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Only a few decades ago scientists would have had a hard time conceiving of the immense quantities of data generated by modern biological research, especially something termed “sequence data.” Now, as much as 50% of biologist time is spent interfacing with a computer doing something called "bioinformatics."
Formally, bioinformatics the application of computer technologies to the processing, storage, and retrieval of these huge quantities of data. In common usage, however, bioinformatics is a term also applied to the analysis of the data, including the development of software programs for that analysis. Just as almost everyone with a desk job must be familiar with the use of Excel, Word, and PowerPoint, nearly all biologists and certainly all biotechnologists are expected to be familiar with programs such as Blast and Clustal.
Our program emphasizes bioinformatic skills development. In this workshop participants use "biotechnology" to generate significant amounts of data in the form of DNA sequence characters. The participants then use “bioinformatics” to process this data into a useful format, and then compare it to data retrieved from massive national databases. The comparisons are then analyzed and described, again using computational tools, in order to tell a scientific story.
The bioinformatic lessons for use in the classroom are based on the same tools and databases the participants use in the course of performing their research on the mussel invasion. These are also the same tools and databases that practicing scientists use for their work. This includes software for designing and validating primers, software for converting chemical chromatograms into DNA sequences, software for retrieving related DNA sequences from the National Center for Biotechnology Information (NCBI), software for aligning those sequences, software for analyzing the statistical significance of those alignments, and software for visualizing the relationships revealed by the comparisons (as cladograms).
If you are attempting to replicate our entire program, note that the first section on collection and dissection of mussels is presented on the Marine Science page. The second section on lab techniques needed to generate the DNA data is presented on the Biotechnology page. Here in the third section, Bioinformatics, we continue by presenting the computer-based techniques required to analyze the DNA data. Each component can be used individually but may require some modification. If you have received your sequence traces from the sequencing vendor (see step 6 from the Biotechnology page) and wish to continue with the original inquiry, we suggest the following order:
As part of this program participant teachers have generated individual lesson plans based on these tools and databases that can be used to support other MBB activities or can be stand-alone activities. The lesson plans are listed near the bottom of this page. ALL lesson plans are also available in our sortable Lesson Plan Matrix.
An example order of activities that could be conducted in a classroom would be
Day 1 - DNA structure makes sense in the context of DNA replication
Show Steve Palumbi video (0:05:00) to inspire students and provide an example of why they should learn this material. Prepare for a short five minute class discussion to be sure the students understood the point of the video (we can use DNA to identify species, i.e., the type of meat). Next show the DNA Structure and Replication powerpoint modified to suit your class (cut it down to about eight slides). After this presentation many teachers will want to incorporate some sort of hands-on activity for about 20 minutes that reinforces the concept of double-stranded complementary A's, G's, T's & C's. Wrapping up the class period with the DNA Structure animation (0:03:30) helps to reinforce the new ideas presented today. The animation may be a bit over the head of many high school students, but is typical of the level of a first year biology course in college.
Day 2 - DNA replication in the cell can be imitated in a test tube
Begin with same animation you closed with the previous class period, but this time play the game at the end of the animation. A vocabulary worksheet should be handed out before showing the DNA Replication animation so that you can stop the animation and let students complete definitions. This is an animation that you will want to play back and forth and pause to discuss, as it is important foundational material for understanding PCR. Next, the teacher could edit and show the PCR and Primer Selection powerpoint followed by PCR Hands-on Activity . To cap off the class period show the PCR Review animation.
Day 3 - Biologists use chemistry tricks to get at the information in DNA
Chain-termination DNA Sequencing powerpoint, Worksheet on DNA Sequencing, DNA Sequencing powerpoint (Session5.ppt)
Day 4 - Biologists use software to convert chemical data into symbols we can understand
Using Chromas to read DNA sequence traces, and using Blast to check DNA sequences
Day 5 - The sequence of A’s, G’s, T’s & C’s is critical and can be compared side by side
Using Clustal to align and compare DNA sequences
Day 1 - PCR Review flash animation followed by PCR hands-on activity
Day 2 - DNA Sequencing Review followed by Using Chromas to convert raw sequencing trace files to A's G's T's & C's
| Title | File Type |
| DNA Sequencing and Using DNA Sequences | PowerPoint |
| Polymerase Chain Reaction and Primer Choice | PowerPoint |
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| The following web links are used to complete the homework designed to illustrate how sequences are used to answer biological questions: | |
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| Title | File Type |
| Paper Primer-Matching Activity to Reinforce the Concept of “PCR” (Polymerase Chain Reaction) | Word |
| Sequence Editing | Word |
| C03 DNA Sequence Activities | Word |
| Sequence Data Validation | Word |
* Use these programs to complete the Bioinformatics Activities
Chromas (application)
clustalx (application)
Cn3D (application)
Cyt_c_Homo.val (example Cn3D file for Cytochrome c)
| Title | File Type |
| Creating Relationship Trees | |
| Mussel Dissection and Nucleotide Differences | |
| DNA and Heredity: A Middle School Classroom Approach | |
| Codon Bracelet & Open Reading Frame Lesson Plan | |
| Codon Bracelet & Open Reading Frame Activity | |
| Telltale Molecules | |
| Global Warming Using Webquest | |
| DNA, Proteins, Dissection, and Pipetting | |
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| We Are All Mutants | |
| Species Determination Using a Virtual Field Study & Virtual Biotech Lab (Overview) | |
| Invasive Species in Elkhorn Slough (Presentation) | |
| Snail Virtual Lab | |
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| Investigating Invertebrates via a "Digital Notebook" | |
| Invertebrate Evolution: Making a Phylogenetic Tree | |
| Concept Mapping: Higher Reasoning Skills | |
| Whose DNA is that? | |
| Catalase: A Bioinformatics Case Study | |
| Biotechnology/Bioinformatics Activity | |
| Tree of Life | |
| Genetic Relationship of the Mustelidae Family: Who is the sea otter related to? | |
| Evolutionary Relationships Based Upon Comparative Genetics |
This presentation introduces the concept of DNA Barcoding using research conducted by Dr. Steve Palumbi and includes an interview with Dr. Palumbi.
| Title | File Type |
| DNA Barcoding | PowerPoint |
| DNA Video (copy into the same folder as the PowerPoint to view in the presentation) | Windows Media |
