1. (less than 20minutes)
Use Pubmed in NCBI's Entrez to find an article written by
Carl R.
Woese (famous scientist, co-discoverer of the Archaea), published in the journal
Proceedings of the National Academy of Sciences of the United States of America
with the words primary kingdoms in the title of the paper. Try to use Boolean operators and field tags; if you cannot recall the tags, use the Preview/Index tool under advanced search (link on top right).
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What query did find the 1977 article?
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How many related citations (link in right hand bar) are linked to this article?
(in the window that gives you the title, authors and abstract, click on the link labeled "related citations ..." select -> all )
When was the most recent published (Hint: In the Display settings pull down menu set the "Sort by" option to Pub Date)?
(Aside: If you wonder why prokaryote was the wrong choice in the exam question on the three domains of life, check the 2009 opinion piece from Norm Pace. A more readable and complete summary of the history is in Jan Sapp's article at http://www.ncbi.nlm.nih.gov/pubmed/18053933 )
2. (ca. 7 minutes) (Note: Entrez' pulldown menus do not always work well in Safari -- use Firefox)
In NCBI's Entrez/pubmed find the earliest paper co-authored by Senejani and Gogarten. What is the topic of the paper?
To learn about inteins, select books as the target database to search (pulldown menu on the left, below the black bar) and search for intein homing, then click on the <see results> link - the image is somewhat informative.
For more information check Wikipedia on inteins
3. (ca. 5 minutes)
Dr. Gogarten seems obsessed by an important protein called ATP synthase. Is he interested in anything else? How many articles has he published that are NOT related to the ATP synthase OR ATPase?
What query did you assemble?
How many articles did you find?
4. (10 minutes)
For a scientist of your choice (e.g., your advisor, or someone who publishes in your field of interest), using
ISI's Web of Science database
(click on the Web of Science tab at the top)
search for articles that cite this author (i.e., you need to use a cited reference search).
Which was the most cited article?
How often was it cited?
When was the most recent citation?
Did you find any interesting article?
Was this article available online?
5. (5 minutes)
Using
Pubmed,
search for articles co-authored by Taiz and Gogarten.
a) How many articles did you retrieve?
b) Using the "find related data" pull down menu in the right bar, display all Nucleotide Links and all Protein Links.
How many did you find?
c) Do all the different protein sequences really refer to different sequences?
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What might explain your finding?
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Go to the nucleotide entry for gi|167559. How many related sequneces (link in right hand bar) does this entry have?
Go to the protein encoded by gi|167559 (167560). How many related sequneces (link in right hand bar) does this entry have?
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6. (10 minutes)
Using
Entrez,
search Protein (use drop-down box to select the Protein database)
for 19888400 (this is a gi number, see historical note)
Click on the BLink link in the lower right-hand corner (under all links from this recored).
Read more about BLink here (especially note the last paragraph)
Do you notice anything interesting about the alignments?
Click on the Tax
BLAST report. Scol through the report, with focus on the Taxonomy Report. In which group of organisms are the most similar homologs to 19888400 mainly found?
7. (8 minutes)
To what domain (super kingdom), phylum (kingdom), and family does Thermoplasma belong? (Use the Taxonomy Search. In the line labeled lineage, if you hover the mouse pointer over the names, it tells you which taxonomic category you are pointing at. )
How many protein and genome sequences are available for Thermoplasma acidophilum, how many are available for the genus Thermoplasma? (In the taxonomy browser go to Thermoplasma and check protein and genome in the header, then click on <Display>)