Educational materials

The assignments presented here incorporate the use of bioinformatic tools at NMPDR to teach biological concepts. These activities were developed with a particular course in mind, then adapted for more general use. Several were developed at the NMPDR Curriculum Developement Workshop held at 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

Pyrimidine Biosynthesis
Biosynthesis of Selenocysteine and Selenoproteins
Bacterial Pathogenesis and Virulence Factors

Assignments

Introduction to bioinformatics and exploration of pyrimidine biosynthesis

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 and GBrowse handout pdf

Student exercise:
Assignment worksheet writable document

Further reading:
The evolutionary history of the first three enzymes in pyrimidine biosynthesis. 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

Exploring selenocysteine biosynthesis across all three Domains using the National Microbial Pathogen Data Resouce

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

Prerequisite reading:
On the road to selenocysteine full text

Using NMPDR and GBrowse handout pdf

Student exercise:
Assignment worksheet writable document

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

Using NMPDR to investigate pathogenesis

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.

Using NMPDR and GBrowse 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 and GBrowse: 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.

^top