This project was prepared as part of a BioQUEST faculty development workshop entitled Implementing Bioinformatics in Introductory Undergraduate Biology Courses:
Exploring Microbiology, Molecular Data and Visualization
at San Diego Supercomputing Center in January 2007. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

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Using BLAST to investigate genes expressed during loblolly pine embryogenesis
Authors          Audiences          Overview           Materials          Resources           Future Directions



Michelle Furlong
Clayton College & State University

Caroline Clower
Clayton State University


Possible Audiences:

This activity can be adopted to any undergraduate course in cell and molecular biology, genetics, microbiology or developmental biology.  


Brief Overview:

All living organisms have thousands of unique genes encoded in their genome, of which only a small fraction are expressed in any individual cell at a given time. Developmental stages in a given organism are driven by changes in gene expression. In order to completely understand development it is useful to identify and characterize those genes that are differentially expressed during various stages of development. The goal of the Loblolly Pine Embryogenesis Project (LPEP) is to sequence expressed sequence tags (ESTs) from loblolly pine embryonic tissues during various stages of embryonic development. The ultimate goal of this project is to use these EST libraries to profile gene expression patterns at various stages of somatic and zygotic embryo development in the loblolly pine.

In this exercise students are given a groups of ESTs generated from the LPEP. The ultimate goal of the exercise is to have the students investigate which genes are expressed during various stages of somatic and zygotic embryo development.  


Project Materials:

EST sequences from the Loblolly Pine Embryogenesis Project (see attachments)
National Center for Biotechnology Information (NCBI)BLAST tool  


Resources and References:

NSF Genomics of Loblolly Pine Embryogenesis Project

National Center for Biotechnology Information (NCBI)

Pullman, G.S., S. Johnson, G. Peter, J. Cairney, and N. Xu. 2003. Improving loblolly pine somatic embryo maturation: comparison of somatic and zygotic embryo morphology, germination and gene expression. Plant Cell Rep., 21: 747-758.  


Future Directions:

Once students have identified various ESTs they can investigate them further by finding homologs to their ESTs and looking at phylogeny of these putative genes and investigating the structure of the gene products.  



- ESTInformation.doc
- EST1.txt
- EST2.txt
- EST3.txt
- EST4.txt
- EST5.txt
- EST6.txt
- worksheet.doc
- BLASTactivity3.doc
- Pullman2.pdf
- embryos.jpg