Links

• Cell Biology/BIO210 videos describing the M. ruber annotation project.  These presentations were created by the BIOL375 students from Winter 2010-11.

  • Presentation Number 1 - This document will upload as a PowerPoint slide presentation.

  • Presentation Number 2 - A humorous look at the M. ruber project, uploaded to YouTube.  You should be able to answer the questions on this document after listening to this video (CLICK HERE).

  • Presentation Number 3 - another PowerPoint slide presentation that describes the M. ruber project.

   

• DOE-JGI Adopt a Genome Project

• IMG-ACT login

Important News. 

• NSF Funding to support MGAN!! 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.

• The project to sequence the M. ruber genome was recently published (click here).

• Dr. Scott and Dr. Chris Kvaal of St. Cloud State University (MN) presented a talk on MGAN at an NSF conference in Washington DC in December of 2010.

• Dr. Scott waits to hear about the status of two other NSF grants (S-STEM and LSAMP) that incorporate the M. ruber genome annotation project as an undergraduate research experience for transfer students and those under-represented in the STEM fields.

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, Black Hawk College, Moline, IL

Additional Collaborators

• Dr. Kristin Douglas, Augustana College
• Dr. Jason Singer, Augustana College
• Dr. Wegman-Geedey, Augustana College
• Dr. Tim Muir, Augustana College
• Alejandra Ratti, Augustana College
• Jason Koontz, Augustana College
• Dr. Matthew Halfhill, St. Ambrose University, Davenport, IA

Contact information - meiothermus@gmail.com

Coming soon: Meiothermus Facebook page

Annotation up-date

• Number of ORFs with completed annotations as of 1-1-11 ...............56

• Number of ORFs with partial annotations as of 1-1-11 ........................20

• Biochemical pathways studied:  glycolysis and arginine & proline metabolic pathways

• Number of undergraduates who have worked in come capacity on this project as of 1-1-11 is 250+ from BIOL375, BIOL210 and independent research projects

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 2009-10 research team annotated 30 M. ruber genes and cloned three of these genes into a pUC18 plasmid. 

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)

5.  Dr. Scott appears to have demonstrated complementation between an E. coli ArgH- auxotroph and a Meiothermus ruber ArgH+ gene cloned into the pKt-1 plasmid.  The technique is one developed by GENI.  M. ruber has two ArgH genes, identified as ArgH1 and ArgH2.  We attempted to complement both genes from M. ruber, but only one of two genes successfully complemented.  The next step is to sequence the two clones to confirm/refute if they are ArgH1 and ArgH2.