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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. 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.

Topics

• Pathogenesis and Virulence Factors of Escherichia coli
• University of Illinois MCB 301 Lab 10: Prediction of biochemical test results
• Listeriolysins
• Phenotype Prediction
• Pyrimidine Biosynthesis
• Biosynthesis of Selenocysteine and Selenoproteins
• Bacterial Pathogenesis and Virulence Factors

Assignments

E.coli pathogenesis for SDSU

Lecture:
PowerPoint view slideshow or download editable slides or 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 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

Lecture:
PowerPoint view slideshow or download editable slides or 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

Lecture:
PowerPoint view slideshow or download editable slides or 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

Lecture:
PowerPoint download 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: MicrobiologyLab? 02-226

Lecture:
PowerPoint download editable slides or handout pdf

Prerequisite reading:
Evolution of Central Metabolic Pathways: Pyrimidine Biosynthesis 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

Lecture:
PowerPoint view slideshow or download editable slides or 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

Lecture:
PowerPoint view slideshow or download editable slides or handout pdf

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

Bacterial Pathogenesis 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

Other Resources

Using NMPDR

NMPDR training workshop handout, illustrated
handout pdf

Annotating Proteins and Adding Proteins to Subsystems—A Worked Example

NMPDR-SEED training workshop handout, illustrated
handout pdf

Suggested References

The National Microbial Pathogen Database Resource (NMPDR)

A genomics platform based on subsystem annotation.: McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.

Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53; [Epub 2006 Dec 1] PMID: 17145713

This paper is the primary description of the data and tools available at NMPDR.

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V.

Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. PMID: 16214803

In this paper, subsystems are defined, and the SEED annotation environment that supports the creation, curation, population and exchange of subsystems is described. The SEED is used by the NMPDR curation staff, and a public version is available for community annotation.

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-- LeslieMcNeil - 04 Apr 2008