BIO520 LAB 1
1/15/2010
Jim Lund

The primary goals of this lab are:
1.	Get used to using the lab computers.
2.	Establish communications.
3.	NCBI publication and reference resources. 					

During the labs I will use certain conventions.  I will try to clearly indicate what answer I want you to return, sometimes by using BOLD.  Help is usually hyperlinked somewhere close by.

Okay, if you are ready to begin, I recommend that you start by opening a file in a text editor like OpenOffice or MS Word with a name derived from your first and last name like the following example: Jim Lund -> LundJ_lab1.rtf.  You will paste your answers into the document.  You do not need to include the questions, just a numbered list of answers from 1 to the end.  When complete labs will be emailed to the TA with a subject line “BIO520 Lab XX”.

Topics for Lab 1:
1.	NCBI PubMed and OMIM.
2.	NCBI Bookshelf.
3.	Screenshots as a help in diagnosis.

1)	Find the page in the Online Mendelian Inheritance in Man (OMIM at the NCBI, linked from the Genetics & Medicine page , or go directly to http://www.ncbi.nlm.nih.gov/omim), which summarizes what is known about hemoglobin A (human gene name HBA1).  What is the country of origin of the woman who has a mutation resulting in a ser3-to-phe (S3F) amino acid substitution?
Answer 1=country, just one word.

2)	Familiarize yourself with the NCBI resources and databases.  The NCBI site contains many biological databases.  Today, we’ll use PubMed, OMIM, and the NCBI Bookshelf.  Pubmed is the major biomedical literature database.  

Starting in the mid-90’s, journals began providing articles online either free or for subscribers.  UK’s library has subscriptions for many biomedical journals and they can be accessed by users on the UK network (UK users off campus can access articles using this proxy server, https://ezproxy.uky.edu/login).  PubMed provides links to access papers online when available.  

Search by author for Watson and Crick and find Watson and Crick’s paper on the structure of DNA.  Provide the Pubmed ID (PMID) for the original publication of this paper (Answer 2a).  The 1953 issues of Nature are not available online, but interestingly this paper has been reprinted in journals that are available online.

	The PubMed Advanced Search page is useful for searching Boolean combinations of author, year of publication, or journal.  Find 1) On how many published papers is the bioinformaticist Lincoln Stein an author?  2) Find the Campbell et al., 1996 paper on cloning by nuclear transfer, 3) Find the environmental shotgun sequencing paper by Venter published in 2004.  Give the number of papers returned in the first case, and the PMID of the paper as the answer for the other questions (Answer 2b, c, d).

3)	The NCBI Bookshelf is a great source of reference and background biological knowledge.  Find a good reference book on molecular biology, genomics, and biochemistry.  Give the title of each book you select [many answers are possible here] (Answer 3a).

	Use the NCBI Bookshelf to find how the location of the TATAAT box/TATA box promoter element with respect to the start of transcription differs between prokaryotes and eukaryotes (Answer 3b).	

4)	Sometimes, it is very helpful to be able to see what is on a computer screen to diagnose a problem.  Please take a screenshot of the entire screen at the NCBI home page and paste it in as Answer 4.

5)	Classify each of the following organisms as eukaryote (E) or prokaryote (P).  This is a sample of typical model organisms used in genomics and in molecular biolgoy.  Your Answer 5 should be a string like P,E,E,P,P,E.

Danio rerio (zebrafish)
Caenorhabditis elegans (nematode)
Saccharomyces cerevisiae (brewer's yeast)
Eschericia coli
Homo sapiens (human)
Zea mays (maize, or corn)
Dictyostelium discoideum (slime mold)

Where do you go for taxonomy help?  You could go to a biology book, or use the NCBI Taxonomy site!

6)	List the amino acids with BASIC side chains (these have a positive charge at neutral pH) in an alphabetic string in one-letter code (eg. ACDE)
You SHOULD know all 20 amino acids and their properties.  The 1-letter code is easiest to use. (Help available at http://elegans.uky.edu/WebReads/web2.htm).

7)	For a typical eukaryotic gene, list the indicated elements in the 5' to 3' order. For two elements that overlap indicate the one the starts most 5' first. The elements are indicated on the drawing (click on the drawing for a full-scale version).  Each term is used only once, although each gene could have more than one of some of these features.  You MUST know the structure of a typical gene!!

As an example, if you feel that the correct order of elements were:  poly A tail, stop codon, promoter, exon 1...your answer would be IDFH....

A.  Intron 1
B.  5'-Untranslated Region
C.  Initiation codon
D.  Stop codon
E.  Exon 2
F.  Basal Promoter
G.  Enhancer
H.  Exon 1

LAB1 HELP

Biology reference page:  http://elegans.uky.edu/WebReads/web2.htm

Find
Find on this web browser page (Ctrl-f) is incredibly useful!

Screenshots
To get a picture of your whole screen, if you are using a Windows OS hit PrintScreen.  Then just paste (CTRL-v) where you want the picture.  To get a picture of just the active window, ALT-PrintScreen, then paste.  On a Mac, use Cmd-Shift-3 or -4, the image is saved to the Desktop.