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Bridges to Structure
Peter Woodruff
Stacey Kiser
Joyce Cadwallader
Organ Organ SystemsSystems …
Traditional “Systems Biology”
DissectionDissection
FormForm
FunctionFunction
…
Building Investigations at Different Levels of Structure
http://www.nsf.gov/od/lpa/forum/colwell/rc03norwaycsis/sld011.htm
Size
Organs
Tissues
Cells
Macro
molecules
Size
Organs
Tissues
Cells
Macro
molecules
Time
ontogeny
Phylogeny
Multidimensional Systems Space
http://tetraspace.alkaline.org/
Brian White’s Course Web Site
Phylogenetic Tree Instructions
Choosing Organisms
Results
Protein Structure Investigation
• The students will investigate protein structure (Problem Posing) by use of the Biology Workbench and NCBI.
• They will get information from the NCBI web site about a protein they think might be representative of a particular organ system.
• They will then gather the materials from that site to dissect the structure of their protein including a visual representation (Problem Solving).
Protein Structure Comparison
• Either using the NCBI or Workbench sequences,they will use Workbench to do additional trees of representative proteins of a particular organ system
• They will present their findings on the proteins in class.
Organ System Protein NCBI
#
#of Hits in GBVET, MAM, INV
Image
(Structure)
Integumentary
Skeletal
Muscular
Digestive
Circulatory
Respiratory
Sensory
Nervous
Reproductive
Endocrine
Immune
Get NCBI Protein File
Get a List of Similar Molecules
Get Structure
Workbench.sdsc.edu
Work in Progress
• Adding activities from Comparative Genome site would be helpful, but time allowed only a start.
• Although we have provided some ascension numbers for proteins, remember only genomic sequences work in this database (Find them at NCBL.).
Workbench (Organisms Used)
Workbench Alignment Data
Organ System
Protein NCBI
#
#of Hits in GBVET, MAM, INV
Image
(Structure)
Integumentary Keratin NoSkeletal collagenMuscular tropomyosin 1IC2Digestive
Circulatory
Respiratory
Sensory Crysallin IA5D 484 Yes(41)Nervous Ach E 2ACK 251 Yes(9)Reproductive E Rece * 196 Yes(22)Endocrine Insulin IEV6 743 Yes(161)Immune Interleukin 1 1IOB Yes
Respiratory: CFTR
http://www.people.virginia.edu/~rjh9u/gif/cftr.gif
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
http://www.brunel.ac.uk/depts/bl/project/biocomp/sequence/seqanal_guide/pds/cftr.jpg
Respiratory: Surfactant Protein D
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
http://ashtoret.tau.ac.il/~sharon/hspd.jpg
Human surfactant protein D (pdb entry:1b08)
Reproductive: Estrogen receptor1ERE
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
http://www.bch.msu.edu/~kuhn/projects/screening/er.jpg
Immune System:Immunoglobulin, Variable Region
& Interleukin-1 BetaCn3D of cd00099.3, IGv
Cn#D of2MIB
Skeletal: Collagen
Cn3D of 1CGD
Muscular: Tropomyosin
http://202.20.99.18/~jjkim/Lecture/Animalphy/Ap10muscle/actin-ca.gif
Cn3D of 1IC2
Workbench Unrooted Tree
www.dcode.org
Data from search for estrogen receptor
Conservation Information for Estrogen Receptor
Bringing Dissection Up to Date
http://www.activehistory.co.uk/2nds/TudorProject/tudor_medicine_and_health.htm
http://mason.gmu.edu/~dgomez2/