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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. 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

Genome Annotation

Lecture: Quicktime movie of slides notes pages editable slides

Prerequisite reading:

• Annotation of bacterial and archaeal genomes: Improving accuracy and consistency. abstract full text
• Tutorial - How to view the annotation provided by the RAST server.

Student exercise: Instructions for finding functional information by comparative analysis Ferroplasma Annotation Ferroplasma Annotation

Further reading:

• The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species. abstract
• Life in acid: pH Homeostasis in acidophiles abstract full text
• Life in hot acid: Pathway analyses in extremely thermoacidophilic archaea abstract full text
• Genome dynamics in a natural archaeal population (complete genome of Ferroplasma acidarmanus ) full text
• Genome sequence of Picrophilus torridus and its implications for life around pH 0 full text
• The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus full text
• The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum full text

Developed for: Eastern Illinois University Bioinformatics seminar

Listeriolysins

Lecture: Quicktime movie of slides notes pages editable slides

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

Biosynthesis of Selenocysteine and Selenoproteins

Lecture: printable slides editable slides

Prerequisite reading:

• On the road to selenocysteine. full text
• Identification and characterization of phosphoseryl-tRNA [Ser]Sec kinase. full text
• Biosynthesis of Selenocysteine on Its tRNA in Eukaryotes. full text

Student exercise: Assignment worksheet writable document

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

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

Lecture: Quicktime movie of slides notes pages 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 assigned genomes

Additional Web Resources:

• Alphabetic list of microbiology lectures, labs, and disease information at the Indiana University School of Medicine in Terre Haute and Evansville.
• Virtual Microbiology Lab with case studies at the University of Florida.
• Comprehensive list of identification tests on the Microbugz site at Austin Community College.

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

Phenotype Prediction

Lecture: 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

Additional Web Resources:

• Alphabetic list of microbiology lectures, labs, and disease information at the Indiana University School of Medicine in Terre Haute and Evansville.
• Virtual Microbiology Lab with case studies at the University of Florida.
• Comprehensive list of identification tests on the Microbugz site at Austin Community College.

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

Pyrimidine Biosynthesis

Lecture: editable slides 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.

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

Bacterial Pathogenesis and Virulence Factors

Lecture: Quicktime movie of slides notes pages editable slides

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.

Student exercise: 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

-- Leslie Mc Neil - 06 Mar 2009