SCCBEP Labs and Kit Application 2016-17
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DESCRIPTION
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Introductory Labs
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DNA SpoolingStudents isolate DNA from strawberries and calf thymus. This is an introductory lab, low in equipment and reagent needs yet brings the wonder of life science while introducing biotechnology. This lab is suitable for all student levels from grades K-12.
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Pipet ArtScience, math and art all in one! The ever popular and much copied orginal. Introduce or review micropipetting skills, self-assessment, with math (using Battleship coordinates), while creating an art work to take home. This lab is suitable for all student levels from grades K-12.
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DNA Fingerprinting Fragile XIntroduction to micropipetting skills and gel electrophoresis, the most basic tools and techniques in biotechnology. Fragile X syndrome incorporates restriction enzyme digest, pedigree and bioethical discussion on genetic counseling. This lab is suitable for all student levels from grades 7-12.
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Fluorescent Protein Labs
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Flourescent Protein Transformation (pGLO, pGFP, pMenlo, pCherry, Rainbow plasmids)An introductory microbiology, genetics, protein lab. pGLO is the old transformation from white to green colonies that can be followed with HIC column purification. pGFP and pMenlo is the new plasmid transformation that can be used with Ni bead affinity purification. This lab is suitable for all student levels from grades 7-12.
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Restriction/Ligation/TransformationThis advanced sequence of labs have students create the plasmid of interest used in transformation. This real-world experience gives students the entire hands-on process of manipulating DNA to create the vectors you need for research. Students get to actually test the results of the plasmid they create by transforming the bacterial for expression. This lab is suitable for advanced biology and biotechnology classes.
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FP Purification by HIC or Ni BeadsAfter expressing a fluorescent protein, a research or industry lab would purify and analyze their protein samples. Protein purification is simple and quick with affinity chromatography due to the his-tagged residues on the protein. Tubes collected from the chromatography step can be visualized for purity in a vertical PAGE (polyacrylamide gel electrophoresis). This lab is suitable for chemistry, advanced biology, and biotechnology classes.
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GFP on Land and SeaThe old GFP lab (Secrets of the Rainforest) is no longer supported but the resource materials for jellyfish and GFP are available upon request.
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SDS-PAGE Protein Gel AnalysisVertical polyacrylamide gel electrophoresis of protein fractions to actually see the purification process. This lab is suitable for chemistry, advanced biology, and biotechnology classes.
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PCR Labs
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ALU PV92Introductory PCR lab where students isolate their cheek cell DNA then amplify the 300bp Alu repeat element on chromosome 16. Students use pre-formulated master and primer mixes in setting up the PCR reactions. After the PCR amplification of the Alu-PV92 locus, samples are analyzed by horizontal agarose gel electrophoresis, stained, and photographed to further analyze and record their Alu-PV92 genotypes. Teachers can post their class data of genotypes on the Allele Server at the DNA Learning Center at Cold Spring Harbor Laboratory. Tech follow-up activities include: determining whether their class is in Hardy-Weinburg equilibrium, plotting the frequency of the “+” allele on a world map, hypothesizing where geographically the insert first occurred and how it has since spread, performing Chi Square analysis to determine if two populations are significantly different, and calculating allele and genotype frequencies using the Hardy-Weinberg equilibrium equation. This lab is recommended as an intro PCR lab for all biology classes.
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Mitochondrial DNA SequencingStudents amplify the mitochondrial control region (the D-loop) from isolated cheek cell DNA to sequence a non-coding, yet variable region on their mitochondrial genomes. The teacher can send the sequencing samples to CSUEB for processing. Once the samples are processed, the sequence data is posted on the Sequence Server of the DNALC web site for the students to analyze. Initially, students can do quick comparisons of their sequences with others using simple alignments. With the sophisticated bioinformatics tools and the database at the DNALC website, students can also count the number of mutations between modern humans to calibrate a molecular clock, a powerful scientific approach in estimating the divergence between humans and Neanderthals. This laboratory is recommended for advanced biology and biotechnology elective classes.
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Wolbachia ProjectDiscover the Microbes Within! With materials and protocols based on those developed by research scientists at the Woods Hole Marine Biological Lab, this unit explores a newly discovered parasitic relationship between a feminizing bacteria, Wolbachia, and their insect hosts. With sections touching on various topics in biology, including ecology, systematics, reproductive biology, symbiotic relationships, biotechnology and bioinformatics, this lab can be incorporated into a variety of biology classes at the high school level. Students go into the field to collect insects, identify the order to which the insect belongs, extract DNA and perform PCR analysis on the insects to determine if they harbor the Wolbachia bacteria. Additional bioinformatics activities are included to analyze the nucleotide sequence of the bacteria DNA, both for students successful at identifying infected insects and and those whose insects were not parasitized by Wolbachia. A new Wolbachia Map created by UCBerkeley students allow class data to be compared across the BABEC schools. This laboratory is recommended for advanced biology and biotechnology elective classes.
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GMO PCRStudents isolate DNA from food samples and/or fresh plant tissue. Using PCR, they amplify Actin, an internal control for successful DNA isolation, and either the Bt gene or the 35S promoter element, which are two common genetic modifications in plants. Students determine the presence or absence of the GM elements in their samples and compare the results to the list of previously tested products. This laboratory is recommended for advanced biology and biotechnology elective classes to follow either Lambda or Alu.
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D1S80 VNTRStudents will amplify a VNTR (variable number of tandem repeats) locus that has 16bp units on chromosome 1 from their cheek cell DNA. Individuals may possess between 14 - 41 of these D1S80 VNTR repeats. PCR is similar to the Alu lab where master mixes and primer mixes are supplied for this amplification reaction. Following PCR, pre-cast vertical polyacrylamide gels are used for electrophoresis to better resolve the smaller fragments of D1S80 alleles. After the gels are stained and photographed, students perform linear regression analysis using Excel to determine their allele sizes. This lab is recommended for all biology and biotechnology elective classes. Please note that only universal gels are provided. If your have vertical gel boxes that require a specific type of gel, that is up to you to procure.
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Lambda PCRPCR reactions of a segment of Lambda bacteriophage. Instead of using pre-made master and primer mixes, this laboratory invites students to take a closer look at the components of PCR and reinforces the various ingredients essential for a PCR reaction. This is appropriate as an introduction to PCR or as a precursor to the advanced PCR Optimization laboratory.
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PCR OptimizationIn this advanced PCR lab, students work in teams to optimize one of the two components of a PCR reaction: MgCl2 and primer. Each team will set up a series of 7 PCR reactions containing different concentrations of MgCl2 or primer. However, students must first calculate the volumes of the various reagents they will need for each reaction, reinforcing their skills on calculating dilutions and working with different units. This exercise is very math intensive and is an excellent way to demonstrate the applicable use of mathematics in science. After PCR, electrophoresis, staining, and imaging, students will analyze their gel photos to determine the optimal primer and magnesium concentrations used for amplification of part of the calf thymus acetylcholinesterase gene. This lab is recommended for advanced biology or biotechnology elective classes after a successful completion of the Lambda PCR lab.
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Technology Labs
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Natural Products Drug DiscoveryStudents extraction bioactive chemical compounds from plants and trees around the school or from home herbal remedies. Extracts are tested in a microbial bioassay to compare zones of inhibition on bacterial and yeast plates. The components in bioactive extracts are analyzed by separation on thin-layer chromatography (TLC). Students calculate Rf values of the various spots. Great lead to independent projects and further characterization of possible active ingredients in plants. We encourage computers use for data analysis after digital camera imaging. Bioethical discussion involves the marketing of products by companies. This lab is suitable for all levels of biology, chemistry, and advanced courses or electives. Please note that this lab is only supported until the blood glucose monitor strips run out.
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Diabetes TechnologyThis lab introduces disease, nutrition, biochemistry, metabolism, and physiology/anatomy using diabetes as the focus. Students learn how to use a blood glucose meter, control solutions to calibrate the meter, and the medical device engineered behind the test strip. Reagents are provided to create unknowns in order for students to predict how a person living with diabetes has to monitor their blood glucose and to balance with diet and exercise. Numerous resource and educational materials are also provided. Lab supported by LifeScan, Inc. Bioethical discussions center around stem cell research. This lab is suitable for all levels of biology, chemistry, anatomy, physiology, nutrition and advanced courses or electives.
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Forensic ScienceEngage students in observing and documenting a crime scene, laboratory analysis of the evidence, career aspects of forensic science, evidence handling, and giving mock trial testimony as an expert witness. Labs include latent fingerprints, blood splatters, skeletal remains, trace evidence, and firearms. PCR and vertical gel electrophoresis is used to analyze the D1S80 VNTR (variable number of tandem repeats) locus (request the D1S80 Kit). Technical advances in capillary electrophoresis and STR analysis will also be covered.
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GMO-ELISA Farmer's DilemmaGMO investigation that examines corn samples with a protein ELISA dipstick. Units includes protein extraction, antibody assay, math, graphing, critical reading and ethics discussion.
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C. elegansThe C. elegans labs consist of a series of experiments designed to expose students to working concepts of a model organism and mutants as well as instruct students in microscopy, micropipetting, and digital analysis. Module 1 gives students the opportunity to observe wild-type and mutant C. elegans morphology, behavior, and life cycle. In Module 2, students study chemotaxis by determining the response of worms to a chemical odorant. In Module 3, students measure the effects of alcohol on worms using time-lapse video microscopy and statistical analysis.
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