Download Using the Inquiry Page in a High School Classroom

A Study of Cystic Fibrosis Using
Web-Based Tools
Anuradha Datta Murphy
Graduate Student, Dept. of Molecular and
Integrative Physiology,
University of Illinois at Urbana-Champaign
Introduction:
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We will use several medical and computational
biology web sites to obtain information on cystic
fibrosis, an inherited respiratory disorder.
Outline of presentation:
– What is cystic fibrosis (CF)?
– Gather information on cause and symptoms of CF from
medical web sites
– Search for cystic fibrosis transmembrane receptor (CFTR)
protein, locate CF-causing mutation, view CFTR structure
using web-based tools
– Obtain information on other inherited disorders of interest
What is cystic fibrosis?
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Cystic fibrosis (CF) is an inherited genetic disease
that affect cells producing sweat, saliva, mucus, and
digestive fluids. Normally thin and slippery, in CF
patients these secretions are sticky and block tubes
and passageways. Most CF patients die of bacterial
infections resulting from blocked airways in the lungs.
Most children with CF have frequent coughing,
wheezing, and respiratory infections.
Symptoms of CF, contd.
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CF also affects the pancreas, liver, and intestines,
leading to poor absorption of nutrients and poor
weight gain. CF patients have salt crystal formation
on their skin when they sweat excessively.
CF slide show available at:
http://www.healthcentral.com/library/April_03/flash_co
ntent/hcplay.asp?id=110
What causes CF?
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A mutation in the gene coding for the CFTR (cystic
fibrosis transmembrane receptor) protein causes CF.
CF is caused when a child inherits two copies of this
defective (mutated) gene, one from each parent.
The CFTR protein is a Cl- channel located on the
plasma membrane of epithelial cells of the lungs,
pancreas, sweat glands, and other tissues.
In non-CF individuals, Cl- transport from the cell is
increased in the presence of ATP. In CF patients this
transport malfunctions, causing salt and water
imbalance in and around the cell.
The CFTR protein:
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A single mutation in the CFTR gene results in cystic
fibrosis.
This mutation involves deletion of three basepairs of
DNA, resulting in deletion of a phenylalanine residue
(delta-F508 mutation) from a normal (wild type)
CFTR sequence.
Theory: deletion of Phe508 prevents the CFTR
protein from being properly delivered to the plasma
membrane, thus causing Cl- transport malfunction.
Properties of the CFTR protein:
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The CFTR gene is located on chromosome 7 in the
human genome
This protein is made up of 1480 amino acids and
contains two domains: (1) membrane association,
and (2) ATP-binding
In CF patients, deletion of Phe 508 causes defective
Cl- transport.
Locating and viewing the CFTR protein:
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In the Biology Student Workbench, search for the
CFTR protein using the following:
– search words: “cystic fibrosis homo sapiens”
– search database: Non-Redundant protein sequence
database
– tool: Ndjinn
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Select SDSCNR:315424, Cystic Fibrosis
Transmembrane Conductance Regulator …, import
sequence.
View sequence, note accession number, P13569.
Use other tools on BSW to learn about CF.
Using the NCBI web site:
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The National Center for Biotechnology Center is
available at the following url:
http://www.ncbi.nlm.nih.gov
Many computational biology tools are available here,
including PubMed (a database of biological
literature), Entrez (a search engine for information on
protein and nucleotide sequences across databases),
BLAST (alignment search tool for protein and
nucleotide sequences), OMIM (Online Mendelian
Inheritance in Man, a directory of human genes and
genetic disorders), and Cn3D (structure viewer).
Study of CFTR using tools on NCBI:
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In the NCBI home page search Entrez for cystic
fibrosis: select Entrez, type “human cystic fibrosis” in
the Search window, click on “Go”.
In the results page; note that our keyword search has
yielded hits on multiple databases contained within
NCBI.
Since CF is an inherited genetic disorder, click on
OMIM to view results within the Online Mendelian
Inheritance in Man database.
In the OMIM hits list page, click on the top hit,
*602421.
Using OMIM:
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Note the exhaustive information on CF available in
OMIM, including cause and symptoms of the disease,
molecular basis, summary of literature on CFTR
mutation research, study of other related diseases
generated by mutations on CFTR, etc.
Click on “Gene map locus 7q31.2” near the top of the
page. This gives the CFTR gene location on the
human genome. Click on “Location” in the following
page to get more detailed information, including a
figure of human chromosome 7 and other genes
located in the vicinity.
Using OMIM:
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Return to the OMIM results page. Scroll down the
page to locate literature on F508 deletion (you can
click on “Edit” in the toolbar header, click on “Find on
This Page” and type delF508). Research indicates
that this deletion causes CF. Click on (602421.0001).
This is the mutated CFTR gene causing CF. In the
displayed page, there is more literature on CFTR
mutation research.
Using NCBI tools:
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Return to the Entrez results page. Click on “Protein”
to examine the CFTR protein sequence. In the hits
page, click on P13569.
Note presence of a phenylalanine residue (F) at
position 508 in the CFTR sequence. There is also
detailed information on various CFTR sequence
mutations and their results.
Using Cn3D structure viewer:
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Return to the Entrez results page. Click on Structure.
Note presence of multiple CFTR structures based on
Phe508 mutation.
Click on 1CKZ, view structure of CFTR segment
affected by Phe508 mutation using Cn3D.
In the MMDB Structure Summary page, click on
“View 3D Structure” button.
Click on amino acid residues below to observe
location on structure. Note absence of “F” residue.
Using NCBI tools:
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Return to the OMIM page.
On the left column, click on “Search Morbid Map”
In the “Search for” window, type in keywords for any
inherited disease of interest (ex., sickle cell anemia,
muscular dystrophy, diabetes, etc.)
Locate the affected gene on the human genome,
view location on the chromosome, view structure of
protein (if available) using Cn3D, and read up on
literature of research (both clinical trials and gene
mutations), all using tools on NCBI!
Closing Notes:
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For more information on CF symptoms and
treatment, see:
– http://www.merck.com/mrkshared/CVMHighLight?file=/mrkshared/
mmanual_home2/sec04/ch053/ch053a.jsp%3Fregion%3Dmerckco
m&word=cystic&word=fibrosis&domain=www.merck.com#hl_ancho
r
– http://www.healthcentral.com/library/librarycontent.cfm?id=222
– http://www.healthcentral.com/library/librarycontent.cfm?id=222