The innovative technology experience for students and teachers used in this project involves a “hands-on” cyber-learning approach, known as GENI-ACT, that will involve participants in a current and global research project while learning basic concepts of biology.
The GENI-ACT consists of nine independent modules:
- Basic Information (DNA coordinates, DNA sequence, Protein Sequence, Isoelectric point)
- Sequence-based Similarity Data (BLAST, CDD, T-Coffee, WebLogo)
- Cellular Localization Data (Gram Stain, TMHMM, SignalP, PSORT-B, Phobius)
- Alternative Open Reading Frame
- Structure-based Evidence (TIGRfam, Pfam, PDB)
- Enzymatic Function (KEGG, MetaCyc, E.C. Number)
- Gene DuplicationGene Degradation (Paralog and Psuedogene Determination)
- Evidence for Horizontal Gene Transfer (Phylogenetic Tree, Gene Context, GC Heat Map)
- RNA Information (Rfam)
Use of the modules encourages participants to:
- Use and master multiple database analysis software packages related to bioinformatics.
- Strengthen library and web-search skills
- Develop skills in making hypotheses and the design of experiments to test them
- Sharpen skills in analysis, synthesis and in the presentation and interpretation of results
- Experience the collaborative nature of science.
The project will use the genome of the bacterium Kytoccocus sedentarius as the source of material for analysis. Kytococcus is one of the Genomic Encyclopedia of Bacteria and Archea (GEBA) organisms. GEBA organisms have had their genomes sequenced to help fill in gaps in the tree of life that exist due to the fact that sequencing had previously been done only for those organisms that were easy to grow or which had clinical significance. A basic summary of the importance of sequencing and annotating GEBA genomes can be found here.
The image below is a scanning electron micrograph showing the characteristic cuboidal appearance of Kytococcus sedentarius in culture. Each one of the sphere-like structures in the micrograph is a single bacterium. Students and teachers participating in the project will help to annotate the genomic sequence of this microbe and, in addition to gaining experience in basic bioinformatic analysis, will contribute to the basic understanding of its biology.
Examples of work on the genome annotation project performed by high school students and MS level students at the university at Buffalo can be seen in the In the news…. page of this website.