BISC209/S12:Schedule: Difference between revisions

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! Monday    !! Tuesday    !! Wednesday !! Thursday  !! Friday   
! Monday    !! Tuesday    !! Wednesday !! Thursday  !! Friday   
|-
|-
| Jan.23 || Jan. 24   No Lab|| Jan. 25<br> Classes begin<br> No Lab || Jan. 26 || Jan. 27
| Jan.23 || Jan. 24 <BR>  '''No Lab'''|| Jan. 25<br> Classes begin<br> '''No Lab''' || Jan. 26 || Jan. 27
|-
|-
| Jan. 30 || Jan. 31 <br>Lab 1 || Feb. 1 <br>Lab 1 || Feb. 2 || Feb. 3  
| Jan. 30 || Jan. 31 <br>'''Lab 1''' || Feb. 1 <br>'''Lab 1''' || Feb. 2 || Feb. 3  
|-
|-
| Feb. 6 || Feb. 7 <br>Lab 2 ||  Feb. 8 <br>Lab 2 ||Feb. 9 || Feb. 10  
| Feb. 6 || Feb. 7 <br>'''Lab 2''' ||  Feb. 8 <br>'''Lab 2''' ||Feb. 9 || Feb. 10  
|-  
|-  
| Feb. 13|| Feb. 14 <br>Lab 3||  Feb. 15 <BR> Lab 3|| Feb. 16 ||  Feb. 17  
| Feb. 13|| Feb. 14 <br>'''Lab 3'''||  Feb. 15 <BR>'''Lab 3'''|| Feb. 16 ||  Feb. 17  
|-
|-
| Feb. 20 <br>'''Presidents' <br>Day''' || Feb. 21 <br> Lab 4||  Feb. 22 <br>Lab 4 || Feb. 23<br>Monday Schedule ||  Feb. 24
| Feb. 20 <br>'''Presidents' Day''' || Feb. 21 <br>'''Lab 4'''||  Feb. 22 <br>'''Lab 4''' || Feb. 23<br>'''Monday Schedule''' ||  Feb. 24
|-
|-
| Feb. 27 || Feb. 28 <br> Lab 5 ||  Feb. 29 <br>Lab 5 || Mar. 1 ||  Mar. 2   
| Feb. 27 || Feb. 28 <br>'''Lab 5''' ||  Feb. 29 <br>'''Lab 5''' || Mar. 1 ||  Mar. 2   
|-
|-
| Mar. 5 || Mar. 6  <br>Lab 6 ||  Mar. 7 <br>Lab 6 || Mar. 8 || Mar. 9  
| Mar. 5 || Mar. 6  <br>'''Lab 6''' ||  Mar. 7 <br>'''Lab 6''' || Mar. 8 || Mar. 9  
|-
|-
| Mar. 12 || Mar. 13  <br>Lab 7 ||  Mar. 14 <br>Lab 7 || Mar. 15 || Mar. 16  
| Mar. 12 || Mar. 13  <br>'''Lab 7''' ||  Mar. 14 <br>'''Lab 7''' || Mar. 15 || Mar. 16  
|-
|-
| Mar. 19<br> '''Spring Break'''  || Mar. 20<br> '''Spring Break'''  ||  Mar. 21<br> '''Spring Break'''  || Mar. 22<br> '''Spring Break''' ||  Mar. 23<br> '''Spring Break'''   
| Mar. 19<br> '''Spring Break'''  || Mar. 20<br> '''Spring Break'''  ||  Mar. 21<br> '''Spring Break'''  || Mar. 22<br> '''Spring Break''' ||  Mar. 23<br> '''Spring Break'''   
|-
|-
| Mar. 26 || Mar. 27 <br> Lab 8||  Mar. 28 <br>Lab 8 || Mar. 29 ||  Mar. 30  
| Mar. 26 || Mar. 27 <br>'''Lab 8'''||  Mar. 28 <br>'''Lab 8''' || Mar. 29 ||  Mar. 30  
|-
|-
| Apr. 2 || Apr. 3  <br>Lab 9<BR> '''Lab Practical''' ||  Apr. 4 <br>Lab 9<BR> '''Lab Practical'''|| Apr. 5 ||  Apr. 6
| Apr. 2 || Apr. 3  <br>'''Lab 9'''<BR> '''Lab Practical'''<BR> start 1pm today ||  Apr. 4 <br>'''Lab 9'''<BR> '''Lab Practical'''|| Apr. 5 ||  Apr. 6
|-
|-
| Apr. 9 || Apr. 10  <br>Lab 10<br>'''Data Analysis & Science Writing Workshop''' ||  Apr. 11<br> Lab 10<br>'''Data Analysis & Science Writing Workshop'''|| Apr. 12 ||  Apr. 13
| Apr. 9 || Apr. 10  <br>'''Lab 10'''<br>'''Data Analysis &<BR> Paper & Presentation Workshop I'''<BR> start 1PM today ||  Apr. 11<br>'''Lab 10'''<br>'''Data Analysis &<BR> Paper & Presentation Workshop I'''|| Apr. 12 ||  Apr. 13
|-
|-
| Apr. 16 <br>'''Patriots' Day''' || Apr. 17  <br> '''Science Writing Workshop II''' ||  Apr. 18 <BR>'''Science Writing Workshop II''' || Apr. 19||  Apr. 20<br>'''Monday Schedule'''
| Apr. 16 <br>'''Patriots' Day''' || Apr. 17  <br>'''Lab 11'''<br> '''Paper & Presentation Workshop II''' ||  Apr. 18<BR>'''Lab 11''' <BR>'''Paper & Presentation Workshop II''' || Apr. 19||  Apr. 20<br>'''Monday Schedule'''
|-
|-
| Apr. 23  || Apr. 24 <br>Lab 12<br>'''NO Lab'''<BR>'''Paper Due''' ||  Apr. 25 <br>'''Rhulman'''<br>'''NO Lab'''<br>'''Paper Due''' || Apr. 26 ||  April 27
| Apr. 23  || Apr. 24 <br>'''NO Lab'''<BR>'''Paper Due''' ||  Apr. 25 <br>'''Rhulman'''<br>'''NO Lab'''<br>'''Paper Due''' || Apr. 26 ||  April 27
|-
|-
| Apr. 30  || May 1 <br>'''Presentations''' ||  May 2 <br>'''Presentations''' || May 3 ||  May 4<br> '''Last day of<br> classes'''  
| Apr. 30  || May 1 <br>'''Lab 12'''<br>'''Presentations''' rm 264 ||  May 2 <br>'''Lab 12'''<br>'''Presentations''' rm 264 || May 3 ||  May 4<br> '''Last day of<br> classes'''  
|}
|}


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|'''Lab #'''
|'''Lab #'''
|'''LAB DATES__'''
|'''LAB DATES__'''
|'''IN LAB WORK________'''
|'''IN LAB WORK__________________'''
|'''OUTSIDE OF LAB WORK________'''
|'''OUTSIDE OF LAB WORK________'''
|'''Assignment/Notes'''
|'''Assignment/Notes'''
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|--
|--
| 1
| 1
| Tues. 1/25-<br>Wed. 1/26
| Tues. 1/31-<br>Wed. 2/1
|Introduction to Microbiology Lab<br>
|Introduction to Microbiology Lab<br>
Lab Safety<br>
Lab Safety<br>
Tools and Techniques of Microbiologist: Aseptic Transfer,<br>  
Tools and Techniques of Microbiologist: Aseptic Transfer,<br>  
Intro to Microbial Diversity Project:Soil sampling in Greenhouse habitat;Begin culture of soil organisms: make soil extract and begin enrichment for ''Azotobacter'' and ''Hypomicrobia bacteria''; <BR> Start Plate Count of Culturable Soil Organisms<BR><br>
Intro to Soil Microbial Community Project:Soil sampling in Greenhouse habitat;Begin culture of soil organisms: make soil extract and begin enrichment for selected bacteria; <BR> Start Plate Count of Culturable Soil Organisms
| Visit the greenhouse and make notes on your selected habitat. Begin to research how to select/enrich for particular soil bacteria.
| Visit the greenhouse and make notes on your selected habitat. Research how to select/enrich for particular soil bacteria. View stained total soil community photomicrographs (provided by your instructor) and do calculations to enumerate microorganisms/g wet soil through a culture independent direct count.
| '''Homework''':  Read all of Lab 2 & outline or make flow diagrams of your lab work in your lab notebook. Check [[BISC209/S11:Resources | Resources]]  section of wiki for information about organizing your lab notebook.<BR>'''Graded Assignment''': .'''Discussion with References''' of how the enrichment culture techniques and media you will use will select soil bacteria of the specific groups we seek and differentiate them from other microbes in the community.  Be sure to read the directions for this assignment found at: [[BISC209/S11: Assignment_209_Lab1 | Assignment: Enrichment for culturable bacteria of specific groups]].
| '''Homework''':  Read all of Lab 2 & outline or make flow diagrams of your lab work in your lab notebook. <BR>Check [[BISC209/S12:Resources | Resources]]  section of wiki for information about organizing your lab notebook.<BR>'''Graded Assignment''': Turn in at the beginning of Lab 2, a '''Discussion with References''' of how the enrichment culture techniques and media you will use will select soil bacteria of the specific groups we seek and differentiate them from other microbes in the community.  Be sure to read the directions for this assignment found at: [[BISC209/S12: Assignment_209_Lab1 | Assignment: Enrichment/Selection/Differentiation of Culturable Bacteria]].
|--
|--
| 2
| 2
| Tues. 2/1-<br>Wed. 2/2
| Tues. 2/7-<br>Wed. 2/8
|  Calibrate Micropipets; Genomic DNA isolation for Culture-Independent Bacteria ID;<BR> Finish Plate Count & quantify cultured microbes;<BR>Practice Streaking for Isolation: Make soil extract from dried soil and set up isolation of spore-forming bacteria; <BR>Continue enrichment & isolation of denitrifying and nitrogen cycling bacteria
|  Finish Plate Count & quantify cultured microbes by culture dependent method; Compare to culture independent method<BR>Practice Streaking for Isolation: Make soil extract from dried soil and set up isolation of spore-forming bacteria; <BR>Continue enrichment & isolation of selected groups of bacteria
| 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; '''BRING TO LAB 3 A NEW SOIL SAMPLE Collected from your group's sampling site. (Materials available for pick up in the lab.) Do not collect it until the day of lab.'''
| Check on your soil bacterial cultures; Assess your isolation streaking; '''BRING TO LAB 3 A NEW SOIL SAMPLE Collected from your group's sampling site. (Materials available for pick up in the lab.) Do not collect it until the day of lab.'''
|'''Homework''' Search the web for photos of colonies of desired bacteria;<BR> Research likely bacterial members of your soil community, differentiating metabolic needs or capabilities, physicial differences, and other useful or differentiating characterisitics. <BR>
|'''Homework''' Search the web for photos of colonies of desired bacteria or to match colonies you've found;<BR>
'''Graded Assignment: '''Make or Fill out a Table''' of the relevant morphologic, physical, and useful metabolic characteristics of expected genera of soil bacterial that you are attempting to find in your habitat. Be sure to read the directions for this assignment found at: Lab 2 Assignment: [[BISC209/S11: Assignment_209_Lab2 | Assignment: Table of Cultured Soil Bacteria Characteristics]].  
'''Graded Assignment:''' Compare your culture dependent and culture dependent estimations of the CFUs/gram of soil (dry wt) calculated in LAB 2 and think about the disparity. (DO NOT explain the discrepancy by criticizing your execution of the experiments!) Write a draft '''Introduction''' section of your final paper that includes a discussion of the "Great Plate Count Anomaly". Be sure to read the full directions for this assignment found at: Lab 2 Assignment: [[BISC209/S12: Assignment_209_Lab2 | Assignment: Introduction]].  


|--
|--
| 3
| 3
| Tues. 2/8-<br>Wed. 2/9
| Tues. 2/14-<br>Wed. 2/15
|  
|  
'''Isolation of Culturable Bacteria:''' Evaluate your success at streaking for isolation;<BR>'''Start CLPP: Community Level Physiological Profiling: Carbon source utilization & nitrogen cycling analysis;'''<BR>Make another soil extract and serial dilution to '''evaluate carbon source utilization;'''<BR> Continue selection & isolation, of desired bacterial groups; <BR> Start '''community exoexyzme profiling''' (starch & cellulose digesters, phosphate solubilizers).
'''Isolation of Culturable Bacteria:''' Evaluate your success at streaking for isolation;<BR>'''Start CLPP: Community Level Physiological Profiling: Carbon source utilization;'''<BR>Make another soil extract and serial dilution to '''evaluate carbon source utilization;'''<BR> Continue selection & isolation, of desired bacterial groups; <BR> Start '''community exoexyzme profiling''' (starch & cellulose digesters, phosphate solubilizers).
| Collect data from BIOLOG ECO plates. Check on cultures and continue isolation. View stained total soil community photomicrographs (provided by your instructor) and do calculations.
| Collect data from BIOLOG ECO plates. Check on cultures and continue isolation.  
| '''Homework''': Quantify the number microorganisms in your soil community from the photomicrographs prepared and stained by your instructors from your Lab 3 soil extract. Compare this estimation to the CFU/gram of soil (dry wt) calculated in LAB 2 and try to explain the disparity, WITHOUT criticizing your execution of the plate count protocols or other procedures involved.  
| '''Homework''': Construct a table (with properly formatted legend) of your experimental evidence for the abundance of microorganisms in your soil community. Write a draft results section. Consult the full directions for this assignment found at: [[BISC209:Assignment_209_Lab3 | Lab 3 Assignment: Colony Count vs. Direct Count Enumeration]]
|--
|--
| 4
| 4
| Tues. 2/14-<br>Wed. 2/15
| Tues. 2/21-<br>Wed. 2/22
| '''Identification of soil community bacteria by 16S rDNA sequencing:''' PCR Amplification of 16S rDNA with "universal" bacterial primers and proofreading polymerase<BR> PCR product clean-up <BR><BR> Run a gel of your cleaned-up pcr product to assess the success of your 16s rRNA gene amplification. Instructor will finish, photograph gel and post the labeled image to the data file;<BR>
| '''Isolation of Culturable Bacteria:'''  Examine cultures and pick unique isolated colonies of your soil bacteria <BR> Exoenzyme assessment; CLPP analysis and calculations of carbon source utilization  
'''Isolation of Culturable Bacteria:'''  Examine enrichment and selective media and pick unique isolated colonies of your soil bacteria to acquire pure cultures for each organism.<BR> Exoenzyme assessment; CLPP analysis and calculations of carbon source utilization and nitrogen cycling.
| Make sure you understand the CLPP analyses and calculations;<BR>  
| Make sure you understand the CLPP analyses and calculations;<BR>  
| '''Homework''':Turn in calculations and graphs for CLPP analyses of carbon source testing.'''Introduction section of final paper.''' Read over the [[BISC209/S11:Project1 | Introduction to the Project]] page in the wiki to identify the topic and experimental questions addressed. Include the history of the "Great Plate Count Anomaly" (the disparity between culturable and unculturable soil community bacteria). Use and cite references in journal ''Cell'' format.  A reference that may be helpful is :[http://www.springerlink.com/content/978-3-540-85464-7#section=183950&page=1&locus=2 | Uncultivated Microorganisms by Slava Epstein in Microbiology Monographs Vol. 10, 2009 DOI: 10.1007/978-3-540-85465-4 available as an e-book through Springerlink at the Wellesley College Library] or as a pdf file in the Resources section of the lab Sakai site.  
| '''Homework''':Analyze prevalence of microbial starch & cellulose digesters and phosphate solubilizers in the soil community. Analyze CLPP data for carbon source utilization; turn in spreadsheet with calculations and make graphs turned into figures with legends. More information about how to use your data in these calculations can be found at [[BISC209/S12: Assignment_209_BIOLOG]].
|--
|--
| 5
| 5
| Tues. 2/22-<br> Wed. 2/23
| Tues. 2/28-<br> Wed. 2/29
| '''Identification of culture-independent soil community bacteria by 16S rDNA sequencing:''' Clone 16s rDNA from successful pcr products into cloning vector<BR> Transform cloning vector into ''E. coli'' and select for transformants on selective media.<BR>
| '''Isolation of Culturable Bacteria:''' Make new cultures from each of your pure cultures of your soil bacteria isolates. <BR>
'''Isolation & of Culturable Bacteria:''' Make new cultures from each of your pure cultures of your soil bacteria isolates.  
Use a pure culture of each isolate to its amplify 16srRNA gene by pcr. Clean up pcr product. Perform agarose gel electrophoresis of pcr product to assess success of amplification.
| Check to see if you have ''E. coli'' transformants on your selection plates. If not, contact your instructor. <BR>
| Send away successfully amplified 16s rDNA for DNA sequencing at a commercial sequencing facility.
| '''Homework''': Write the M&M section (what you've done so far) for your final paper. Refer to the assignment directions in the [[BISC209/S11:Assignments]] section.
| '''Homework''': '''M&M''': Compose a draft of your Materials and Methods section of your final paper with the following three general sections:<br> 1)Community level physiological testing: carbon source profiling, exoenzymes profiling; <BR> 2) Identification of bacteria by 16S rRNA gene sequencing from soil genomic DNA;<br> 3) Selection and isolation of soil community bacteria to pure culture. More information can be found at Lab 5 Assignment:  [[BISC209/S12: Assignment_209_Lab5 | Materials & Methods]]
 
|--
|--
| 6
| 6
| Tues.3/1. - <br> Wed. 3/2
| Tues.3/6 - <br> Wed. 3/7
| '''Identification of culture-independent soil community bacteria by 16S rDNA sequencing:'''Select 48/per pair (96 per soil habitat) well-isolated, transformants from selective media and grow in broth overnight. <BR>
| '''Isolate Testing:''' Perform physical characteristics tests: smear slide, Gram stain, confirm Gram stain with selective media, start an antibiotic production test.<BR>
'''Isolation & of Cultured Bacteria:''' Perform physical characteristics tests: smear slide, Gram stain, Confirm Gram stain with selective media, start an antibiotic production test.<BR>
|   
|  Send away frozen glycerol stocks of overnight cultures of transformed bacteria for 16S rDNA sequencing. Results should be back within 2 weeks.
| '''Homework''': Write a brief summary of the theory behind the following techniques that we used to identify our bacterial species by molecular tools: polymerase chain amplification of the 16srRNA gene and DNA sequencing by the newer fluorescent-labeled ddNPTs chain -termination (Sanger) method. Directions found at: Lab 6 Assignment:  [[BISC209/S12: Assignment_209_Lab6 | Assignment: Theory Summary ]]
| '''Homework''': Write a brief summary of the theory behind the following techniques that we used to identify our bacterial species by molecular tools: genomic DNA isolation, polymerase chain amplification of part of the 16s rRNA genes, use of the Zero Blunt® TOPO® PCR Cloning Kit to create a library of unique plasmid vector with our 16S rRNA gene inserts and then select, One Shot® TOP10 Competent E. coli Cells that allowed us to select and separate our 16S rRNA genes for sequencing, and DNA sequencing by the Sanger method.  
|--
|--


|--
|--
| 7
| 7
| Tues. 3/8- <br> Wed. 3/9
| Tues. 3/13- <br> Wed. 3/14
| '''Cultured bacteria assessment''': Start SIMs test; Continue antibiotic production test; Read Gram stain confirmation by selective media, Start Quorum Sensing & Bacterial interactions tests.
| '''Isolates Testing''': Start motility test and MNM tests; Continue antibiotic production test; Read Gram stain confirmation by selective media, Start Bacterial interactions test.
| Complete, read, or set up fresh cultures as needed.
| Complete, read, or set up fresh cultures as needed.
| '''Homework''': Write a partial Results section with figures/tables: Read more about this assignment at: [[BISC209/S11: Assignment_209_Lab7 | Assignment: Partial Results section with Fig/Tables]]. 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 [[BISC209/S11:Resources| 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.
| '''Homework''': '''Annotated Bibliography''' of appropriate references for the discussion section of your paper<BR>'''Graphical abstract''': See models in research reports found in recent issues of the journal ''Cell''. A description and examples of Graphical Abstracts can be found at http://www.elsevier.com/wps/find/authorsview.authors/graphicalabstracts [http://www.elsevier.com/wps/find/authorsview.authors/graphicalabstracts]. More information on this assignment found at: [[BISC209/S12: Assignment_209_Lab8 | Assignment: Annotated Bibliography/Graphical Abstract]]
|--
|--
| 8
| 8
| Tues. 3/15- <br> Wed. 3/16
| Tues. 3/27- <br> Wed. 3/28
| Cont. '''Cultured bacteria assessment:''' Complete and read antibiotic production test, quorum sensing, interactions, SIMS tests. Confirm results with special stains or other motility tests as needed.  
| Cont. '''Isolates testing:''' Complete and read antibiotic production test, interactions, MNM tests. Special Staining as indicated.  
| Make sure you have signed up for an account on the RDB and received a username and password before you come to RDP Lab (9). Link to the RDB:<BR>
|  
[http://rdp.cme.msu.edu/index.jsp].
| '''Homework''': Study for your Lab Practical. Your instructor will give you more instructions about what that test will include and how to study.
| '''Homework''': Results section on isolates work and Graphical Abstract.  
|--
|--
| 9
| 9
| Tues. 3/28- <br> Wed. 3/29
| Tues. 4/3- <br> Wed. 4/4
| Meet in a computer lab (TBA) for data analysis of your 16S rDNA sequencing results.  
| '''Lab Practical'''<BR>  
| Complete all work on cultured bacterial isolates to provide evidence for functional co-operation and/or competition in your soil community
| Make sure you have signed up for an account on the RDB and received a username and password. Link to the RDB:<BR>
| '''Homework''': Study for your Lab Practical that will be given in Lab 10. Your instructor will give you more instructions about what that test will include and how to study.<BR>Analyze your sequencing data from 16S rDNA sequencing of the soil genomic DNA sequences and start preparing phylogenic trees with identification information for the bacteria in your soil community. Make figures or other displays of these data to supply evidence for the diversity and evolutionary relationships of some of the bacteria in your soil community .
[https://rdp.cme.msu.edu/index.jsp].
| '''Homework''': '''Write a draft results section of your work on your isolates.''' Construct a table of the tests performed on the isolates from your soil community (your isolates and your teammates from the same sampling site) and write a complete results narrative. You should include in the table: Gram stain, description of the colony morphology, description of the individual bacteria and any characteristic arrangement (cocci, rods, with descriptors ie., large, small, bullet shaped, in chains, etc.), evidence of spores (either endospore stain positive or visualization of empty areas in vegetative cells on Gram stain), motility, evidence for nitrogen cycling capabilities, sole carbon source (citrate or mannitol) . Make a separate figure from a photograph of your interactions assay and your antibiotic production assays and analyze those data.  
|--
|--
| 10
| 10
| Tues. 4/5- <br> Wed. 4/6
| Tues. 4/10- <br> Wed. 4/11
| '''Lab Practical'''<BR>
| '''Data Analysis & Science Writing Workshop I'''
| Conference with your instructor to discuss your data analysis& poster presentation.
|  
| '''Homework''': Prepare your group (4 students- 1 soil community) "virtual" poster presentation to be presented in LAB 11
| '''Homework''': Analyze your 16s rRNA gene sequences identification of your isolates and make a table of bacteria isolated from your soil community. Construct a tree from your group's data showing taxonomic diversity among these bacteria. We will use your figures in a Science Writing Workshop next time.


|--
|--
| 11
| 11
| Tues. 4/12-<br> Wed. 4/13
| Tues. 4/17-<br> Wed. 4/18
| "Virtual" Poster presentation in groups by habitat
| '''Science Writing Workshop II'''
|  
|  
| '''Homework''': Write your final paper in the form of a scientific paper. See the [[BISC209/S11:Resources |Resources]] section for an extensive handout on How to Write in Scientific Style and a link to Wellesley Library information
| '''Homework''': Write your final paper in the form of a scientific paper. See the [[BISC209/S12:Resources |Resources]] section for an extensive handout on How to Write in Scientific Style. <BR> Information on your final paper found at: [[BISC209/S12: Assignment_209_Lab10 | Assignment: Final Paper]]


|--
|--
| Conferences
| '''NO LAB'''<BR>'''PAPER DUE'''
| Wed. 4/20-<br> Tues. 4/26
| Tues. 4/24-<br> Wed. 4/25
| Meet with your instructor to discuss your final paper.<BR> When & where at discretion<BR> of your instructor.
| '''Final Paper''' Due by 4pm uploaded to Sakai AND in hard copy to your instructor's office.  
|
| '''Homework''': Prepare your group presentation. See information in Resources in Sakai lab site
|--
|--
| 12
| 12
| Tues. 5/3-<br> Wed. 5/4
| Tues. 5/1-<br> Wed. 5/2
| Final Paper due on your lab day.<BR> When & where at discretion<BR> of your instructor.
| '''Group Presentation'''
| Information on your final paper found at: [[BISC209/S11: Assignment_209_Lab12 | Assignment: Final Paper]]
|  
| End of lab
| End of lab
|--
|--
Line 147: Line 146:
<br>
<br>
<div class=noprint>
<div class=noprint>
==Links to Labs==
==Links to Labs==
[[BISC209/S12: Lab1 | Lab 1 ]]<br>
[[BISC209/S12: Lab1 | Lab 1 ]]<br>

Latest revision as of 13:14, 19 January 2012

Wellesley College-BISC 209 Microbiology -Spring 2012


BISC209 S12 Lab Calendar

Monday Tuesday Wednesday Thursday Friday
Jan.23 Jan. 24
No Lab		 Jan. 25
Classes begin
No Lab		 Jan. 26 Jan. 27
Jan. 30 Jan. 31
Lab 1		 Feb. 1
Lab 1		 Feb. 2 Feb. 3
Feb. 6 Feb. 7
Lab 2		 Feb. 8
Lab 2		 Feb. 9 Feb. 10
Feb. 13 Feb. 14
Lab 3		 Feb. 15
Lab 3		 Feb. 16 Feb. 17
Feb. 20
Presidents' Day		 Feb. 21
Lab 4		 Feb. 22
Lab 4		 Feb. 23
Monday Schedule		 Feb. 24
Feb. 27 Feb. 28
Lab 5		 Feb. 29
Lab 5		 Mar. 1 Mar. 2
Mar. 5 Mar. 6
Lab 6		 Mar. 7
Lab 6		 Mar. 8 Mar. 9
Mar. 12 Mar. 13
Lab 7		 Mar. 14
Lab 7		 Mar. 15 Mar. 16
Mar. 19
Spring Break		 Mar. 20
Spring Break		 Mar. 21
Spring Break		 Mar. 22
Spring Break		 Mar. 23
Spring Break
Mar. 26 Mar. 27
Lab 8		 Mar. 28
Lab 8		 Mar. 29 Mar. 30
Apr. 2 Apr. 3
Lab 9
Lab Practical
start 1pm today		 Apr. 4
Lab 9
Lab Practical		 Apr. 5 Apr. 6
Apr. 9 Apr. 10
Lab 10
Data Analysis &
Paper & Presentation Workshop I
start 1PM today		 Apr. 11
Lab 10
Data Analysis &
Paper & Presentation Workshop I		 Apr. 12 Apr. 13
Apr. 16
Patriots' Day		 Apr. 17
Lab 11
Paper & Presentation Workshop II		 Apr. 18
Lab 11
Paper & Presentation Workshop II		 Apr. 19 Apr. 20
Monday Schedule
Apr. 23 Apr. 24
NO Lab
Paper Due		 Apr. 25
Rhulman
NO Lab
Paper Due		 Apr. 26 April 27
Apr. 30 May 1
Lab 12
Presentations rm 264		 May 2
Lab 12
Presentations rm 264		 May 3 May 4
Last day of
classes

Weekly Planner

BISC209 Weekly Lab Planner

Lab # LAB DATES__ IN LAB WORK__________________ OUTSIDE OF LAB WORK________ Assignment/Notes
1 Tues. 1/31-
Wed. 2/1 		Introduction to Microbiology Lab

Lab Safety
Tools and Techniques of Microbiologist: Aseptic Transfer,
Intro to Soil Microbial Community Project:Soil sampling in Greenhouse habitat;Begin culture of soil organisms: make soil extract and begin enrichment for selected bacteria;
Start Plate Count of Culturable Soil Organisms

Visit the greenhouse and make notes on your selected habitat. Research how to select/enrich for particular soil bacteria. View stained total soil community photomicrographs (provided by your instructor) and do calculations to enumerate microorganisms/g wet soil through a culture independent direct count. Homework: Read all of Lab 2 & outline or make flow diagrams of your lab work in your lab notebook.
Check Resources section of wiki for information about organizing your lab notebook.
Graded Assignment: Turn in at the beginning of Lab 2, a Discussion with References of how the enrichment culture techniques and media you will use will select soil bacteria of the specific groups we seek and differentiate them from other microbes in the community. Be sure to read the directions for this assignment found at: Assignment: Enrichment/Selection/Differentiation of Culturable Bacteria.
2 Tues. 2/7-
Wed. 2/8 		Finish Plate Count & quantify cultured microbes by culture dependent method; Compare to culture independent method
Practice Streaking for Isolation: Make soil extract from dried soil and set up isolation of spore-forming bacteria;
Continue enrichment & isolation of selected groups of bacteria 		Check on your soil bacterial cultures; Assess your isolation streaking; BRING TO LAB 3 A NEW SOIL SAMPLE Collected from your group's sampling site. (Materials available for pick up in the lab.) Do not collect it until the day of lab. Homework Search the web for photos of colonies of desired bacteria or to match colonies you've found;

Graded Assignment: Compare your culture dependent and culture dependent estimations of the CFUs/gram of soil (dry wt) calculated in LAB 2 and think about the disparity. (DO NOT explain the discrepancy by criticizing your execution of the experiments!) Write a draft Introduction section of your final paper that includes a discussion of the "Great Plate Count Anomaly". Be sure to read the full directions for this assignment found at: Lab 2 Assignment: Assignment: Introduction.

3 Tues. 2/14-
Wed. 2/15

Isolation of Culturable Bacteria: Evaluate your success at streaking for isolation;
Start CLPP: Community Level Physiological Profiling: Carbon source utilization;
Make another soil extract and serial dilution to evaluate carbon source utilization;
Continue selection & isolation, of desired bacterial groups;
Start community exoexyzme profiling (starch & cellulose digesters, phosphate solubilizers).

Collect data from BIOLOG ECO plates. Check on cultures and continue isolation. Homework: Construct a table (with properly formatted legend) of your experimental evidence for the abundance of microorganisms in your soil community. Write a draft results section. Consult the full directions for this assignment found at: Lab 3 Assignment: Colony Count vs. Direct Count Enumeration
4 Tues. 2/21-
Wed. 2/22 		Isolation of Culturable Bacteria: Examine cultures and pick unique isolated colonies of your soil bacteria
Exoenzyme assessment; CLPP analysis and calculations of carbon source utilization 		Make sure you understand the CLPP analyses and calculations;
 Homework:Analyze prevalence of microbial starch & cellulose digesters and phosphate solubilizers in the soil community. Analyze CLPP data for carbon source utilization; turn in spreadsheet with calculations and make graphs turned into figures with legends. More information about how to use your data in these calculations can be found at BISC209/S12: Assignment_209_BIOLOG.
5 Tues. 2/28-
Wed. 2/29 		Isolation of Culturable Bacteria: Make new cultures from each of your pure cultures of your soil bacteria isolates.

Use a pure culture of each isolate to its amplify 16srRNA gene by pcr. Clean up pcr product. Perform agarose gel electrophoresis of pcr product to assess success of amplification.

Send away successfully amplified 16s rDNA for DNA sequencing at a commercial sequencing facility. Homework: M&M: Compose a draft of your Materials and Methods section of your final paper with the following three general sections:
1)Community level physiological testing: carbon source profiling, exoenzymes profiling;
2) Identification of bacteria by 16S rRNA gene sequencing from soil genomic DNA;
3) Selection and isolation of soil community bacteria to pure culture. More information can be found at Lab 5 Assignment: Materials & Methods
6 Tues.3/6 -
Wed. 3/7 		Isolate Testing: Perform physical characteristics tests: smear slide, Gram stain, confirm Gram stain with selective media, start an antibiotic production test.
 Homework: Write a brief summary of the theory behind the following techniques that we used to identify our bacterial species by molecular tools: polymerase chain amplification of the 16srRNA gene and DNA sequencing by the newer fluorescent-labeled ddNPTs chain -termination (Sanger) method. Directions found at: Lab 6 Assignment: Assignment: Theory Summary
7 Tues. 3/13-
Wed. 3/14 		Isolates Testing: Start motility test and MNM tests; Continue antibiotic production test; Read Gram stain confirmation by selective media, Start Bacterial interactions test. Complete, read, or set up fresh cultures as needed. Homework: Annotated Bibliography of appropriate references for the discussion section of your paper
Graphical abstract: See models in research reports found in recent issues of the journal Cell. A description and examples of Graphical Abstracts can be found at http://www.elsevier.com/wps/find/authorsview.authors/graphicalabstracts [1]. More information on this assignment found at: Assignment: Annotated Bibliography/Graphical Abstract
8 Tues. 3/27-
Wed. 3/28 		Cont. Isolates testing: Complete and read antibiotic production test, interactions, MNM tests. Special Staining as indicated. Homework: Study for your Lab Practical. Your instructor will give you more instructions about what that test will include and how to study.
9 Tues. 4/3-
Wed. 4/4 		Lab Practical
 Make sure you have signed up for an account on the RDB and received a username and password. Link to the RDB:

[2].

Homework: Write a draft results section of your work on your isolates. Construct a table of the tests performed on the isolates from your soil community (your isolates and your teammates from the same sampling site) and write a complete results narrative. You should include in the table: Gram stain, description of the colony morphology, description of the individual bacteria and any characteristic arrangement (cocci, rods, with descriptors ie., large, small, bullet shaped, in chains, etc.), evidence of spores (either endospore stain positive or visualization of empty areas in vegetative cells on Gram stain), motility, evidence for nitrogen cycling capabilities, sole carbon source (citrate or mannitol) . Make a separate figure from a photograph of your interactions assay and your antibiotic production assays and analyze those data.
10 Tues. 4/10-
Wed. 4/11 		Data Analysis & Science Writing Workshop I Homework: Analyze your 16s rRNA gene sequences identification of your isolates and make a table of bacteria isolated from your soil community. Construct a tree from your group's data showing taxonomic diversity among these bacteria. We will use your figures in a Science Writing Workshop next time.
11 Tues. 4/17-
Wed. 4/18 		Science Writing Workshop II 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.
Information on your final paper found at: Assignment: Final Paper
NO LAB
PAPER DUE 		Tues. 4/24-
Wed. 4/25 		Final Paper Due by 4pm uploaded to Sakai AND in hard copy to your instructor's office. Homework: Prepare your group presentation. See information in Resources in Sakai lab site
12 Tues. 5/1-
Wed. 5/2 		Group Presentation 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

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