Lab Reports

Wrapping up IMG-ACT Genome Annotation Online notebook should be completed for all 3 genes Final reports are comprised of the imgACT online reports (one for each gene) and a team summary of the project –Each student on the team should complete the online reports for all 3 assigned genes. The reports must be printed out and turned in with your team project summary & cover page. –Each team should collectively summarize the results of their annotation project. The summary must be printed out and one copy turned in to your T.A., together with individual reports for each gene. DUE DATES

Provide a COVER PAGE for your report: Include your team name as well as the full names (and UIDs) of student team members. Include a LIST of the pathways or cell structures assigned to your team. (some teams have only one while others have two). Include a LIST of the gene OIDs that were annotated as part of this report. Wrapping up IMG-ACT Genome Annotation

Online Reports Access REPORT from team coursework page. “Click” on the link under step name column.

For each module, enter requested results in report (from notebook). Note that this format is compatible for eventual upload to IMG database. Online Reports

CLICK when finished Note: Surmised from the analysis of data from ALL modules. Skip Module 9 – we did not annotate RNA molecules Online Reports

PRINTING your report: Delete “edit” from URL then press [Enter] Online Reports

Notice entry boxes have been removed. Select [Print] from drop-down menu. Include hard copy with team report.

Team Project Summary Include a graphical representation of your pathway or cellular structure, highlighting genes annotated by team, as well as a summary table EX: CELLULAR STRUCTURE Reference Gene Reference Organism Gene OID (P. limnophilus) Proposed Gene Annotation ABC-type nitrate/sulfonate/bicarbonate Transport system, periplasmic component SSuA Rhodopirellula baltica SSuC SSuB Rhodopirellula baltica ABC-type nitrate/sulfonate/bicarbonate Transport system, permease component ABC-type nitrate/sulfonate/bicarbonate Transport system, ATPase component Escherichia coli ATCC 8739 Corresponding gene in P. limnophilus ABC Transport Systems in Planctomyces limnophilus DSM 3776

Team Project Summary EX: PATHWAY EC Number Reference Organism Gene OID (P. limnophilus) Proposed Gene Annotation narB; nitrate reductase catalytic subunit Rhodopirellula baltica Corresponding gene in P. limnophilus nitrite reductase (NAD(P)H) large subunit Rhodopirellula baltica glutamine synthetase Rhodopirellula baltica

Team Project Summary Provide a 2-3 page DESCRIPTIVE SUMMARY: (1) TEAM: Based on gene content, what parts of the pathway or cellular structure that your team annotated appears to be functional (i.e., all components present in P. limnophilus genome)? What components are missing from various steps or cell structures? Propose an experiment to hunt for missing genes**. The experiment may be computationally-based or one performed in the wet laboratory – be creative! (No more than 5-6 sentences) (2) INDIVIDUAL: For each assigned gene, provide a BRIEF summary of some of the key results that enabled you to conclude that the functional annotation is accurate as well as any interesting or surprising results that you encountered while annotating your genes. (No more than 3-4 sentences per gene) **NOTE: For those lab sections in which multiple teams shared one pathway or structure, you should SHARE results – a gene isn’t missing if it was assigned to someone else.

Team BRUIN Josie Bruin ( ) Joe Bruin ( ) Jackie Bruin ( ) Jerry Bruin ( ) Assigned pathway: Nitrogen Metabolism Annotated Gene OIDs: Assemble report & turn in to your T.A.

Finally, take post-annotation survey Cookies must be enabled for survey to work properly.