Virtual Appendix
The following links are meant to be a "virtual appendix" to the four modules in the 7.02 laboratory manual.
Module 1: Genetics
| ONLINE RESOURCES | DESCRIPTIONs |
|---|---|
| Antibiotic Resistance | Images from Dr. Delliss' virtual Molecular Biology LabBook at College of Charleston |
| Streaked Plate Examples | "The good, the bad, and the ugly" from College of Charleston. The streaking method shown is slightly different from that used in 7.02, but a nice demonstration of single colonies! |
| Plating Cells | Examples show why we tell you to "Streak your plate to dryness!" |
| Schleif, Robert. "Regulation of the L-arabinose operon of Escherichia coli." Trends in Genetics 16, no. 12 (December 1, 2000): 559-565. | This review article, entitled "Regulation of the L-arabinose operon of Escherichia coli" describes the experiments that led to the current model of araBAD regulation and is a good source of references. |
Module 2: Protein Biochemistry
| ONLINE RESOURCES | DESCRIPTIONs |
|---|---|
| Animated Alpha Helices and Beta Sheets | These QuickTime® movies from the University of Arizona Department of Chemistry allow you to visualize these secondary structure elements in 3D. |
| Tutorial on Dilutions | From the Concepts in Biology page at Wellesley College. |
| Beer-Lambert Law (Spectrophotometry) | From Sheffield Hallam University's Division of Chemistry. |
| Search for animations on Gel Filtration Chromatography, Ion Exchange Chromatography, and Affinity Chromatography on the Amersham Biosciences web site. | From Amersham Biosciences. |
| More Chromatography Resources! | From the Laboratory Info section of the Natural Toxins Research Center at Texas A&M University-Kingsville. |
| Preparing the SDS-PAGE Precast Gel | Images from the Virtual Molecular Biology LabBook at the College of Charleston. |
| Setting up the SDS-PAGE Apparatus | Images from College of Charleston's Virtual Molecular Biology LabBook. In our lab, we will have two groups run gels on the same apparatus. |
| Gel Electrophoresis Simulator | From the Rochester Institute of Technology (RIT). |
| Short Animations on Antibody Structure and an Example of use of Antibody Staining "in situ" | From the Neurogenesis section of the Neuron Connection page at Wellesley College. |
| Michaelis-Menton Enzyme Kinetics I | From the MIT Biology Hypertextbook. Includes derivation of the Michaelis-Menton equation. |
| Enzyme Kinetics Animations | From the Concepts in Biology page at Wellesley College. |
Module 3: Recombinant DNA Methods
| ONLINE RESOURCES | DESCRIPTIONs |
|---|---|
| New England Biolabs (NEB) | NEB is a Massachusetts-company that is the leader in the isolation and production of restriction enzymes. Their Web site has a number of excellent resources related to restriction and other DNA/RNA modifying enzymes. Every laboratory scientist I know has a copy of the NEB catalog--it's just that useful! |
| Restriction Enzymes Overview | This page from New England Biolabs gives an overview of restriction enzymes, specifically their role in nature and the three types of REs (Type I, Type II, and Type III). |
| The BLAST Tutorial | Tutorial on searching online databases. |
| BLAST Tutorial Worksheet (PDF) | Download this worksheet before beginning the BLAST tutorial! |
| BLAST Tutorial Answer Key (PDF) | Answers to the BLAST tutorial worksheet. |
| DNAi | "DNA interactive" site from Cold Spring Harbor DNA Learning Center. |
| DNAi-Manipulations | Subpage of DNAi containing animations of RDM topics (restriction enzymes, ligations, PCR, etc.) |
| DNA in 3D! | This page from the University of Arizona Department of Chemistry contains some great 3D views of the DNA double helix, as well as G-C basepairing. |
| Chalfie, Martin, Yuan Tu, Ghia Euskirchen, William W. Ward, and Douglas C. Prasher. "Green Fluorescent Protein as a Marker for Gene Expression." Science 263, no. 5148 (Feb. 11, 1994): 802-805. (New Series) | The original Science paper describing GFP's use as a reporter of protein expression. |
Module 4: Development
| ONLINE RESOURCES | DESCRIPTIONs |
|---|---|
| ZFin | A University of Oregon site providing a copy of The Zebrafish Book, The Zebrafish Science Monitor, stock lists, references and many addresses of interest to the Zebrafish research community. |
| Stages of Embryonic Development of the Zebrafish | Check out this extensive reference, also at University of Oregon. |
| FishScope | Early cleavage to organ formation: Time-lapse movies of zebrafish morphogenesis. |
| An Atlas of Zebrafish Anatomy | This site shows zebrafish embryos at four different stages of development, to provide help in understanding how the zebrafish embryo looks inside. Select different developmental stages at 24h, 48h, 72h, and 120h. You will find an overview image for each stage, with links (click on numbers on image) to images of the sections. |
| Zebrafish Info Center | Why use zebrafish to study? |
| "Making a Splash with Zebrafish" | A 1997 BioScience article about the development of zebrafish as a model organism. |
| Zebrafish Drawings | A complete collection of drawings of early zebrafish development from Zfin. |
| Stages of Zebrafish Development | All links from Stages of Embryonic Development of the Zebrafish found within Zfin. |
| Glossary of Developmental Terms | From Stages of Embryonic Development of the Zebrafish from Zfin. |
| Northern Blot QuickTime® Movie (MOV - 4.6 MB) (Courtesy of Dr. Katherine Schneider. Used with permission.) | Watch this short movie detailing how to set up the Northern transfer apparatus before lab on Development session 71! |
| Hybridization Conditions for Northern and Southern Blots | This excellent resource from North Dakota State University explains the effect of salt, formamide, and extent of homology between probe and target on the effectiveness of hybridization. Written for Southern blots, but the same principles apply for northern blots. Includes formulas for calculating effective Tms. |