NMPDR> Main Web>FrontPage > OtherResources>TeachingMaterials  

 

Teaching and Learning with NMPDR

The assignments presented here incorporate the use of bioinformatics tools at NMPDR to teach biological concepts. These activities were developed with a particular course in mind, and may be adapted for more general use. Several were developed at the NMPDR Curriculum Development Workshop held at the University of Illinois in July, 2007. Some of the assignments have not yet been updated for use with the present user interface.

For each topic below we provide lecture slides, suggested readings that provide context for the activity, the student activity, and suggestions for further reading. Please feel free to make use of the materials. We will be happy to work with you to adapt the assignments to fit the learning objectives of your course, or to design a new unit. Please contact us with new ideas or about problems encountered by you or your students.

Assignments

University of Illinois MCB 301 Lab 10--Prediction of biochemical test results

view slideshow

editable slides

handout pdf

Prerequisite reading:
Culture and Identification of Infectious Agents Bacteriology Ch 2 full text from Microbiology and Immunology On-Line, by Alvin Fox, published by The University of South Carolina School of Medicine.

Student exercise:
Assignment worksheet writable document with links to assigned genomes

Developed for:
Laboratory class at University of Illinois: MCB 301 Experimental Microbiology

Listeriolysins

view slideshow

editable slides

handout pdf

Prerequisite reading:
Listeria monocytogenes and Listeriosis full text from Todar's Online Textbook of Bacteriology

Identified Virulence Factors of Listeria: Toxin in the Virulence Factors Data Base

Student exercise:
Assignment worksheet writable document

Further reading:
The cell biology of Listeria monocytogenes infection: the intersection of bacterial pathogenesis and cell-mediated immunity. full text

Developed for:
Laboratory class at University of Illinois: MCB 428 Bacterial Pathogens Lab

Phenotype Prediction

editable slides

Prerequisite reading:
Culture and Identification of Infectious Agents Bacteriology Ch 2 full text from Microbiology and Immunology On-Line, by Alvin Fox, published by The University of South Carolina School of Medicine.

Student exercise:
Assignment worksheet writable document with links to online protocols

Developed for:
Laboratory class at Lewis University: Microbiology Lab? 02-226

Pyrimidine Biosynthesis

editable slides

handout pdf

Prerequisite reading:
Evolution of Central Metabolic Pathways: Pyrimidine Biosynthesis%PUBMED% Chs 7.0 and 7.2 full text from Sequence - Evolution - Function: Computational Approaches in Comparative Genomics by Eugene V. Koonin & Michael Y. Galperin, Kluwer Academic Publishers.

Biosynthesis of Pyrimidine Ribonucleotides Ch 6.2 pdf from The Organic Chemistry of Biological Pathways by John E. McMurry and Tadhg P. Begley, Roberts & Company Publishers.

Using NMPDR handout pdf

Student exercise:
Assignment worksheet writable document

Further reading:
The evolutionary history of the first three enzymes in pyrimidine biosynthesis. PubMed"> abstract

Biochemical and enzymological aspects of the symbiosis between the deep-sea tubeworm Riftia pachyptila and its bacterial endosymbiont. full text

Developed for:
Introductory class at William Woods: BIO 301 Genetics

Biosynthesis of Selenocysteine and Selenoproteins

view slideshow

editable slides

handout pdf

Prerequisite reading:
On the road to selenocysteine. full text

Using NMPDR handout pdf

Student exercise:
Assignment worksheet writable document

Developed for:
Advanced classes at Illinois: MCB 432 Computing in Molecular Biology, CPSC 569 Applied Bioinformatics

Bacterial Pathogenesis and Virulence Factors

view slideshow

editable slides

handout pdf

Prerequisite reading:
Mechanisms of Bacterial Pathogenesis full text from Todar's Online Textbook of Bacteriology

Bacterial Pathogenesis %PUBMED% Ch 7 full text from Medical Microbiology, edited by Samuel Baron, published by The University of Texas Medical Branch at Galveston.

General Aspects of Bacterial Pathogenesis Bacteriology Ch 10 full text from Microbiology and Immunology On-Line, by Alvin Fox, published by The University of South Carolina School of Medicine.

Using NMPDR handout pdf

Student exercise:
Inquiry Unit worksheet writable document

On-line Inquiry Units focused on Campylobacter, Listeria, Staphylococci, Streptococci, or Vibrio are writable after registration at the iLab site that hosts our user forums.

Developed for:
Advanced discussion section at Illinois: MCB 426 Bacterial Pathogenesis

Pathogenesis and Virulence Factors of Escherichia coli

view slideshow

editable slides

handout pdf

Prerequisite reading:
About pathogenic Escherichia coli Center for Infectious disease Research and Policy at University of Minnesota

Mechanisms of Bacterial Pathogenesis full text from Todar's Online Textbook of Bacteriology

Bacterial Pathogenesis %PUBMED% Ch 7 full text from Medical Microbiology, edited by Samuel Baron, published by The University of Texas Medical Branch at Galveston.

General Aspects of Bacterial Pathogenesis Bacteriology Ch 10 full text from Microbiology and Immunology On-Line, by Alvin Fox, published by The University of South Carolina School of Medicine.

Using NMPDR handout pdf

Student exercise:
Inquiry Unit worksheet writable document

-- Leslie Mc Neil - 04 Apr 2008

• NMPDRworkshop.mht: NMPDRworkshop.mht