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MEIOTHERMUS RUBER
GENOME ANNOTATION PROJECT
Principle Project Collaborators:
- Dr. Lori Scott, Augustana College, Rock Island, IL
- Ms. Angela Ghrist, Scott Community College, Bettendorf, IA
- Dr. Todd Linscott, BlackHawk College, Moline, IL
- Dr. Matthew Halfhill, St. Ambrose University, Davenport, IA
Additional Collaborators
- Dr. Kristin Douglas, Augustana College
- Dr. Jason Singer, Augustana College
- Dr. Wegman-Geedey, Augustana College
- Dr. Tim Muir, Augustana College
Important News.
- The newly formed network called the Microbial Genome Annotation Network (MGAN), whose PIs include Dr. Lori Scott (Augustana College), Dr. Cheryl Kerfeld (JGI) and Dr. Chris Kvaal (St. Cloud State Univ.), was awarded a $500,000 RCN-UBE grant from NSF to promote the network and its utilization of the DOE JGI's Adopt-a-Genome program. The grant provides travel awards to JGI workshop participants and the development of curricular tools for utilizing the JGI's IMG-ACT/edu bioinformatics toolbox. The Meiothermus ruber Genome Annotation Project is an offshoot of this larger network.
Important Publications and Documents
- A student version of the instructions for Modules 1-5 of the IMG-ACT annotation for Meiothermus ruber is available for network members only; request a copy by emailing Lori Scott. Instructions for the remaining modules will be available soon.
Annotation up-date
Number of ORFs with completed annotations as of 07-01-10 ...............35
Number of ORFs with partial annotations as of 07-01-10 ........................10
Latest research findings
1. Genomic DNA from Meiothermus ruber was isolated from a 1-day overnight culture using the Wizard SV DNA Purification System. We followed the instructions provided by McDonald, R. and Hill, O. (2004) Isolation of genomic DNA from bacterial cells using the Wizard® SV Genomic DNA Purification System. eNotes.
Figure 1: Isolation of gDNA from M. ruber and E. coli and the Subsequent Amplification of the 16S rRNA gene. This project was performed by the BI375/Molecular Genetics students from Winter 2009-10
- Average concentration of M. ruber gDNA = 6.4ug in 200ul elution buffer
- Average concentration of E. coli gDNA = 2.5ug in 200ul elution buffer
2. The BI375 research team is currently annotating 30 M. ruber genes and cloning a subset of these genes. The outcome of this project will be presented at the ISAS meeting in April, 2010.
3. Angela Ghrist (EICCD/Scott Community College) and Nicole Oldfather confirmed through restriction enzyme analysis that we had successfully amplified the 16SrRNA gene(s) using universal primers purchased from IDT (Coralville, IA). They are working to clone the beta-galactosidase gene into a suitable vector.
4. A poster was presented at the 2010 Illinois State Academy of Sciences 102nd annual meeting from the collaborative work of the 2009-10 BI375 students, and A. Ghrist and N. Oldfather from Scott Community College (Click Here)