BISC209/S11: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 for culturable bacteria of specific groups.	10
2	3	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: Assignment: Table of Cultured Soil Bacteria Characteristics.	5
3	4	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.	5
4	5	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/S11: Assignment_209_BIOLOG Write an Introduction section of final paper. Full directions and useful references can be found at Lab 4 Assignment: Assignment: Introduction	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: 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 newer fluorescent-labeled ddNPTs chain -termination (Sanger) method. Directions found at: Lab 6 Assignment: Assignment: Theory Summary	5
7	8	Partial Results section with figures/tables: Enumeration of bacteria in a soil community and Culture-based Soil Community Physiological Profiling, including results from the exoezyme community tests, BIOLOG Eco plate carbon source testing, the MPN of nitrogen cyclers testing, and from evidence of metabolic and physiologic capabilities in cultured isolates. Read more about this assignment at: Assignment: Partial Results section with Fig/Tables	10
8	9	Make 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 results narrative for it. 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), quorum sensing, antibiotic production, motility, indole, and H2S, nitrogen cycling results (maybe--if they worked). Make a separate figure from a photograph of your interactions assay and analyze those data. 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: Graphical Abstract/Discussion Info	5
9	10	Study for Lab practical.Make trees from your phylogenetic relationships among your 16s rRNA identified and unindentified bacteria. Complete your graphical abstract if you want to add a tree.
10	10	Lab practical	45
10	11		25
11	12	Lab notebook	5
	April 24 or 25	Final Paper due by 4pm to your dropbox in Sakai & hard copy to instructor's office	60
12	12	Group Oral Presentation Note that the 15pt group total includes points for Individual Contribution to Group points--assigned by consensus of your project and presentation group	15
Other		CLEAN-UP points	5

Assignments

Lab 1 Assignment: Assignment: Enrichment for culturable bacteria of specific groups
Lab 2 Assignment: Assignment: Table of Cultured Soil Bacteria Characteristics
Lab 3 Assignment: Assignment: Culturable vs. Total Microbial Estimation
Lab 4 Assignment: Assignment: Introduction
Lab 5 Assignment: Assignment: Materials & Methods
Lab 6 Assignment: Assignment: Theory Summary
Lab 7 Assignment: Assignment: Partial Results section with Fig/Tables
Lab 19 Assignment: Assignment: Graphical Abstract
Lab 12 Assignment: Assignment: Final Paper

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