A full suite of standards-aligned PowerPoint presentations was developed for teachers to cover a diversity of interrelated program topics that bridge ecology, environmental science, evolution, genetics, biochemistry, molecular, cellular, and developmental biology, and bioinformatics. These presentations, which incorporate scientific animations, embedded video files, and other multimedia, form a central part of the program curriculum and were designed to help teachers integrate scientific concepts, processes, and principles from different life science disciplines. Because these materials are undergoing periodic revisions based on teacher feedback, viewing access is currently offered through authorSTREAM.
A companion laboratory manual provides step-by-step instructions to guide students through each protocol in the laboratory segment of the DNA barcoding pipeline. This manual was specifically designed for use in conjunction with the multimedia presentations developed for the Barcoding Life’s Matrix program. The manual is currently being offered in draft format. A revised manual will be available in February 2013.
Introduction to DNA Barcoding
PowerPoint presentation
This introductory presentation provides a brief history of DNA barcoding, a description of the DNA barcoding pipeline, and an introduction to the International Barcode of Life (iBOL) project and the Barcode of Life Data Systems (BOLD). It bears noting that emphasis has been placed upon program-specific barcoding efforts, particularly student-led efforts to create a reference DNA barcode library for rockfishes of the genus Sebastes found in the waters surrounding California’s northern Channel Islands. This material is included to specifically accommodate active teacher participants in the Barcoding Life’s Matrix program. For a more general introduction, please use the Prezi link to the Program Primer that appears on the home page. To provide an appropriate context for subsequent discussions centered on a role for DNA barcoding in species identification and discovery, this Program Primer compares estimated rates of species loss with the rate of species identification using Linnaean taxonomy.
Beyond the Barcode Metaphor
PowerPoint presentation
DNA barcoding is a species identification system that pairs a standardized gene sequence with other types of retrievable information stored in an electronic database (the Barcode of Life Data Systems). This unit begins by comparing and contrasting the UPC (Universal Product Code) barcode system used to track consumer products, with the DNA barcode system developed by iBOL scientists to identify species groups. To prepare students for the laboratory segment of the program and help them understand the evolutionary constraints imposed on the DNA barcode sequence, the unit guides them through an extensive review of fundamental molecular life science topics.
Entering the barcoding pipeline in the lab: isolating genomic DNA from target marine specimens
PowerPoint presentation
The laboratory segment of the DNA barcoding pipeline begins with the isolation of genomic DNA (gDNA) from specimen tissue. To foster an understanding of the key steps involved in this laboratory procedure, this unit reviews a number of fundamental topics in cell biology, including intercellular junctions, the extracellular matrix, proteolytic enzymes, and biological macromolecules. More advanced topics, including chaotropism and non-covalent forces (e.g. hydrogen bonds, van der Waals forces, and hydrophobic effects), are also covered to help students understand the biochemistry underlying the lab procedures executed in this unit.
Using polymerase chain reaction to copy and amplify a segment of the CO1 gene
PowerPoint presentation
The next step of the DNA barcoding pipeline involves the use of polymerase chain reaction (PCR) to copy and amplify a 650 base pair region of the mitochondrial CO1 gene. Because PCR draws heavily upon our knowledge of the key biomolecular events that occur during DNA synthesis in the cell, this unit begins with a review of cell cycle checkpoints, leading and lagging strand synthesis, and replication fork dynamics. The unit concludes by comparing and contrasting DNA replication in the cell with DNA replication in a test tube using PCR.
Examining DNA using agarose gel electrophoresis
PowerPoint presentation
In this laboratory unit, students use agarose gel electrophoresis to confirm that CO1 gene fragments of the expected size were generated by PCR. A number of central issues associated with this standard separation technique, including migration rates, resolving power, pH and its effects on charge, the selection of molecular weight size markers (e.g. DNA ladders), and the spectral properties of ethidium bromide, are examined in this unit.
Purifying CO1 amplicons using silica-based spin column technology
PowerPoint presentation
CO1 amplicons generated by PCR must be isolated from other reaction components that may obscure the analysis and interpretation of automated DNA sequencing results. In this laboratory unit, CO1 amplicons are purified from the PCR reaction mixture using silica-based spin columns. To help students understand the biochemistry behind the key steps of this widely used separation technique, this unit discusses the behavior of DNA in the presence of chaotropic salts and alcohol.
Automated DNA Sequencing
PowerPoint presentation
Purified CO1 amplicons are sequenced using a PCR-based technology that relies on the use of fluorescently labeled dideoxynucleotide chain terminators. This unit provides an in-depth examination of this commonly used method of automated DNA sequencing, and provides supplemental material that includes a discussion of reading frames, the absence of stop codons within a correctly edited sequence, and the non-universality of the mitochondrial genetic code.
Analyzing, Editing and Uploading Sequence Data to the BOLD Student Data Portal (BOLD-SDP)
PowerPoint presentation
CURRENTLY UNDER DEVELOPMENT; PLEASE CHECK BACK SOON
The DNA barcoding pipeline culminates in the submission of raw trace files and edited CO1 sequence data to BOLD. For sequence data submitted by members of the professional community, BOLD currently deploys a suite of automatic tools to identify data anomalies such as contaminated sequences, sequences with stop codons, and low quality trace file reads. This information is then conveyed to a team of data curators, who vet and annotate records according to their validity.
The BOLD Student Data Portal (BOLD-SDP) is a customized workspace and analytical workbench that was specifically designed for educational users. BOLD-SDP permits additional sequence classification and tagging to further ensure the accuracy and consistency of barcode data entering BOLD from the educational community. This unit outlines the steps involved in analyzing, editing, and uploading sequence data to BOLD-SDP.
Next Generation Sequencing Technologies and Environmental Barcoding Applications
PowerPoint presentation
CURRENTLY UNDER DEVELOPMENT; PLEASE CHECK BACK SOON
