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| {{Template:BISC220/S10}} | | {{Template:BISC220/S10}} |
| <div style="padding: 10px; width: 720px; border: 5px solid #66999;"> | | <div style="padding: 10px; width: 720px; border: 5px solid #669999;"> |
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| ==BISC220 S10 Lab Calendar== | | ==BISC220 S10 Lab Calendar== |
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| |- | | |- |
| | Jan. 25 <br><br> | | | Jan. 25 <br><br> |
| | Jan. 26 <br>Lab 1<br> Enzymes 1 ||Jan. 27 <br> Lab 1<br> Enzymes 1 || Jan. 28 <br> Lab 1<br> Enzymes 1 || Jan. 29 <br><br> || | | | Jan. 26 <br>Lab 1<br> Enzymes 1 |
| | | Jan. 27 <br> Lab 1<br> Enzymes 1 |
| | | Jan. 28 <br> Lab 1<br> Enzymes 1 |
| | | Jan. 29 <br><br> |
| |- | | |- |
| | Feb. 1<br><br> | | | Feb. 1<br><br> |
| | Feb. 2 <br>Lab 2 <br> Enzymes 2|| Feb. 3 <br>Lab 2<br>Enzymes 2 || Feb. 4 <br>Lab 2<br>Enzymes 2 || Feb. 5 <br><br> || | | | Feb. 2 <br>Lab 2 <br> Enzymes 2 |
| | | Feb. 3 <br>Lab 2<br>Enzymes 2 |
| | | Feb. 4 <br>Lab 2<br>Enzymes 2 |
| | | Feb. 5 <br><br> |
| |- | | |- |
| | Feb. 8 <br><br> | | | Feb. 8 <br><br> |
| | Feb. 9 <br>Lab 3<br> Enzymes 3 || Feb. 10 <br>Lab 3<br> Enzymes 3 || Feb. 11 <br>Lab 3<br> Enzymes 3 ||Feb. 12 <br><br> || | | | Feb. 9 <br>Lab 3<br> Enzymes 3 |
| | | Feb. 10 <br>Lab 3<br> Enzymes 3 |
| | | Feb. 11 <br>Lab 3<br> Enzymes 3 |
| | | Feb. 12 <br><br> |
| |- | | |- |
| | Feb. 15 <br><br> | | | Feb. 15 <br>'''President's Day'''<br> |
| | Feb. 16 <br>'''Monday Schedule'''<br> '''NO LAB''' || Feb. 17 <br> '''NO LAB''' <br> || Feb. 18 <br> '''NO LAB''' <br>|| Feb. 19 <br><br>|| | | | Feb. 16 <br>'''Monday Schedule'''<br> '''NO LAB''' |
| | | Feb. 17 <br> '''NO LAB''' <br> |
| | | Feb. 18 <br> '''NO LAB''' <br> |
| | | Feb. 19 <br><br> |
| |- | | |- |
| | Oct. 5 <br>Lab 4 | | | Feb. 22 <br><br> |
| | Oct. 6 <br>Lab 5 || Oct. 7 <br>Lab 5 || Oct. 8 <br>Lab 5 || Oct. 9 <br>Lab 5 || | | | Feb. 23 <br>Lab 4 <br> Enzymes 4 |
| | | Feb. 24 <br>Lab 4 <br> Enzymes 4 |
| | | Feb. 25 <br>Lab 4 <br> Enzymes 4 |
| | | Feb. 26 <br><br> |
| |- | | |- |
| | Oct. 12 <br>'''Fall Break''' <br> '''No Lab''' | | | Mar. 1 <br> <br> |
| | Oct. 13 <br>'''No Lab''' || Oct. 14 <br> '''Wed. follows Mon.<br> Schedule''' <br>Lab 5 || Oct. 15 <br>'''No Lab''' || Oct. 16 <br>'''No Lab'''|| | | | Mar. 2 <br>Lab 5 <br> '''Science Writing''' |
| | | Mar. 3 <br> Lab 5 <br> '''Science Writing''' |
| | | Mar. 4 <br>Lab 5 <br> '''Science Writing''' |
| | | Mar. 5 <br><br> |
| |- | | |- |
| | Oct. 19 <br>Lab 6 | | | Mar. 8 <br><br> |
| | Oct. 20 <br>Lab 6 || Oct. 21 <br>Lab 6 || Oct. 22 <br>Lab 6 || Oct. 23 <br>Lab 6|| | | | Mar. 9 <br>Lab 6<br> Yeast 1<br> '''''Paper 1 due''''' |
| | | Mar. 10 <br>Lab 6<br> Yeast 1<br> '''''Paper 1 due''''' |
| | | Mar. 11 <br>Lab 6<br> Yeast 1<br> '''''Paper 1 due''''' |
| | | Mar. 12 <br><br> |
| |- | | |- |
| | Oct. 26 <br>Lab 7 | | | Mar. 15 <br><br> |
| | Oct. 27 <br>Lab 7 || Oct. 28 <br>Lab 7 || Oct. 29 <br>Lab 7 || Oct. 30 <br>Lab 7|| | | | Mar. 16 <br>Lab 7<br> Yeast 2 |
| | | Mar. 17<br>Lab 7<br>Yeast 2 |
| | | Mar. 18 <br>Lab 7<br> Yeast 2 |
| | | Mar. 19 <br><br> |
| |- | | |- |
| | Nov. 2 <br>'''No Monday Lab''' | | | Mar. 22 <br>'''Spring Break''' |
| | Nov. 3 <br> '''Tanner Conference''' <br> '''No Lab''' || Nov. 4 <br>Lab 8 || Nov. 5 <br>Lab 8 || Nov. 6 <br>Lab 8|| | | | Mar. 23 <br> '''Spring Break''' |
| | | Mar. 24 <br>'''Spring Break''' |
| | | Mar. 25 <br>'''Spring Break''' |
| | | Mar. 26 <br>'''Spring Break''' |
| |- | | |- |
| | Nov. 9 <br> Lab 8 | | | Mar. 29 <br> <br> |
| | Nov. 10 <br>Lab 8 || Nov. 11 <br>Lab 9 || Nov. 12 <br>Lab 9 || Nov. 13 <br>Lab 9|| | | | Mar. 30 <br>Lab 8 <br> Yeast 3 |
| | | Mar. 31 <br>Lab 8 <br> Yeast 3 |
| | | April 1 <br>Lab 8 <br> Yeast 3 |
| | | April 2 <br><br> |
| |- | | |- |
| | Nov. 16 <br> Lab 9 | | | April 5 <br> <br> |
| | Nov. 17 <br>Lab 9 || Nov. 18 <br>Lab 10 || Nov. 19 <br>Lab 10 || Nov. 20 <br>Lab 10|| | | | April 6 <br>Lab 9 <br> Cell Culture |
| | | April 7 <br>Lab 9 <br> Cell Culture |
| | | April 8 <br>Lab 9 <br> Cell Culture |
| | | April 9 <br><br> |
| |- | | |- |
| | Nov. 23 <br> Lab 10 | | | April 12 <br> |
| | Nov. 24 <br>Lab 10 || Nov. 25 <br>'''No Lab''' || Nov. 26 <br>'''Thanksgiving Holiday'''|| Nov. 27 <br>'''Thanksgiving Holiday'''<br> '''No Lab'''|| | | | April 13<br>Lab 10 <br> Cytoskeleton 1 <br> '''''Paper 2 due''''' |
| | | April 14 <br>Lab 10 <br> Cytoskeleton 1 <br> '''''Paper 2 due''''' |
| | | April 15 <br>Lab 10 <br> Cytoskeleton 1 <br> '''''Paper 2 due''''' |
| | | April 16 <br><br> |
| |- | | |- |
| | Nov. 30 <br> Lab 11 | | | April 19 <br> '''Patriot's Day''' |
| | Dec. 1 <br>Lab 11 || Dec. 2 <br>Lab 11 || Dec. 3 <br>Lab 11 || Dec. 4 <br>Lab 11|| | | | April 20 <br>Lab 11<br> Cytoskeleton 2 |
| | | April 21 <br>Lab 11 <br> Cytoskeleton 2 |
| | | April 22 <br>'''Monday Schedule''' |
| | | April 23 <br><br> |
| |- | | |- |
| | Dec. 7 <br> Lab 12 | | | April 26 <br> <br> |
| | Dec. 8 <br>Lab 12 || Dec. 9 <br>Lab 12 || Dec. 10 <br>Lab 12 || Dec. 11 <br>Lab 12|| | | | April 27 <br>Lab 12<br> Presentations |
| | | April 28 <br> '''Rhulman'''<br> '''NO LAB''' |
| | | April 29 <br>Lab 12 <br> Presentations |
| | | April 30 <br><br> |
| | |- |
| | | May 3 <br><br> |
| | | May 4 <br> '''NO LAB''' |
| | | May 5 <br> Lab 12 <br> Presentations |
| | | May 6 <br> '''Last day of classes''' <br> '''''Paper 3 due''''' |
| | | May 7 <br><br> |
| |- | | |- |
| |} | | |} |
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| |- | | |- |
| ! 1 | | ! 1 |
| | Gene Mapping | | | Enzyme Structure/Function |
| | 1-5 | | | 1-5 |
| |- | | |- |
| !2 | | !2 |
| | RNA interference | | | Yeast Genetics and the Secretory Pathway |
| | 5-8 | | | 6-8 |
| |- | | |- |
| !3 | | !3 |
| | Plant Genetic Engineering | | | Cell Culture and the Cytoskeleton |
| | 1,4,7-10 | | | 9-12 |
| |- | | |- |
| |} | | |} |
| | <br> |
| | <br> |
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| ==Graded Assignments== | | ==Graded Assignments== |
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| |+ | | |+ |
| ! Lab Assigned !! Lab Due !! Assignment<br> description !! Point Value <br>(Total 200) | | ! Lab Assigned !! Lab Due !! Assignment<br> description !! Point Value <br>(Total 200) |
| | |- |
| | ! Lab 1 |
| | | Lab 2 |
| | | RasMol/ClustalW |
| | | 10 |
| |- | | |- |
| ! Lab 2 | | ! Lab 2 |
| | Lab 3 | | | Lab 3 |
| | Autosomal vs. X-linked analysis | | | Calculations from Lab 2 |
| | | 10 |
| | |- |
| | ! Lab 3 |
| | | Lab 4 |
| | | Calculations from Lab 3 |
| | 15 | | | 15 |
| |- | | |- |
| ! Lab 5 | | ! Lab 4 |
| | Friday, October 23rd by 5 pm | | | Lab 6 <br> Week of March 8th |
| | Gene Mapping Paper | | | β-galactosidase paper |
| | 40 | | | 40 |
| |- | | |- |
| ! Lab 5 | | ! Lab 6 |
| | Wednesday, October 14th by 5 pm <br> | | | Lab 7 |
| '''Monday Lab ONLY:''' Monday October 19th by 5 pm<br>
| | | Yeast growth predictions/BLAST |
| |Materials and Methods Write-up: <br> Two M&M sections for your paper | |
| | 15 | | | 15 |
| |- | | |- |
| ! Lab 8 | | ! Lab 8 |
| | Lab 9 | | | Lab 10 <br> Week of April 12 |
| | Sequence Analysis write up
| | | Yeast Secretory Pathway Paper |
| | 10
| |
| |- | |
| ! Lab 8
| |
| | Tuesday, November 17th by 5 pm
| |
| | RNAi paper - Full paper
| |
| | 45 | | | 45 |
| |- | | |- |
| ! Lab 9 | | ! Lab 10 |
| | Wednesday, December 2nd by 5 pm | | | Lab 12 |
| | Revision of Paper #2 | | | Cytoskeleton Imaging Oral Presentations |
| | 20 | | | 25 |
| |- | | |- |
| ! Lab 10 | | ! Lab 11 |
| | Friday, December 11th by 5 pm | | | May 6 - Last Day of Classes |
| | Transgenic Plant Paper - Science Style | | | Cytoskeleton Partial Paper |
| | 50 | | | 35 |
| |- | | |- |
| ! Other | | ! Other |
| | | | | |
| | Discretionary Points: <br> Preparation & Participation | | | "P" Points - Participation and Preparation |
| | 5 | | | 5 |
| |- | | |- |
| |} | | |} |
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| <br>
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| ==BISC219 F09 Weekly Lab Planner==
| |
| {| border="1"
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| |+
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| ! '''Lab''' !! '''Date''' !! '''In-Lab Work''' !! '''Outside of Lab Work''' !! '''Assignment'''
| |
| |-
| |
| ! 1
| |
| | Tues. 9/9 to <br>Mon. 9/14
| |
| | Start tobacco transformation <br><br>Examine ''C. elegans'' and learn to identify the stages and sexes <br><br> Practice picking worms<br><br>Set up your first crosses to examine autosomal vs. X-linkage ('''3 plates total)''' <br><br> Perform a mutant hunt: Pick (3) Dumpy mutants to separate plates ('''3 plates total''')
| |
| |3-5 days after Lab 1 transfer tobacco leaf tissue to new media '''''with''''' antibiotics<br><br> 3-4 days after setting up your crosses pick 2 wild type worms from each autosomal vs. X-linked cross to new plates ('''3 plates total''') be sure to examine the F1 progeny taking note of male and hermaphrodite phenotypes <br><br> Examine mutants from hunt - check phenotype. If '''Dumpy''' then cross L4 mutant hermaphrodites by L4 wild type (N2) males ('''2 plates - duplicates''')
| |
| | Familiarize yourself with the information in the [[BISC_219/2009:Resources]] section. <br><br> Read the Introduction, Tools and Techniques, and first two labs in the '''Gene Mapping''' series: [[BISC 219/2009:Gene Mapping]]<br><br>Read the Background and Creating the Transgenic Plants in the '''Creating a Transgenic Organism''' series: [[BISC 219/2009:Creating a Transgenic Organism]]
| |
| |-
| |
| ! 2
| |
| | Tue. Sept. 15 to <br> Mon. Sept 21
| |
| | Calibrate micropipettes <br><br>Count and examine phenotypes of autosomal vs. X-linked crosses <br><br> '''Linkage''': cross males from last cross to the (4) test strains ('''4 plates total''')
| |
| |'''3 days after lab:'''<br> '''Linkage''': transfer (2) L4 hermaphrodites from each cross to 2 new plates ('''8 plates total''')
| |
| | '''Homework:'''Data Analysis (Results)of your autosomal vs. X-linked testing (15pt) due next lab. Grading rubric & Assignment info at: [[BISC_219: Assignment Help- Data Analysis 1]]
| |
| |-
| |
| ! 3
| |
| | Tues. Sept. 22 to <br> Mon. Sept. 28
| |
| | '''Linkage''': examine phenotypes and count to determine linkage <br><br> '''Mapping''': pick (5) Dpy worms from linkage plate to separate plates ('''5 plates total''')
| |
| | '''3 days after lab:''' <br> '''Mapping''': Pick (3) double mutants to separate plates ('''3 plates total''')<br><br> '''Complementation''': Cross Dpy mutant worms to N2 males ('''2 plates total''')
| |
| | '''Homework:''' Read journal article #1 for discussion in Lab 4: Bruinsma et al., Identification of Mutations in Caenorhabditis elegans That Cause Resistance to High Levels of Dietary Zinc and Analysis Using a Genomewide Map of Single Nucleotide Polymorphisms Scored by Pyrosequencing. ''Genetics.'' 2008 June; 179(2): 811–828.
| |
| doi: 10.1534/genetics.107.084384. Full text available from PubMed or from Wellesley College Library at [http://luna.wellesley.edu/search~S3?/tGenetics/tgenetics/1,42,45,B/l856~b1919161&FF=tgenetics&2,,4,2,0]
| |
| |-
| |
| ! 4
| |
| | Tues. Sept. 29 to <br> Mon. Oct. 5
| |
| | '''Plant''': Transfer tobacco shoots to root inducing medium <br><br> '''Mapping''': cross N2 males with double mutants ('''2 plates total''')<br><br>'''Complementation''': pick males from complementation cross #1 and mate with known Dpy strains ('''4 plates total''') <br><br> '''RNAi''': pick a single colony – circle and save for next week <br><br> Discuss Paper #1
| |
| | '''3 days after lab:'''<br> '''Mapping''': pick 3-4 males from previous cross to 2 plates and cross with d u/d u hermaphrodites for a test cross ('''2 plates total''') <br><br> '''Complementation''': examine cross plates for Dpy males <br><br> Set up an overnight culture of your colony on the day before next lab
| |
| | '''Homework:''' Start working on Mapping Partial Paper (Introduction section). See [[BISC_219/2009:Resources]] and [[BISC_219: Assignment Help- Partial Paper Mapping]] for help.
| |
| |-
| |
| ! 5
| |
| | Tues. Oct. 6 to<br> Wed. Oct. 14
| |
| | '''Mapping''': SCORE <br><br> '''RNAi''': Plasmid DNA isolation (mini-prep) <br><br> Transform the miniprep into the feeding bacterial strain
| |
| | Determine map distance between your mutant gene and the known reference mutation. <br><br> Make sure all transformations are successful. If not, contact instructor to problem solve <br><br> '''The day before lab''': Set up an overnight culture of your transformation
| |
| | '''Homework:''' Work on Gene Mapping Partial paper – Title, Abstract, Intro, Results, References – '''due 10/23'''. See [[BISC_219/2009:Resources]] and [[BISC_219: Assignment Help- Partial Paper Mapping]] for help. <br><br> Write up practice M &M sections (15 points) on plasmid isolation and transformation [[BISC_219: Assignment Help- Materials and Methods]] – '''due Wednesday October 14th by 5 pm'''<br><br>
| |
| Read journal articles:<br>
| |
| 1) Fire et al, ''Potent and specific genetic interference by ds RNA in C. elegans'' in ''Nature'' Feb.19,1998 Vol.391 pages 806-811 (doi:10.1038/nature07759. Available at: [http://www.nature.com/nature/journal/v391/n6669/index.html]<br>
| |
| 2)Steiner and Plasterk's preview of the Yigid article, ''Knocking out the Argunautes'', found in ''Cell'' 127, Nov. 17, 2006, DOI: doi:10.1016/j.cell.2006.11.004 available at: [http://www.cell.com/archive?year=2006]<br>
| |
| 3) Yigid et al, ''Analysis of the C. elegans Argonaute Family Reveals that Distinct Argonautes Act Sequentially during RNAi'' in ''Cell'' Volume 127, Issue 4, 17 November 2006, Pages 747-757, (doi:10.1016/j.cell.2006.09.033), available at [http://www.cell.com/archive?year=2006] for discussion in Lab 6.
| |
| |-
| |
| ! 6
| |
| | Mon. Oct. 19 to <br> Fri. Oct. 23
| |
| | '''RNAi''': induction of bacteria for RNAi feeding <br><br> Seed plates with induced bacteria and allow to dry <br><br> Paper discussion
| |
| | '''4 days after lab:'''<br> Add 2 L4 worms to your plates – N2, ''rrf-3''
| |
| | '''Homework''': Gene Mapping partial paper due Friday October 23rd by 5 pm for all students
| |
| |-
| |
| ! 7
| |
| | Mon. Oct. 26 to <br> Fri. Oct. 30
| |
| | '''Plant''':Transfer plantlets to soil and remove them from their sterile world <br><br> '''RNAi''': examine the three sets of worms and determine their phenotypes <br>
| |
| Set up single worm PCR RNAi treated and mutant worms <br><br> Run agarose gel of PCR results <br><br> Practice sequencing data analysis with ''Sequencher'' software
| |
| | Complete Practice sequencing exercise
| |
| | '''Homework''': Work on M&M revisions for RNAi paper and additional M&M protocols
| |
| |-
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| ! 8
| |
| | Wed. Nov. 4 to <br> Tues. Nov. 10
| |
| | '''RNAi''': Clean up PCR reactions <br><br> Run sequencing reaction and cleanup (columns)<br><br> Load samples into
| |
| Sequencer <br><br> '''Plants''': Plant chromosomal DNA extraction from leaf tissue <br><br> PCR amplification of transgene <br><br> Histochemical GUS enzyme activity assay
| |
| | Instructors will post your sequencing data to the conference – analyze your results<br><br> Examine and score histochemial data according to instructors directions
| |
| | '''Homework''': Write up practice sequencing data analysis (10 points). [[BISC_219: Assignment Help- Sequence Analysis]]<br> Due in lab next week.<br>
| |
| Read for next lab: Apse, G.P., Aharon, G.S., Snedden, W.A., Blumwald, E. "Salt Tolerance Conferred by Overexpression of a Vacuolar Na+/H+ Antiport in Arabidopsis" ''Science'' (1999) 285: 1256-1258. Available at: http://www.sciencemag.org/cgi/content/full/285/5431/1256 or in pdf form at http://0-www.sciencemag.org.luna.wellesley.edu:80/cgi/reprint/285/5431/1256.pdf and the ''Science'' perspectives article by Frommer ''Taking Transgenic Plants with a Pinch of Salt, '' Science 20 August 1999: Vol. 285. no. 5431, pp. 1222 - 1223. DOI: 10.1126/science.285.5431.1222 at [http://0-www.sciencemag.org.luna.wellesley.edu/cgi/content/full/285/5431/1222]
| |
| <br>
| |
| and Uddin MI et al., "Overexpression of a New Rice Vacuolar Antiporter Regulating Protein OsARP Improves Salt Tolerance in Tobacco". ''Plant and Cell Physiology'' (2008), Volume 49, Number 6 Pp. 880-890. Available at: http://pcp.oxfordjournals.org/cgi/content/full/49/6/880 <br>
| |
| and a Feb. 5, 2002 Boston Globe'' article by ME Malone, ''SCIENTISTS FOCUS ON THE TOBACCO PLANT AS A POSSIBLE CANCER-FIGHTER GENETICALLY ALTERED CROPS MAY SOMEDAY PRODUCE DRUGS TO COMBAT MANY DISEASES''. Available from Lexus/Nexus Academic http://0-www.lexisnexis.com.luna.wellesley.edu/us/lnacademic/search/flap.do?flapID=news&random=0.7807457835138732
| |
| <br><br> Work on Paper #2 – Full Paper – Title, Abstract, Intro, Materials and Methods, Results, Discussion, References – [[BISC_219: Assignment Help- RNAi full paper]]- DUE Nov. 17th at 5 pm
| |
| |-
| |
| ! 9
| |
| | Wed. Nov. 11 to <br> Tues. Nov. 17
| |
| | '''Plants''': Restriction enzyme digest of PCR reactions <br><br> Agarose gel electrophoresis of cut PCR product<br><br> Paper Discussion #3
| |
| | _
| |
| | Work on Paper #2 – Full Paper – Title, Abstract, Intro, Materials and Methods, Results, Discussion, References – [[BISC_219: Assignment Help- RNAi full paper]]- DUE Nov. 17th at 5 pm
| |
| |-
| |
| ! 10
| |
| | Wed. Nov. 18 to <br> Tues. Nov. 24
| |
| | '''Plants:'''Spectrophotometric GUS enzyme activity assay <br><br> Phenotypic analysis of plants<br><br> Paper #2 review returned in lecture 11/24 for revision<br>Discuss ''The Science of Science Writing'' by Gopen and Swan from the ''American Scientist'' (Nov.-Dec. 1990, Vol78, 550-558 (Available in the E-Reserves folder on the BISC219 course First Class) conference
| |
| | _
| |
| | '''Homework''': Analyze all data & create figures/tables from course ''gusA'' and GUS data for the Workshop. Assignment help at [[BISC 219/2009: Mod 3 Analyzing the data on the putative transgenic and control plants]]<br>
| |
| <br><br> Work on revision of Paper #2 for resubmission by 12/2 at 5 pm<br>
| |
| |-
| |
| ! 11
| |
| | Mon. Nov. 30 to<br> Fri. Dec 4
| |
| | '''Data Analysis''':Effective Figure Design Workshop
| |
| | _
| |
| | '''Homework''': Write final paper on Genetic Engineering in ''Science'' style'''. Due: December 11, 2009 by 5 pm'''. Instructions at [[BISC 219: Assignment Help- Transgenic plants research report ]]
| |
| |-
| |
| ! 12
| |
| | Mon. Dec.7 to <br> Fri. Dec. 11
| |
| | TBA
| |
| | TBA
| |
| | TBA
| |
| |-
| |
| |}
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| <br>
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| <br>
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| </div>
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