BISC209/S10:Schedule
From OpenWetWare
BISC209 S10 Lab Calendar
| Monday | Tuesday | Wednesday | Thursday | Friday |
|---|---|---|---|---|
| Jan.25 | Jan. 26 Lab 1 |
Jan. 27 Lab 1 |
Jan. 28 | Jan. 29 |
| Feb. 1 | Feb. 2 Lab 2 |
Feb. 3 Lab 2 |
Feb. 4 | Feb. 5 |
| Feb. 8 | Feb. 9 Lab 3 |
Feb. 10 Lab 3 |
Feb. 11 | Feb. 12 |
| Feb. 15 President's Day |
Feb. 16 Monday schedule NO LAB |
Feb. 17 NO LAB |
Feb. 18 | Feb. 19 |
| Feb. 22 | Feb. 23 Lab 4 |
Feb. 24 Lab 4 |
Feb. 25 | Feb. 26 |
| Mar. 1 | Mar. 2 Lab 5 |
Mar. 3 Lab 5 |
Mar. 4 | Mar. 5 |
| Mar. 8 | Mar. 9 Lab 6 |
Mar. 10 Lab 6 |
Mar. 11 | Mar. 12 |
| Mar. 15 | Mar. 16 Lab 7 |
Mar. 17 Lab 7 |
Mar. 18 | Mar. 19 |
| Mar. 22 Spring Break |
Mar. 23 Spring Break |
Mar. 24 Spring Break |
Mar. 25 Spring Break |
Mar. 26 Spring Break |
| Mar. 29 | Mar. 30 Lab 8 Lab Practical |
Mar. 31 Lab 8 Lab Practical |
Apr. 1 | Apr. 2 |
| Apr. 5 | Apr. 6 Lab 9 Data analysis |
Apr. 7 Lab 9 Data Analysis |
Apr. 7 | Apr. 8 |
| Apr. 12 | Apr. 13 Lab 10 Conference |
Apr. 14 Lab 10 Conference |
Apr. 15 | Apr. 16 |
| Apr. 19 Patriots' Day NO LAB |
Apr. 20 Lab 11 Presentations |
Apr. 21 Lab 11 Presentations |
Apr. 22 Monday Schedule |
Apr. 23 |
| Apr. 26 | Apr. 27 NO Lab |
Apr. 28 Rhulman NO Lab |
Apr. 29 | April 30 |
| May 3 | May 4 Lab 12 Paper Due |
May 5 Lab 12 Paper Due |
May 6 Last day of classes |
April 30 |
Assignments
BISC110 Assignments/ Weekly Lab Planner
| Lab # | LAB DATES__ | IN LAB WORK________ | OUTSIDE OF LAB WORK________ | Assignment/Notes | ||
| 1 | Tues. 1/26- Wed. 1/27 |
Introduction to Microbiology Lab Lab Safety |
Homework: Visit the greenhouse and make notes on your selected habitat (see Lab 2 Part A for how to focus your observations). Begin to research how to select/enrich for particular soil bacteria. References posted to the Lab First Class conference (Reference Folder) and lots of information in the Protocols section of the wiki. Read all of Lab 2 & outline or make flow diagrams for your lab work Answer the Questions found at the end of LAB 1 and turn them in at the beginning of Lab 2 | |||
| 2 | Tues. 2/2- Wed. 2/3 |
Soil sampling in Greenhouse habitat Begin culture of soil organisms on selective, differential and enrichment media Standard Plate Count of Culturable Soil Organisms Genomic DNA isolation for Non-Culturable Bacterial ID |
Check on your soil bacterial enrichment and selection cultures; Assess your isolation streaking; check on your plate count plates and move any in danger of overgrowing to cold room | Homework Search the web for photos of colonies of desired bacteria; Research morphology of likely members found in your soil community, differentiating metabolic needs or capabilities used for culture, habitat range, and role in the soil or in the environment of these desired groups of bacteria: cellulolytic, Actinomycetes such as the Streptomyces, Bacillus species, Fruiting myxobacteria, Gliding bacteria such as Beggiotoa, Azotobacter, Aerobic methanol oxidizers, Sulfur oxidizers, Nitrosomonas, and Nitrobacter | ||
| 3 | Tues. 2/9- Wed. 2/10 |
Identification of Unculturable Bacterial by 16S rDNA sequencing: Assess success of soil DNA isolation using Nanodropper to measure DNA conc.; Dilute or conc. DNA isolate to 100ng/μL; PCR Amplification of 16S rDNA with "universal" bacterial primers and proofreading polymerase PCR product clean-up Run a gel of your cleaned-up pcr product to assess the success of your amplification. Instructor will finish, photograph it and post the results to the data file in First Class Lab conference Isolation of Culturable Bacteria: Complete Standard Plate Count counting & calculation |
Check on cultures and continue isolation | Homework: Write up your procedure for genomic DNA isolation and amplification of 16S rDNA from a soil sample as a Materials & Methods section for your final scientific paper. Use the information in the Methods section in the "Guidelines for Science Writing" handout found in the Resources section of the wiki and/or model your protocol descriptions like those in the journal articles in the References folder on the First Class Lab Conference. | ||
| 4 | Tues. 2/23- Wed. 2/24 |
Identification of Unculturable Bacterial by 16S rDNA sequencing: Clone 16s rDNA from successful pcr products into cloning vector Transform cloning vector into E. coli and select for transformants on selective media. Isolation of Culturable Bacteria: Examine enrichment and selective media and pick unique isolated colonies of your soil bacteria to make 2 fresh slants per organism. |
Continue isolation and identification of soil bacteria; Check to see if you have E. ooli transformants on your selection plates. If not, contact your instructor. |
Homework: Write the Introduction section of your final paper. Use the Introduction section of the "Guidelines for Science Writing" handout found in the Resources section of the wiki and model your protocol descriptions like those in the journal articles in the References folder on the First Class Lab Conference. You will need to cite sources in the Name/Year style of the journal Cell. See the Wellesley library e-data base for recent issues of this journal to use as models for your citations. | ||
| 5 | Tues. 3/2- Wed. 3/3 |
Identification of Unculturable Bacterial by 16S rDNA sequencing:Select 48/per pair (96 per soil habitat) well-isolated, transformants from selective media and grow in broth overnight. Isolation & Id of Culturable Bacteria: Make new stock slants from each of your pure cultures of your soil bacteria. Perform stains, physical, metabolic and morphologic tests to differentiate soil bacteria. |
Prepare glycerol stocks of overnight cultures of transformed bacteria to send away frozen for 16S rDNA sequencing. Results should be back within 2 weeks. | Homework: Write the following protocols as M&M sections for your final paper (You may refer to your organisms by a code number or group name if you don't yet know the genus and species name: Isolation of soil bacteria to pure culture & ID of cultured soil organisms by DNA sequencing | ||
| 6 | Tues.3/9. - Wed. 3/10 |
Isolation & Id of Culturable Bacteria: Perform physical characteristics tests: start a motility test by inoulating SIM tube or a soft agar deep; perform other differentiating tests as needed. Start the ID of Cultured Bacteria by 16srDNA Sequencing and Analysis: Prepare lysates from pure colonies of your soil organisms of interest; pcr amplification of lysate DNA using "universal" bacterial primers and Taq polymerase. |
Complete or set up differential tests for bacterial id as needed. | Homework: Partial Results section with figures/tables: Staining & Morphology of Culturable Soil Bacteria. (You may refer to each organism with a group name or code number if you haven't completed your identification.) Refer to the Results section (including the information on effective figure design and how to write figure legends in the "Guidelines for Science Writing" found in the Resources section of the wiki. Using other published journal articles as models is also an effective way to learn to write a good results analysis. | ||
| 7 | Tues. 3/16- Wed. 3/17 |
16S rDNA sequencing: Clean-up pcr products and run a gel to assess success at amplification of 16s rDNA from each of your soil bacteria to id. Cultured bacteria ID: Read last weeks tests; Continue with new differential ID tests; Start Antibiotic sensitivity and nitogen recycling tests; add other "role" tests as needed. |
Complete, read, or set up differential tests for bacterial id as needed. | Homework: Study for your Lab Practical that will be given in the first part of Lab 8. Your instructor will give you more instructions about what that test will include and how to study. | ||
| 8 | Tues. 3/30- Wed. 3/31 |
Lab Practical Cont. Cultured bacteria ID: cont. with tests to differentiate and id your cultured bacteria. |
The Prokaryotes]through Springer ebooks; Link to the electronic edition of | Bergey's Manualsthrough Springer ebooks | |||
| 9 | Tues. 4/6- Wed. 4/7 |
Meet in a computer lab (TBA) for data analysis of your 16S rDNA sequencing results. | Complete tests to ID cultured bacteria | Homework: Analyze your sequencing data and write a partial Results section with figures/tables on the Soil Community Diversity Results from 16S rDNA sequencing of the soil genomic DNA (you do not have to include the 16S rDNA sequencing results of the cultured bacteria) | ||
| 10 | Tues. 4/13- Wed. 4/14 |
Conference with your instructor to discuss your data analysis, poster presentation or your progress on your final paper. | Homework: Prepare your group (4 students- 1 habitat) "virtual" poster presentation to be presented in LAB 11 | |||
| 11 | Tues. 4/20- Wed. 4/22 |
"Virtual" Poster presentation in groups by habitat | Homework: Write your final paper in the form of a scientific paper. See the Resources section for an extensive handout on How to Write in Scientific Style and a link to Wellesley Library information | |||
| 12 | Tues. 5/4- Wed. 5/5 |
Final Paper due by 5pm on your lab day
|
End of lab | |||
Links to Labs
Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10
Lab11
Lab 12
