyzed simultaneously using modern analytical instrumentation. This analysis is particularly useful for studies of adaptive responses to light and temperature stress (metabonomics). Detailed metabolomics analysis of the model plant Arabidopsis can reveal novel features of the regulatory program which determines plant tolerance to changes in the environment. The objective of this project is to prepare samples of Arabidopsis tissues for analysis using metabolomics instrumentation.

Student participation
The student will learn standardized metabolomics protocols. This will consist of making extracts of preserved Arabidopsis tissue and preparing these samples for analysis by gas chromatography and liquid chromatography – mass spectrometry. Participation in instrumental analysis and the analysis of data will also form part of student training.

Project 3: Identifying new genes in plant essential oil biosynthesis
Background and objectives
Many plant species produce volatile essential oils with fragrant, pleasing aromas that have made them popular in cooking, floristry, aromatherapy, and gardening. Yet these oils also possess potent biological activities which impact other organisms in the environment. However, most aromatic plants have received little experimental attention, and the biosynthetic genes for many promising essential oils remain unknown. Two widely used aromatic plants, rose geranium and cilantro, produce oils with potent anti-microbial properties and have shown great promise in reducing food borne illnesses. The objective of this project is to clone and express genes involved in essential oil biosynthesis in these non-model species using molecular biology techniques.

Student participation
The student will consult transcript data from aromatic plants and select candidate genes possibly involved in essential oil biosynthesis for cloning and characterization. This approach will be complemented by an unbiased screening strategy which will involve the construction of a cDNA expression library for high throughput screening. Molecular biology techniques such as genomic DNA extraction, PCR genotyping, molecular cloning, primer design, and sequencing are other skills the student will learn during this project.

Project 4: Comparative analysis of auxin and auxin-related metabolites in charophyte algae
Background and objectives
There is strong genomic and morphological evidence that charophyte fresh water algae are the most closely related living members of the ancestral group that gave rise to the embryophytes (land plants). In angiosperms auxin plays an essential role in regulating development, and the regulation and transport of this hormone appears to have grown in complexity with the evolution of these higher plants from earlier, more ‘primitive’ plant taxa. Identifying the most primitive plants that use auxins would reveal new insights into the evolution of early plants. Comparative genomic studies between the charophytes and other embryophytes has revealed some evidence for the presence of key genes involved in synthesizing auxin in these algae. However, the auxin and auxin-metabolite content of charophyte tissues has not been well characterized. Our objective is to characterize the auxin profile of a charophyte alga and compare it with representative land plants using mass spectrometry.

Student participation
The student will grow and sample a charophyte alga and some primitive land plants. Obtain tissue samples from the various species and prepare them for analysis by mass spectrometry. The student will then participate in the analysis of the mass-spec data generated by these experiments.

Feel free to contact me for details or visit the link above to the ROP website.

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