Molecular and Cellular Biology Seminar | Emmalynn Canaday, Oct. 31

The Molecular and Cellular Biology Seminar series (MCB7410) features Emmalynn Canaday  on Oct. 31 at 3:30 PM in Porter Hall Room 104.

Canaday is a graduate student in the departments of Environmental and Plant Biology and Molecular and Cellular Biology at Ohio University.

Abstract:  The rapid changes in RNA technologies has required new computational tools to handle large data. Microarrays used hybridization with known primers to identify sequences. While microarrays opened up new abilities to quantify transcriptomes,  it was also unable to identify novel transcripts and assess splice variants. Advancements in RNAseq have given us the ability to assess both areas. RNAseq can return terabytes of sequences which requires fast computationally light algorithms to process. Genome alignment tools such as Star and Bowtie can take these sequences and align them to a reference genome to quantify expression of genes. Genome aligners can have limitations such as high demands on processing as well as still being unable to identify splice variants. The newest generation of technologies uses a reference transcriptome instead of a genome to find splice aware alignment, referred to as pseudo alignment. Tools like Salmon and Kallisto have made alignment faster, easier and given more depth to the data produced. Kallisto in particular has become a popular tool for plant transcriptome analysis. A group studying the effects of heat stress on pollen tubes used RNAseq to identify genes important for plant reproduction in a heating climate (Lohani et al., 2021). Kallisto was also used to identify when plants shift between splice variants when responding to pathogenic stress (Bazin et al., 2020). Alignment tools let us make sense of large data and find subtle shifts with biological impact.   

Lohani, N., Singh, M. B., & Bhalla, P. L. (2021). RNA-seq highlights molecular events associated with impaired pollen-pistil interactions following short-term heat stress in Brassica napus. Frontiers in plant science, 11, 622748. 

Bazin, J., Mariappan, K., Jiang, Y., Blein, T., Voelz, R., Crespi, M., & Hirt, H. (2020). Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis. PLoS pathogens, 16(4), e1008401.