Optimizing RNA Extraction from Fungal-Algal Tissues for Transcriptomic Gene Expression Analysis

Hohl, Michael J. (2016) Optimizing RNA Extraction from Fungal-Algal Tissues for Transcriptomic Gene Expression Analysis. Undergraduate thesis, under the direction of Erik Hom from Biology, University of Mississippi.

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Abstract

Extracting high-quality RNA is critical for downstream applications such a qRT-PCR and RNA-Seq based transcriptomics. Single-stranded RNA is readily susceptible to degradation by environmental RNases, necessitating rapid and sterile homogenization techniques; freezing at -80°C, lysis buffer addition, and short bursts of beadbeating have been shown to increase yields and quality of extracted RNA. Utilizing fungal-algal tissues from the model symbiosis between the filamentous fungi Aspergillus nidulans and the green alga Chlamydomonas reinhardtii, three different commercial homogenizers and six RNA extractions kits were assessed and an optimized extraction protocol for total RNA from fungal-algal tissues was determined. Using the protocol designed in this study, the relationship between Chlamydomonas reinhardtii and the budding yeast Saccharomyces cerevisiae when grown under circadian-based light conditions prior to co-culturing will be assessed using RNA-Seq to determine changes gene expression patterns in response to co-culturing under a new light condition to look for synchrony. A phenotypic study of this system was performed and while no significant differences in biomass were observed, it is believed that with the fungus Neurospora crassa, a model organism for studying circadian rhythms, a light regimen-dependent phenotypic resonse will be observed.

Item Type: Thesis (Undergraduate)
Uncontrolled Keywords: RNA, Circadian Rhythm, Fungi, Algae, Model Organisms, Nucleic Acid Extraction
Creators: Hohl, Michael J.
Student's Degree Program(s): B.S. in Biology
Thesis Advisor: Erik Hom
Thesis Advisor's Department: Biology
Institution: University of Mississippi
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QP Physiology
Depositing User: Michael J Hohl
Date Deposited: 13 May 2016 12:51
Last Modified: 13 May 2016 12:51
URI: http://thesis.honors.olemiss.edu/id/eprint/529

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