RNA Extraction from Variovorax isolates under various growth conditions for transcriptome analysis.

Poster Number

4B

Lead Author Major

Biological Sciences

Lead Author Status

Sophomore

Second Author Major

Pre-Dentistry

Second Author Status

Sophomore

Third Author Major

Biological Sciences

Third Author Status

Sophomore

Format

Poster Presentation

Faculty Mentor Name

Paul Orwin

Faculty Mentor Department

Biological Sciences

Abstract/Artist Statement

Variovorax paradoxus and related species within the genus play a vital role in soil health and plant growth. Further understanding of its biofilm formation and mechanisms of horizontal gene transfer may provide new opportunities for its application as a biofertilizer or plant growth promoting additive. Determining which genes change in expression levels under biofilm growth conditions is an important step in building this knowledge. Because the resulting datasets are very large and complex, a reproducible experimental strategy is critical to getting useful data. Reproducible high quality RNA extraction is a prerequisite to obtaining useful transcriptome analysis results. This process includes streaking and inoculating bacterial cultures, creating frozen stock bullets of identical density and provenance, then utilizing these bullets to grow cultures in different conditions. Once grown, RNA extraction is performed utilizing the Direct-Zol kit from Zymo Research. Purity and concentration of RNA are measured using the NanoDrop spectrophotometer. Four strains of Variovorax were studied; MF375, MF160, MF369, NFACC270, and KK3. These strains were grown in liquid culture to logarithmic phase and stationary phase as well as in static biofilms. The extracted RNA from these strains will next be used for transcriptome analysis to determine which genes are upregulated and downregulated in these various growth conditions.

Location

Information Commons, William Knox Holt Memorial Library and Learning Center

Start Date

29-4-2023 10:00 AM

End Date

29-4-2023 1:00 PM

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Apr 29th, 10:00 AM Apr 29th, 1:00 PM

RNA Extraction from Variovorax isolates under various growth conditions for transcriptome analysis.

Information Commons, William Knox Holt Memorial Library and Learning Center

Variovorax paradoxus and related species within the genus play a vital role in soil health and plant growth. Further understanding of its biofilm formation and mechanisms of horizontal gene transfer may provide new opportunities for its application as a biofertilizer or plant growth promoting additive. Determining which genes change in expression levels under biofilm growth conditions is an important step in building this knowledge. Because the resulting datasets are very large and complex, a reproducible experimental strategy is critical to getting useful data. Reproducible high quality RNA extraction is a prerequisite to obtaining useful transcriptome analysis results. This process includes streaking and inoculating bacterial cultures, creating frozen stock bullets of identical density and provenance, then utilizing these bullets to grow cultures in different conditions. Once grown, RNA extraction is performed utilizing the Direct-Zol kit from Zymo Research. Purity and concentration of RNA are measured using the NanoDrop spectrophotometer. Four strains of Variovorax were studied; MF375, MF160, MF369, NFACC270, and KK3. These strains were grown in liquid culture to logarithmic phase and stationary phase as well as in static biofilms. The extracted RNA from these strains will next be used for transcriptome analysis to determine which genes are upregulated and downregulated in these various growth conditions.