BISC209/S12:Assignments

Graded Lab Assignments

Lab Assigned	Lab Due	Assignment description	Point Value (Total 200)
1	2	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.	10
2	3	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.	5
3	4	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	5
4	5	Analyze your community level diversity and behavior data including the prevalence of microbial starch & cellulose digesters and phosphate solubilizers in the soil community and the carbon source utilization patterns and CMD measurement. Write a results section with figures/tables and narrative. Full directions and useful references for this assignment can be found at Lab 4 Assignment: Assignment: Results Section Community Level Assessments	10
5	6	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	10
6	7	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	5
7	8	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	5
8	9	Study for Lab practical
9	9	Lab practical	45
9	10	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	April 24 or 25	Final Paper: Information found at: Assignment: Final Paper	60
11	12	Lab notebook	5
11	12	Group Presentation Note that the 25pt includes 10 points of Individual Contribution to Group points--assigned by consensus of your project and presentation group. Information found in Resources in Sakai (folder Group Presentation) and in Lab 12 in the wiki	25
Other		CLEAN-UP points	5

Assignments

Lab 1 Assignment: Assignment: Enrichment/Selection/Differentiation of Culturable Bacteria
Lab 2 Assignment: Assignment: Introduction
Lab 3 Assignment: Assignment: Colony Count vs. Direct Count Enumeration
Lab 4 Assignment: Assignment: Results Section Community Level Assessments
Lab 5 Assignment: Assignment: Materials & Methods
Lab 6 Assignment: Assignment: Theory Summary
Lab 7 Assignment: Assignment: Annotated Bibliography/Graphical Abstract
Lab 10 Assignment: Assignment: Final Paper